============================================== 2025-02-18 16:32:08 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_MHS_i5006_DY330_rep2_17267.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_MHS_i5006_DY330_rep2_17267.PE.a.GPS ============================================== 2025-02-18 16:32:08 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_HS_i5006_DY330_rep2_17274.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_HS_i5006_DY330_rep2_17274.PE.a.GPS Original read count stats: _IP Bases: 53848 HitCounts: 136870.0 Original read count stats: _IP Bases: 89554 HitCounts: 198246.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 14 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 18 reads. The genome is segmented into 3173 regions for analysis. Running with 1 threads ... The genome is segmented into 6845 regions for analysis. ============================================== 2025-02-18 16:32:09 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep4_21314.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep4_21314.PE.a.GPS Original read count stats: _IP Bases: 124241 HitCounts: 186962.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 24 reads. ============================================== 2025-02-18 16:32:10 ============================================== 2025-02-18 16:32:10 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_HS_i5006_DY330_rep1_20229.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_HS_i5006_DY330_rep1_20229.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_HS_i5006_DY330_rep2_20230.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_HS_i5006_DY330_rep2_20230.PE.a.GPS The genome is segmented into 7546 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 72614 HitCounts: 103874.0 Original read count stats: _IP Bases: 73661 HitCounts: 105598.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 16 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 17 reads. ============================================== 2025-02-18 16:32:11 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_HS_i5006_DY330_rep1_19786.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_HS_i5006_DY330_rep1_19786.PE.a.GPS The genome is segmented into 4828 regions for analysis. ============================================== 2025-02-18 16:32:11 Original read count stats: ============================================== 2025-02-18 16:32:11 The genome is segmented into 4929 regions for analysis. ============================================== 2025-02-18 16:32:11 ============================================== 2025-02-18 16:32:11 ============================================== 2025-02-18 16:32:12 Running with 1 threads ... ============================================== 2025-02-18 16:32:12 ============================================== 2025-02-18 16:32:12_IP Bases: 680597 HitCounts: 1187656.0 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep1_20231.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep1_20231.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep3_21313.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep3_21313.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep2_20240.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep2_20240.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep2_17280.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep2_17280.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep2_20232.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep2_20232.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep2_20228.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep2_20228.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep1_20227.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep1_20227.PE.a.GPS Original read count stats: _IP Bases: 183440 HitCounts: 512120.0 Original read count stats: _IP Bases: 165138 HitCounts: 446192.0 Original read count stats: _IP Bases: 418150 HitCounts: 822736.0 ============================================== 2025-02-18 16:32:13 Original read count stats: _IP Bases: 187281 HitCounts: 492290.0 ============================================== 2025-02-18 16:32:13 Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_MHS_i5006_DY330_rep2_20222.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_MHS_i5006_DY330_rep2_20222.PE.a.GPS Original read count stats: Original read count stats: _IP Bases: 486233 HitCounts: 782198.0 _IP Bases: 450144 HitCounts: 716172.0 _IP Bases: 287469 HitCounts: 970416.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_2.1x36mers.unique.GPS ============================================== 2025-02-18 16:32:13 At Poisson p-value 1.0e-03, in a 301bp window, expect 44 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep1_19790.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep1_19790.PE.a.GPS Original read count stats: _IP Bases: 258949 HitCounts: 448002.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 53 reads. Original read count stats: _IP Bases: 571035 HitCounts: 657365.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 110 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 78 reads. The genome is segmented into 2598 regions for analysis. ============================================== 2025-02-18 16:32:14 At Poisson p-value 1.0e-03, in a 301bp window, expect 58 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 73 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_2.SE.a.GPS Original read count stats: _IP Bases: 414702 HitCounts: 1247126.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 48 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 79 reads. The genome is segmented into 2987 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 97 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 70 reads. Running with 1 threads ... The genome is segmented into 7670 regions for analysis. The genome is segmented into 8002 regions for analysis. The genome is segmented into 8358 regions for analysis. Original read count stats: ============================================== 2025-02-18 16:32:14 ============================================== 2025-02-18 16:32:14 ============================================== 2025-02-18 16:32:15_IP Bases: 598377 HitCounts: 707006.0 The genome is segmented into 8323 regions for analysis. The genome is segmented into 7810 regions for analysis. ============================================== 2025-02-18 16:32:15 The genome is segmented into 7949 regions for analysis. The genome is segmented into 6968 regions for analysis. ============================================== 2025-02-18 16:32:14 At Poisson p-value 1.0e-03, in a 301bp window, expect 123 reads. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_MHS_i5006_DY330_rep1_20221.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_MHS_i5006_DY330_rep1_20221.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep1_17265.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep1_17265.PE.a.GPS Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep2_17273.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep2_17273.PE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_HS_i5006_DY330_rep2_20238.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_HS_i5006_DY330_rep2_20238.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_HS_i5006_DY330_rep1_17259.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_HS_i5006_DY330_rep1_17259.PE.a.GPS The genome is segmented into 8207 regions for analysis. ============================================== 2025-02-18 16:32:16 Original read count stats: Original read count stats: _IP Bases: 441474 HitCounts: 1310132.0 _IP Bases: 523824 HitCounts: 1061760.0 Original read count stats: Running with 1 threads ... _IP Bases: 301403 HitCounts: 1442792.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep3_21307.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep3_21307.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 75 reads. Original read count stats: _IP Bases: 533796 HitCounts: 1234136.0 ============================================== 2025-02-18 16:32:17 Original read count stats: _IP Bases: 1482498 HitCounts: 3175842.0 The genome is segmented into 8246 regions for analysis. Original read count stats: _IP Bases: 388073 HitCounts: 1854138.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep3_21327.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep3_21327.PE.a.GPS Running with 1 threads ... The genome is segmented into 8454 regions for analysis. ============================================== 2025-02-18 16:32:17 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_HS_i5006_DY330_rep1_17261.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_HS_i5006_DY330_rep1_17261.PE.a.GPS Original read count stats: _IP Bases: 1021653 HitCounts: 1824548.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 85 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 97 reads. ============================================== 2025-02-18 16:32:17 At Poisson p-value 1.0e-03, in a 301bp window, expect 102 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep1_19784.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep1_19784.PE.a.GPS Original read count stats: _IP Bases: 475505 HitCounts: 1459048.0 The genome is segmented into 8202 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 134 reads. Running with 1 threads ... Original read count stats: _IP Bases: 623692 HitCounts: 1704348.0 The genome is segmented into 6477 regions for analysis. ============================================== 2025-02-18 16:32:18 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep2_20220.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep2_20220.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 169 reads. The genome is segmented into 8246 regions for analysis. ============================================== 2025-02-18 16:32:18 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep3_21322.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep3_21322.PE.a.GPS ============================================== 2025-02-18 16:32:18 The genome is segmented into 8234 regions for analysis. ============================================== 2025-02-18 16:32:18 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep1_20223.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep1_20223.PE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_MHS_i5006_DY330_rep1_19780.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_MHS_i5006_DY330_rep1_19780.PE.a.GPS The genome is segmented into 7953 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 166 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 127 reads. Running with 1 threads ... Original read count stats: _IP Bases: 1391608 HitCounts: 3633854.0 Original read count stats: _IP Bases: 917436 HitCounts: 3371698.0 The genome is segmented into 8156 regions for analysis. Original read count stats: _IP Bases: 519606 HitCounts: 3452990.0 Original read count stats: _IP Bases: 1021168 HitCounts: 1945622.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 163 reads. The genome is segmented into 8028 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 263 reads. Running with 1 threads ... ============================================== 2025-02-18 16:32:20 The genome is segmented into 8245 regions for analysis. ============================================== 2025-02-18 16:32:20 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep4_21306.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep4_21306.PE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep3_21320.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep3_21320.PE.a.GPS ============================================== 2025-02-18 16:32:20 ============================================== 2025-02-18 16:32:20 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_2.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 968615 HitCounts: 1962960.0 ============================================== 2025-02-18 16:32:20 ============================================== 2025-02-18 16:32:20 ============================================== 2025-02-18 16:32:20 Original read count stats: Original read count stats: Original read count stats: ============================================== 2025-02-18 16:32:21 ============================================== 2025-02-18 16:32:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_1.1x36mers.unique.GPS ============================================== 2025-02-18 16:32:21 At Poisson p-value 1.0e-03, in a 301bp window, expect 168 reads. ============================================== 2025-02-18 16:32:21 ============================================== 2025-02-18 16:32:21 ============================================== 2025-02-18 16:32:22 At Poisson p-value 1.0e-03, in a 301bp window, expect 285 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 295 reads. The genome is segmented into 7900 regions for analysis. _IP Bases: 1687970 HitCounts: 3324397.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 179 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep2_20236.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep2_20236.PE.a.GPS ============================================== 2025-02-18 16:32:21_IP Bases: 2165662 HitCounts: 3119754.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 294 reads. _IP Bases: 1097330 HitCounts: 2214232.0 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep3_21323.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep3_21323.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep4_21324.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep4_21324.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_1.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep1_17257.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep1_17257.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep1_20219.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep1_20219.PE.a.GPS ============================================== 2025-02-18 16:32:23 The genome is segmented into 6866 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep3_21315.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep3_21315.PE.a.GPS Running with 1 threads ... ============================================== 2025-02-18 16:32:23 Original read count stats: _IP Bases: 703762 HitCounts: 4072330.0 ============================================== 2025-02-18 16:32:23 The genome is segmented into 8140 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1167065 HitCounts: 3961472.0 Original read count stats: _IP Bases: 1066920 HitCounts: 3988016.0 Original read count stats: _IP Bases: 1953345 HitCounts: 4389034.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_2.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_2.1x36mers.unique.GPS Original read count stats: The genome is segmented into 7932 regions for analysis. _IP Bases: 1483852 HitCounts: 4703384.0 Running with 1 threads ... Original read count stats: _IP Bases: 1571309 HitCounts: 4200526.0 Original read count stats: ============================================== 2025-02-18 16:32:23_IP Bases: 1790554 HitCounts: 3634616.0 The genome is segmented into 7947 regions for analysis. Original read count stats: Original read count stats: Original read count stats: _IP Bases: 2185373 HitCounts: 3383306.0 _IP Bases: 1473988 HitCounts: 3836664.0 _IP Bases: 1755383 HitCounts: 4080521.0 The genome is segmented into 8216 regions for analysis. Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_2.1x36mers.unique.GPS Original read count stats: Running with 1 threads ... _IP Bases: 695937 HitCounts: 5080032.0 ============================================== 2025-02-18 16:32:23 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep3_21305.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep3_21305.PE.a.GPS Original read count stats: _IP Bases: 1540452 HitCounts: 2276189.0 Original read count stats: _IP Bases: 1767394 HitCounts: 4123733.0 Original read count stats: _IP Bases: 1900893 HitCounts: 4263208.0 Original read count stats: _IP Bases: 1162993 HitCounts: 2525756.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 195 reads. ============================================== 2025-02-18 16:32:24 ============================================== 2025-02-18 16:32:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep2_20224.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep2_20224.PE.a.GPS ============================================== 2025-02-18 16:32:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_2.1x36mers.unique.GPS ============================================== 2025-02-18 16:32:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 04-E.coli-ArgR-GSE60546/ArgR_arg_rep2.1x36mers.unique.bam --out 04-E.coli-ArgR-GSE60546/ArgR_arg_rep2.1x36mers.unique.GPS ============================================== 2025-02-18 16:32:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoB_2.1x36mers.unique.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoB_2.1x36mers.unique.GPS ============================================== 2025-02-18 16:32:25 At Poisson p-value 1.0e-03, in a 301bp window, expect 279 reads. ============================================== 2025-02-18 16:32:25 ============================================== 2025-02-18 16:32:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_1.SE.a.GPS The genome is segmented into 8019 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 286 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep1_17260.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep1_17260.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_1.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_1.1x36mers.unique.GPS ============================================== 2025-02-18 16:32:25 Running with 1 threads ... Original read count stats: _IP Bases: 682268 HitCounts: 5004434.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoB_1.1x36mers.unique.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoB_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 241009 HitCounts: 5702723.0 Original read count stats: _IP Bases: 1607573 HitCounts: 5320582.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 202 reads. Original read count stats: _IP Bases: 1618403 HitCounts: 4739985.0 Original read count stats: _IP Bases: 777235 HitCounts: 5673978.0 Original read count stats: _IP Bases: 1585789 HitCounts: 5415469.0 The genome is segmented into 8257 regions for analysis. Original read count stats: _IP Bases: 1642500 HitCounts: 2492751.0 ============================================== 2025-02-18 16:32:25 Running with 1 threads ... Original read count stats: _IP Bases: 1821232 HitCounts: 2505475.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoB_2.SE.a.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoB_2.SE.a.GPS ============================================== 2025-02-18 16:32:26 At Poisson p-value 1.0e-03, in a 301bp window, expect 304 reads. ============================================== 2025-02-18 16:32:26 The genome is segmented into 8011 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 04-E.coli-ArgR-GSE60546/ArgR_arg_rep1.1x36mers.unique.bam --out 04-E.coli-ArgR-GSE60546/ArgR_arg_rep1.1x36mers.unique.GPS Running with 1 threads ... Original read count stats: _IP Bases: 1673120 HitCounts: 5250822.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 296 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_2.1x36mers.unique.GPS ============================================== 2025-02-18 16:32:26 ============================================== 2025-02-18 16:32:26 At Poisson p-value 1.0e-03, in a 301bp window, expect 344 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 307 reads. ============================================== 2025-02-18 16:32:26 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_MHS_i5006_DY330_rep1_17253.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_MHS_i5006_DY330_rep1_17253.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 338 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 234 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 341 reads. ============================================== 2025-02-18 16:32:26 At Poisson p-value 1.0e-03, in a 301bp window, expect 372 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 04-E.coli-ArgR-GSE60546/ArgR_arg_rep2.SE.a.bam --out 04-E.coli-ArgR-GSE60546/ArgR_arg_rep2.SE.a.GPS Original read count stats: Original read count stats: _IP Bases: 1622652 HitCounts: 5166553.0 _IP Bases: 554728 HitCounts: 6069441.0 ============================================== 2025-02-18 16:32:26 The genome is segmented into 8079 regions for analysis. The genome is segmented into 8096 regions for analysis. ============================================== 2025-02-18 16:32:26 At Poisson p-value 1.0e-03, in a 301bp window, expect 339 reads. Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_2.SE.a.GPS The genome is segmented into 8172 regions for analysis. The genome is segmented into 8273 regions for analysis. Original read count stats: _IP Bases: 1709225 HitCounts: 5435299.0 Running with 1 threads ... Original read count stats: Running with 1 threads ... _IP Bases: 1835925 HitCounts: 2673012.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 361 reads. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 339 reads. _IP Bases: 1501990 HitCounts: 5804828.0 ============================================== 2025-02-18 16:32:26 Original read count stats: _IP Bases: 1810502 HitCounts: 2466644.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 150 reads. ============================================== 2025-02-18 16:32:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 267279 HitCounts: 6134545.0 ============================================== 2025-02-18 16:32:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_1.SE.a.GPS The genome is segmented into 8098 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoB_1.SE.a.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoB_1.SE.a.GPS The genome is segmented into 8298 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 342 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 415 reads. ============================================== 2025-02-18 16:32:27 ============================================== 2025-02-18 16:32:27 Running with 1 threads ... Original read count stats: _IP Bases: 1850186 HitCounts: 2695555.0 The genome is segmented into 8296 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_2.SE.a.GPS Original read count stats: _IP Bases: 1895202 HitCounts: 6225039.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_MHS_i5006_DY330_rep2_17269.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_MHS_i5006_DY330_rep2_17269.PE.a.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 219 reads. ============================================== 2025-02-18 16:32:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 04-E.coli-ArgR-GSE60546/ArgR_arg_rep1.SE.a.bam --out 04-E.coli-ArgR-GSE60546/ArgR_arg_rep1.SE.a.GPS The genome is segmented into 8376 regions for analysis. Original read count stats: _IP Bases: 1763292 HitCounts: 5674213.0 The genome is segmented into 8137 regions for analysis. The genome is segmented into 8101 regions for analysis. The genome is segmented into 8237 regions for analysis. Original read count stats: _IP Bases: 1907600 HitCounts: 6308264.0 Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8098 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 225 reads. Running with 1 threads ... Original read count stats: _IP Bases: 1675720 HitCounts: 5701076.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 362 reads. ============================================== 2025-02-18 16:32:28 Original read count stats: _IP Bases: 1137507 HitCounts: 6443714.0 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_HS_i5006_DY330_rep2_17276.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_HS_i5006_DY330_rep2_17276.PE.a.GPS Original read count stats: _IP Bases: 1717195 HitCounts: 5955316.0 ============================================== 2025-02-18 16:32:28 ============================================== 2025-02-18 16:32:28 Original read count stats: _IP Bases: 607199 HitCounts: 6606419.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_1.SE.a.GPS The genome is segmented into 8168 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep3_21299.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep3_21299.PE.a.GPS The genome is segmented into 8104 regions for analysis. Running with 1 threads ... The genome is segmented into 7939 regions for analysis. Original read count stats: _IP Bases: 570062 HitCounts: 2725132.0 Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8346 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 226 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 239 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 163 reads. ============================================== 2025-02-18 16:32:28 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 229 reads. The genome is segmented into 8288 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep3_21316.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep3_21316.PE.a.GPS Original read count stats: Original read count stats: _IP Bases: 1339830 HitCounts: 7080250.0 _IP Bases: 1771946 HitCounts: 6222577.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 415 reads. The genome is segmented into 8481 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 351 reads. Running with 1 threads ... The genome is segmented into 8192 regions for analysis. Running with 1 threads ... The genome is segmented into 8183 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 403 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 238 reads. Running with 1 threads ... The genome is segmented into 8048 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 450 reads. Original read count stats: _IP Bases: 800568 HitCounts: 7178086.0 The genome is segmented into 7611 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 382 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 405 reads. The genome is segmented into 8176 regions for analysis. The genome is segmented into 8226 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 365 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 202 reads. ============================================== 2025-02-18 16:32:30 At Poisson p-value 1.0e-03, in a 301bp window, expect 256 reads. The genome is segmented into 8176 regions for analysis. The genome is segmented into 8014 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 445 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 418 reads. The genome is segmented into 8352 regions for analysis. The genome is segmented into 8510 regions for analysis. ============================================== 2025-02-18 16:32:31 The genome is segmented into 8480 regions for analysis. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 395 reads. Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep4_21317.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep4_21317.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_MHS_i5006_DY330_rep1_20234.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_MHS_i5006_DY330_rep1_20234.PE.a.GPS Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 485 reads. The genome is segmented into 8211 regions for analysis. The genome is segmented into 8375 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 452 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 490 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 435 reads. Running with 1 threads ... Original read count stats: _IP Bases: 736179 HitCounts: 8122668.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 438 reads. Original read count stats: _IP Bases: 2515859 HitCounts: 7378876.0 The genome is segmented into 8458 regions for analysis. Running with 1 threads ... The genome is segmented into 8688 regions for analysis. The genome is segmented into 7992 regions for analysis. The genome is segmented into 8652 regions for analysis. Running with 1 threads ... The genome is segmented into 8292 regions for analysis. ============================================== 2025-02-18 16:32:33 Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep2_17275.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep2_17275.PE.a.GPS The genome is segmented into 8480 regions for analysis. Running with 1 threads ... The genome is segmented into 8097 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 456 reads. The genome is segmented into 8473 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 582 reads. The genome is segmented into 8307 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 904153 HitCounts: 8851466.0 The genome is segmented into 8483 regions for analysis. The genome is segmented into 7980 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 566 reads. The genome is segmented into 8212 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:32:38 At Poisson p-value 1.0e-03, in a 301bp window, expect 620 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 551 reads. Original read count stats: _IP Bases: 1936530 HitCounts: 1.0173744E7 The genome is segmented into 8146 regions for analysis. Running with 1 threads ... The genome is segmented into 7815 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 660 reads. Running with 1 threads ... The genome is segmented into 8196 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 713 reads. The genome is segmented into 8488 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:32:51 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoD_2.1x36mers.unique.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoD_2.1x36mers.unique.GPS ============================================== 2025-02-18 16:32:51 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoD_1.1x36mers.unique.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoD_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 919518 HitCounts: 1.511547E7 Original read count stats: _IP Bases: 941384 HitCounts: 1.5762234E7 --------------------------- Events discovered Significant: 2 Insignificant: 3 Filtered: 1 Finish binding event prediction: 45.4s Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 609 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 632 reads. ============================================== 2025-02-18 16:32:57 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep1_17252.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep1_17252.PE.a.GPS --------------------------- Events discovered Significant: 7 Insignificant: 18 Filtered: 7 Finish binding event prediction: 49.1s Running with 1 threads ... The genome is segmented into 8592 regions for analysis. Running with 1 threads ... The genome is segmented into 8589 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1811030 HitCounts: 1.7383904E7 ============================================== 2025-02-18 16:32:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoD_2.SE.a.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoD_2.SE.a.GPS Original read count stats: _IP Bases: 1007508 HitCounts: 1.810954E7 ============================================== 2025-02-18 16:33:02 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoD_1.SE.a.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoD_1.SE.a.GPS Original read count stats: _IP Bases: 1034491 HitCounts: 1.9330964E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 800 reads. The genome is segmented into 8789 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 848 reads. --------------------------- Events discovered Significant: 82 Insignificant: 2 Filtered: 16 The genome is segmented into 8774 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 1327 reads. Finish binding event prediction: 1.0m Refine read distribution from 19 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 3 Filtered: 1 Finish binding event prediction: 18.1s --------------------------- Events discovered Significant: 141 Insignificant: 3 Filtered: 7 Finish binding event prediction: 1.0m Refine read distribution from 24 binding events. Running with 1 threads ... The genome is segmented into 8076 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 134 Insignificant: 0 Filtered: 7 Finish binding event prediction: 1.0m Refine read distribution from 27 binding events. Running with 1 threads ... ============================================== 2025-02-18 16:33:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_MHS_i5006_DY330_rep1_17251.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_MHS_i5006_DY330_rep1_17251.PE.a.GPS ============================================== 2025-02-18 16:33:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep2_17268.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep2_17268.PE.a.GPS Original read count stats: Original read count stats: _IP Bases: 3557248 HitCounts: 2.4581446E7 _IP Bases: 1762347 HitCounts: 2.4228782E7 --------------------------- Events discovered Significant: 104 Insignificant: 22 Filtered: 5 Finish binding event prediction: 17.1s Refine read distribution from 85 binding events. At Poisson p-value 1.0e-03, in a 301bp window, expect 1746 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 1900 reads. The genome is segmented into 7989 regions for analysis. Running with 1 threads ... The genome is segmented into 8176 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 18 Filtered: 7 Finish binding event prediction: 46.1s --------------------------- Events discovered Significant: 82 Insignificant: 24 Filtered: 21 Finish binding event prediction: 1.7m Refine read distribution from 18 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 138 Insignificant: 28 Filtered: 4 Finish binding event prediction: 44.4s Refine read distribution from 127 binding events. --------------------------- Events discovered Significant: 142 Insignificant: 37 Filtered: 3 Finish binding event prediction: 49.1s Refine read distribution from 131 binding events. --------------------------- Events discovered Significant: 18 Insignificant: 0 Filtered: 5 Finish binding event prediction: 1.8m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 54 Insignificant: 55 Filtered: 14 Finish binding event prediction: 1.8m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 61 Insignificant: 66 Filtered: 22 Finish binding event prediction: 1.8m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 60 Insignificant: 69 Filtered: 22 Finish binding event prediction: 2.0m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 18 Insignificant: 0 Filtered: 5 Finish binding event prediction: 2.0m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 340 Insignificant: 0 Filtered: 106 Finish binding event prediction: 2.1m Refine read distribution from 247 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 37 Insignificant: 0 Filtered: 0 Finish binding event prediction: 24.1s Refine read distribution from 33 binding events. --------------------------- Events discovered Significant: 28 Insignificant: 58 Filtered: 18 Finish binding event prediction: 2.3m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 88 Insignificant: 1 Filtered: 29 Finish binding event prediction: 2.3m Refine read distribution from 64 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 34 Insignificant: 0 Filtered: 0 Finish binding event prediction: 18.1s Refine read distribution from 30 binding events. --------------------------- Events discovered Significant: 51 Insignificant: 83 Filtered: 17 Finish binding event prediction: 2.2m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 130 Insignificant: 55 Filtered: 31 Finish binding event prediction: 2.5m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 532 Insignificant: 22 Filtered: 85 Finish binding event prediction: 2.5m Refine read distribution from 174 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 70 Insignificant: 65 Filtered: 15 Finish binding event prediction: 2.2m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 22 Insignificant: 29 Filtered: 6 Finish binding event prediction: 2.5m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 10 Insignificant: 51 Filtered: 16 Finish binding event prediction: 2.5m Refine read distribution from 4 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 163 Insignificant: 47 Filtered: 3 Finish binding event prediction: 58.2s Refine read distribution from 121 binding events. --------------------------- Events discovered Significant: 22 Insignificant: 55 Filtered: 11 Finish binding event prediction: 1.8m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 52 Insignificant: 79 Filtered: 16 Finish binding event prediction: 2.6m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 27 Insignificant: 41 Filtered: 8 --------------------------- Events discovered Significant: 57 Insignificant: 41 Filtered: 16 Finish binding event prediction: 2.6m --------------------------- Events discovered Significant: 78 Insignificant: 39 Filtered: 18 Finish binding event prediction: 2.7m Finish binding event prediction: 2.6m Refine read distribution from 5 binding events. Running with 1 threads ... Refine read distribution from 18 binding events. Refine read distribution from 17 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 57 Insignificant: 67 Filtered: 19 Finish binding event prediction: 2.8m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 270 Insignificant: 0 Filtered: 82 Finish binding event prediction: 2.9m Refine read distribution from 81 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 47 Insignificant: 68 Filtered: 14 --------------------------- Events discovered Significant: 115 Insignificant: 40 Filtered: 23 Finish binding event prediction: 2.7m Finish binding event prediction: 2.8m Refine read distribution from 5 binding events. Running with 1 threads ... Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 64 Insignificant: 52 Filtered: 12 Finish binding event prediction: 2.6m Refine read distribution from 3 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 207 Insignificant: 0 Filtered: 69 Finish binding event prediction: 2.6m Refine read distribution from 55 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 152 Insignificant: 25 Filtered: 34 Finish binding event prediction: 3.1m Refine read distribution from 24 binding events. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 190 Insignificant: 1 Filtered: 37 Finish binding event prediction: 3.2m Refine read distribution from 38 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 987 Insignificant: 9 Filtered: 152 Finish binding event prediction: 3.0m Refine read distribution from 722 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 176 Insignificant: 0 Filtered: 58 --------------------------- Events discovered Significant: 1520 Insignificant: 394 Filtered: 3 Finish binding event prediction: 3.0m Finish binding event prediction: 1.1m Refine read distribution from 143 binding events. Running with 1 threads ... Refine read distribution from 1181 binding events. --------------------------- Events discovered Significant: 81 Insignificant: 25 Filtered: 25 Finish binding event prediction: 3.1m Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 810 Insignificant: 4 Filtered: 80 Finish binding event prediction: 3.2m Refine read distribution from 450 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 34 Insignificant: 62 Filtered: 14 Finish binding event prediction: 3.2m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 113 Insignificant: 32 Filtered: 1 Finish binding event prediction: 51.2s Refine read distribution from 88 binding events. --------------------------- Events discovered Significant: 78 Insignificant: 69 Filtered: 17 Finish binding event prediction: 3.5m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 166 Insignificant: 0 Filtered: 52 Finish binding event prediction: 3.2m Refine read distribution from 145 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 8 Insignificant: 20 Filtered: 5 Finish binding event prediction: 3.3m Running with 1 threads ... --------------------------- Events discovered Significant: 264 Insignificant: 58 Filtered: 1 Finish binding event prediction: 36.1s Refine read distribution from 210 binding events. --------------------------- Events discovered Significant: 81 Insignificant: 83 Filtered: 20 Finish binding event prediction: 3.1m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 201 Insignificant: 71 Filtered: 3 Finish binding event prediction: 1.3m Refine read distribution from 157 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.4m Running with 1 threads ... --------------------------- Events discovered Significant: 137 Insignificant: 29 Filtered: 3 Finish binding event prediction: 52.1s Refine read distribution from 102 binding events. --------------------------- Events discovered Significant: 14 Insignificant: 21 Filtered: 3 Finish binding event prediction: 3.5m Refine read distribution from 6 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 12 Insignificant: 0 Filtered: 3 Finish binding event prediction: 3.5m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 105 Insignificant: 100 Filtered: 14 Finish binding event prediction: 3.6m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 748 Insignificant: 3 Filtered: 67 Finish binding event prediction: 3.7m --------------------------- Events discovered Significant: 230 Insignificant: 43 Filtered: 18 Finish binding event prediction: 37.1s Refine read distribution from 428 binding events. Running with 1 threads ... Refine read distribution from 218 binding events. --------------------------- Events discovered Significant: 168 Insignificant: 27 Filtered: 3 Finish binding event prediction: 1.4m Refine read distribution from 108 binding events. --------------------------- Events discovered Significant: 102 Insignificant: 100 Filtered: 25 Finish binding event prediction: 2.5m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 169 Insignificant: 69 Filtered: 3 Finish binding event prediction: 1.1m Refine read distribution from 128 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.7m Running with 1 threads ... --------------------------- Events discovered Significant: 126 Insignificant: 40 Filtered: 0 Finish binding event prediction: 1.3m Refine read distribution from 107 binding events. --------------------------- Events discovered Significant: 115 Insignificant: 27 Filtered: 31 Finish binding event prediction: 3.6m Refine read distribution from 45 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 142 Insignificant: 51 Filtered: 2 Finish binding event prediction: 2.1m Refine read distribution from 113 binding events. --------------------------- Events discovered Significant: 76 Insignificant: 21 Filtered: 30 Finish binding event prediction: 3.2m Refine read distribution from 27 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 284 Insignificant: 0 Filtered: 93 Finish binding event prediction: 3.8m Refine read distribution from 179 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 116 Insignificant: 40 Filtered: 3 --------------------------- Events discovered Significant: 329 Insignificant: 0 Filtered: 107 --------------------------- Events discovered Significant: 118 Insignificant: 22 Filtered: 33 Finish binding event prediction: 1.2m Finish binding event prediction: 3.7m Finish binding event prediction: 3.7m Refine read distribution from 61 binding events. Refine read distribution from 48 binding events. Running with 1 threads ... Refine read distribution from 265 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 90 Insignificant: 81 Filtered: 19 Finish binding event prediction: 3.7m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 147 Insignificant: 48 Filtered: 2 --------------------------- Events discovered Significant: 134 Insignificant: 51 Filtered: 3 --------------------------- Events discovered Significant: 139 Insignificant: 48 Filtered: 4 Finish binding event prediction: 1.2m --------------------------- Events discovered Significant: 1374 Insignificant: 408 Filtered: 1 Finish binding event prediction: 2.2m Finish binding event prediction: 2.0m Finish binding event prediction: 1.2m Refine read distribution from 123 binding events. Refine read distribution from 92 binding events. Refine read distribution from 95 binding events. Refine read distribution from 1066 binding events. --------------------------- Events discovered Significant: 516 Insignificant: 179 Filtered: 37 Finish binding event prediction: 41.1s Refine read distribution from 370 binding events. --------------------------- Events discovered Significant: 42 Insignificant: 75 Filtered: 13 Finish binding event prediction: 2.7m Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 144 Insignificant: 61 Filtered: 6 Finish binding event prediction: 1.4m --------------------------- Events discovered Significant: 186 Insignificant: 27 Filtered: 4 Finish binding event prediction: 59.1s Refine read distribution from 140 binding events. Refine read distribution from 87 binding events. --------------------------- Events discovered Significant: 151 Insignificant: 26 Filtered: 0 Finish binding event prediction: 53.1s Refine read distribution from 124 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 37 Insignificant: 0 Filtered: 0 Finish binding event prediction: 30.1s Refine read distribution from 33 binding events. --------------------------- Events discovered Significant: 172 Insignificant: 0 Filtered: 57 Finish binding event prediction: 4.0m Refine read distribution from 147 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 130 Insignificant: 41 Filtered: 2 Finish binding event prediction: 50.1s Refine read distribution from 91 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 143 Insignificant: 61 Filtered: 6 No valid binding event was found. --------------------------- Events discovered Significant: 131 Insignificant: 1 Filtered: 31 --------------------------- Events discovered Significant: 106 Insignificant: 101 Filtered: 17 Finish binding event prediction: 1.8m --------------------------- Events discovered Significant: 234 Insignificant: 11 Filtered: 44 --------------------------- Events discovered Significant: 13 Insignificant: 0 Filtered: 4 Finish binding event prediction: 4.2m Finish binding event prediction: 4.3m Refine read distribution from 87 binding events. Finish binding event prediction: 4.1m Running with 1 threads ... Finish binding event prediction: 4.1m Refine read distribution from 49 binding events. Running with 1 threads ... Refine read distribution from 18 binding events. Running with 1 threads ... Refine read distribution from 6 binding events. Running with 1 threads ... Refine read distribution from 60 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 163 Insignificant: 1 Filtered: 53 Finish binding event prediction: 4.1m Refine read distribution from 134 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 157 Insignificant: 41 Filtered: 1 Finish binding event prediction: 1.5m Refine read distribution from 132 binding events. --------------------------- Events discovered Significant: 322 Insignificant: 0 Filtered: 100 --------------------------- Events discovered Significant: 182 Insignificant: 1 Filtered: 38 Finish binding event prediction: 4.1m Finish binding event prediction: 4.2m Refine read distribution from 61 binding events. Running with 1 threads ... Refine read distribution from 249 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 44 Insignificant: 17 Filtered: 0 Finish binding event prediction: 45.1s Refine read distribution from 26 binding events. --------------------------- Events discovered Significant: 237 Insignificant: 0 Filtered: 76 Finish binding event prediction: 4.3m Refine read distribution from 77 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 102 Insignificant: 63 Filtered: 23 Finish binding event prediction: 4.0m Refine read distribution from 24 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 124 Insignificant: 62 Filtered: 4 Finish binding event prediction: 1.1m Refine read distribution from 68 binding events. --------------------------- Events discovered Significant: 117 Insignificant: 47 Filtered: 3 Finish binding event prediction: 2.0m Refine read distribution from 66 binding events. --------------------------- Events discovered Significant: 1415 Insignificant: 387 Filtered: 6 Finish binding event prediction: 2.3m Refine read distribution from 1133 binding events. --------------------------- Events discovered Significant: 691 Insignificant: 176 Filtered: 11 Finish binding event prediction: 2.1m Refine read distribution from 551 binding events. --------------------------- Events discovered Significant: 123 Insignificant: 3 Filtered: 31 --------------------------- Events discovered Significant: 63 Insignificant: 44 Filtered: 1 Finish binding event prediction: 4.5m Finish binding event prediction: 2.0m --------------------------- Events discovered Significant: 242 Insignificant: 66 Filtered: 2 Finish binding event prediction: 2.0m Refine read distribution from 54 binding events. Refine read distribution from 29 binding events. Running with 1 threads ... Refine read distribution from 202 binding events. --------------------------- Events discovered Significant: 33 Insignificant: 0 Filtered: 0 Finish binding event prediction: 30.1s Refine read distribution from 29 binding events. --------------------------- Events discovered Significant: 372 Insignificant: 0 Filtered: 120 Finish binding event prediction: 4.8m Refine read distribution from 228 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 311 Insignificant: 0 Filtered: 95 Finish binding event prediction: 4.9m Refine read distribution from 257 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 8 Insignificant: 20 Filtered: 5 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 102 Insignificant: 11 Filtered: 36 Finish binding event prediction: 4.1m Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 106 Insignificant: 47 Filtered: 0 Finish binding event prediction: 56.2s Refine read distribution from 65 binding events. --------------------------- Events discovered Significant: 585 Insignificant: 16 Filtered: 102 --------------------------- Events discovered Significant: 389 Insignificant: 0 Filtered: 126 --------------------------- Events discovered Significant: 746 Insignificant: 1 Filtered: 169 Finish binding event prediction: 4.8m --------------------------- Events discovered Significant: 612 Insignificant: 2 Filtered: 120 Finish binding event prediction: 4.8m Finish binding event prediction: 4.8m Finish binding event prediction: 4.8m Refine read distribution from 147 binding events. Running with 1 threads ... Refine read distribution from 165 binding events. Refine read distribution from 310 binding events. Running with 1 threads ... Running with 1 threads ... Refine read distribution from 188 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 174 Insignificant: 62 Filtered: 2 Finish binding event prediction: 1.6m Refine read distribution from 149 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 79 Insignificant: 17 Filtered: 31 Finish binding event prediction: 4.5m Refine read distribution from 34 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 130 Insignificant: 110 Filtered: 8 Finish binding event prediction: 1.4m Refine read distribution from 99 binding events. --------------------------- Events discovered Significant: 1573 Insignificant: 439 Filtered: 2 Finish binding event prediction: 1.4m --------------------------- Events discovered Significant: 212 Insignificant: 0 Filtered: 70 Finish binding event prediction: 5.3m Refine read distribution from 1210 binding events. Refine read distribution from 64 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 527 Insignificant: 0 Filtered: 164 Finish binding event prediction: 5.2m Refine read distribution from 400 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 746 Insignificant: 417 Filtered: 28 Finish binding event prediction: 2.2m Refine read distribution from 584 binding events. --------------------------- Events discovered Significant: 101 Insignificant: 18 Filtered: 38 Finish binding event prediction: 4.6m Refine read distribution from 41 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 285 Insignificant: 99 Filtered: 6 Finish binding event prediction: 1.2m Refine read distribution from 242 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 1.7m --------------------------- Events discovered Significant: 514 Insignificant: 0 Filtered: 157 Finish binding event prediction: 5.4m Refine read distribution from 382 binding events. --------------------------- Events discovered Significant: 146 Insignificant: 69 Filtered: 4 --------------------------- Events discovered Significant: 1488 Insignificant: 471 Filtered: 1 Finish binding event prediction: 1.9m Running with 1 threads ... Finish binding event prediction: 1.2m Refine read distribution from 120 binding events. Refine read distribution from 1159 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.1m --------------------------- Events discovered Significant: 1373 Insignificant: 212 Filtered: 5 Finish binding event prediction: 2.5m Refine read distribution from 967 binding events. --------------------------- Events discovered Significant: 154 Insignificant: 62 Filtered: 2 Finish binding event prediction: 1.4m Refine read distribution from 114 binding events. --------------------------- Events discovered Significant: 189 Insignificant: 3 Filtered: 41 Finish binding event prediction: 5.6m Refine read distribution from 65 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 208 Insignificant: 69 Filtered: 2 Finish binding event prediction: 2.0m Refine read distribution from 166 binding events. --------------------------- Events discovered Significant: 394 Insignificant: 0 Filtered: 130 Finish binding event prediction: 5.8m Refine read distribution from 232 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 448 Insignificant: 100 Filtered: 5 Finish binding event prediction: 2.0m Refine read distribution from 315 binding events. --------------------------- Events discovered Significant: 1489 Insignificant: 372 Filtered: 1 Finish binding event prediction: 1.2m Refine read distribution from 1150 binding events. --------------------------- Events discovered Significant: 500 Insignificant: 81 Filtered: 4 Finish binding event prediction: 1.8m Refine read distribution from 354 binding events. --------------------------- Events discovered Significant: 1564 Insignificant: 488 Filtered: 0 Finish binding event prediction: 3.1m Refine read distribution from 1195 binding events. --------------------------- Events discovered Significant: 733 Insignificant: 192 Filtered: 13 Finish binding event prediction: 1.1m Refine read distribution from 583 binding events. --------------------------- Events discovered Significant: 379 Insignificant: 0 Filtered: 116 Finish binding event prediction: 5.9m Refine read distribution from 285 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 257 Insignificant: 77 Filtered: 4 Finish binding event prediction: 1.8m Refine read distribution from 205 binding events. --------------------------- Events discovered Significant: 432 Insignificant: 108 Filtered: 4 Finish binding event prediction: 2.5m Refine read distribution from 299 binding events. --------------------------- Events discovered Significant: 1299 Insignificant: 217 Filtered: 8 Finish binding event prediction: 2.9m Refine read distribution from 954 binding events. --------------------------- Events discovered Significant: 895 Insignificant: 21 Filtered: 188 Finish binding event prediction: 6.2m Refine read distribution from 671 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 144 Insignificant: 71 Filtered: 2 Finish binding event prediction: 2.5m Refine read distribution from 112 binding events. --------------------------- Events discovered Significant: 1709 Insignificant: 451 Filtered: 2 Finish binding event prediction: 1.7m Refine read distribution from 1280 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 1341 Insignificant: 200 Filtered: 10 Finish binding event prediction: 2.5m Refine read distribution from 959 binding events. --------------------------- Events discovered Significant: 441 Insignificant: 64 Filtered: 3 Finish binding event prediction: 2.3m Refine read distribution from 283 binding events. --------------------------- Events discovered Significant: 959 Insignificant: 256 Filtered: 4 Finish binding event prediction: 1.7m Refine read distribution from 744 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 517 Insignificant: 84 Filtered: 0 Finish binding event prediction: 2.1m Refine read distribution from 357 binding events. --------------------------- Events discovered Significant: 197 Insignificant: 87 Filtered: 9 Finish binding event prediction: 1.6m Refine read distribution from 124 binding events. --------------------------- Events discovered Significant: 517 Insignificant: 0 Filtered: 163 Finish binding event prediction: 6.7m Refine read distribution from 391 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 496 Insignificant: 168 Filtered: 16 Finish binding event prediction: 3.3m Refine read distribution from 371 binding events. --------------------------- Events discovered Significant: 1566 Insignificant: 523 Filtered: 1 Finish binding event prediction: 1.8m Refine read distribution from 1203 binding events. --------------------------- Events discovered Significant: 824 Insignificant: 211 Filtered: 6 Finish binding event prediction: 2.1m Refine read distribution from 655 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 689 Insignificant: 72 Filtered: 25 Finish binding event prediction: 2.4m Refine read distribution from 232 binding events. --------------------------- Events discovered Significant: 1332 Insignificant: 224 Filtered: 8 Finish binding event prediction: 3.0m Refine read distribution from 962 binding events. --------------------------- Events discovered Significant: 1476 Insignificant: 296 Filtered: 10 Finish binding event prediction: 3.2m Refine read distribution from 1039 binding events. --------------------------- Events discovered Significant: 743 Insignificant: 384 Filtered: 54 Finish binding event prediction: 1.2m Refine read distribution from 547 binding events. --------------------------- Events discovered Significant: 752 Insignificant: 106 Filtered: 25 Finish binding event prediction: 2.3m Refine read distribution from 301 binding events. --------------------------- Events discovered Significant: 1582 Insignificant: 307 Filtered: 5 Finish binding event prediction: 2.4m Refine read distribution from 1067 binding events. --------------------------- Events discovered Significant: 1533 Insignificant: 276 Filtered: 13 Finish binding event prediction: 4.0m Refine read distribution from 1049 binding events. ============================================== 2025-02-18 16:40:17 ============================================== 2025-02-18 16:40:17 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp.SE.a.GPS Original read count stats: _IP Bases: 249264 HitCounts: 292606.0 Original read count stats: _IP Bases: 298261 HitCounts: 365756.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 36 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 44 reads. The genome is segmented into 8413 regions for analysis. Running with 1 threads ... The genome is segmented into 8573 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:40:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_1.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_1.1x36mers.unique.GPS ============================================== 2025-02-18 16:40:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc.1x36mers.unique.GPS Original read count stats: _IP Bases: 403577 HitCounts: 1956914.0 Original read count stats: _IP Bases: 879852 HitCounts: 2870506.0 ============================================== 2025-02-18 16:40:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 62 reads. Original read count stats: _IP Bases: 170791 HitCounts: 1654337.0 ============================================== 2025-02-18 16:40:23 The genome is segmented into 8424 regions for analysis. ============================================== 2025-02-18 16:40:23 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 28 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_1.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS The genome is segmented into 8493 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 149 reads. Original read count stats: Original read count stats: _IP Bases: 585366 HitCounts: 3124186.0 _IP Bases: 1038960 HitCounts: 3517299.0 ============================================== 2025-02-18 16:40:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS ============================================== 2025-02-18 16:40:24 Original read count stats: ============================================== 2025-02-18 16:40:24_IP Bases: 251784 HitCounts: 2038834.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 106 reads. The genome is segmented into 8162 regions for analysis. ============================================== 2025-02-18 16:40:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 44 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS Running with 1 threads ... The genome is segmented into 8429 regions for analysis. ============================================== 2025-02-18 16:40:25 ============================================== 2025-02-18 16:40:25 Original read count stats: _IP Bases: 1187307 HitCounts: 3006417.0 Running with 1 threads ... The genome is segmented into 8456 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:40:25 ============================================== 2025-02-18 16:40:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS ============================================== 2025-02-18 16:40:25 Original read count stats: Original read count stats: ============================================== 2025-02-18 16:40:25 ============================================== 2025-02-18 16:40:26 ============================================== 2025-02-18 16:40:26 ============================================== 2025-02-18 16:40:27 ============================================== 2025-02-18 16:40:27 At Poisson p-value 1.0e-03, in a 301bp window, expect 233 reads. ============================================== 2025-02-18 16:40:25 ============================================== 2025-02-18 16:40:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 245 reads. ============================================== 2025-02-18 16:40:26 ============================================== 2025-02-18 16:40:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS ============================================== 2025-02-18 16:40:27_IP Bases: 1749494 HitCounts: 2918843.0 _IP Bases: 1450451 HitCounts: 3253124.0 ============================================== 2025-02-18 16:40:27 ============================================== 2025-02-18 16:40:27 ============================================== 2025-02-18 16:40:27 ============================================== 2025-02-18 16:40:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_1.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_2.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_2.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_2.1x36mers.unique.GPS ============================================== 2025-02-18 16:40:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_2.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp.SE.a.GPS Original read count stats: _IP Bases: 43126 HitCounts: 4641200.0 ============================================== 2025-02-18 16:40:27 ============================================== 2025-02-18 16:40:27 Original read count stats: _IP Bases: 108011 HitCounts: 4093880.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc.1x36mers.unique.GPS The genome is segmented into 8364 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS Original read count stats: _IP Bases: 422303 HitCounts: 4330588.0 Original read count stats: Original read count stats: _IP Bases: 201974 HitCounts: 2111315.0 _IP Bases: 370472 HitCounts: 3715975.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 16 reads. Original read count stats: _IP Bases: 1815087 HitCounts: 2871295.0 ============================================== 2025-02-18 16:40:28 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 20 reads. Original read count stats: _IP Bases: 658719 HitCounts: 2511341.0 _IP Bases: 1170659 HitCounts: 2046616.0 Original read count stats: Running with 1 threads ... _IP Bases: 1352171 HitCounts: 1862734.0 Original read count stats: _IP Bases: 915950 HitCounts: 2287249.0 The genome is segmented into 8356 regions for analysis. Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif.SE.a.GPS Original read count stats: _IP Bases: 2043716 HitCounts: 2922358.0 Original read count stats: _IP Bases: 1093392 HitCounts: 1955404.0 _IP Bases: 294160 HitCounts: 2531484.0 Original read count stats: _IP Bases: 903223 HitCounts: 2090759.0 The genome is segmented into 2372 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 49864 HitCounts: 3196328.0 Original read count stats: _IP Bases: 1973635 HitCounts: 3023774.0 Running with 1 threads ... Original read count stats: _IP Bases: 1122611 HitCounts: 2513055.0 Original read count stats: Original read count stats: _IP Bases: 1794159 HitCounts: 2976561.0 _IP Bases: 1256873 HitCounts: 4854615.0 Original read count stats: _IP Bases: 96119 HitCounts: 4944494.0 Original read count stats: The genome is segmented into 8270 regions for analysis. _IP Bases: 2118413 HitCounts: 3492695.0 Original read count stats: ============================================== 2025-02-18 16:40:28 Running with 1 threads ... _IP Bases: 1899921 HitCounts: 3590135.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 15 reads. ============================================== 2025-02-18 16:40:28 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 18 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 44 reads. The genome is segmented into 4937 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 59 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp.SE.a.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 77 reads. The genome is segmented into 8116 regions for analysis. Original read count stats: _IP Bases: 1200936 HitCounts: 2203541.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 72 reads. The genome is segmented into 8692 regions for analysis. ============================================== 2025-02-18 16:40:28 Running with 1 threads ... The genome is segmented into 8295 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_1.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_1.SE.a.GPS Original read count stats: _IP Bases: 131208 HitCounts: 5110059.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 120 reads. Original read count stats: _IP Bases: 1402243 HitCounts: 2155081.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 128 reads. ============================================== 2025-02-18 16:40:29 At Poisson p-value 1.0e-03, in a 301bp window, expect 153 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 160 reads. The genome is segmented into 8463 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 169 reads. The genome is segmented into 8635 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 31 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 150 reads. Running with 1 threads ... The genome is segmented into 8248 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 239 reads. Running with 1 threads ... Original read count stats: _IP Bases: 1003959 HitCounts: 5736651.0 ============================================== 2025-02-18 16:40:29 At Poisson p-value 1.0e-03, in a 301bp window, expect 174 reads. The genome is segmented into 8298 regions for analysis. ============================================== 2025-02-18 16:40:29 ============================================== 2025-02-18 16:40:29 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 248 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS Original read count stats: _IP Bases: 1119996 HitCounts: 2105800.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_2.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_2.1x36mers.unique.GPS The genome is segmented into 8102 regions for analysis. Original read count stats: Running with 1 threads ... _IP Bases: 298289 HitCounts: 2198544.0 ============================================== 2025-02-18 16:40:29 At Poisson p-value 1.0e-03, in a 301bp window, expect 171 reads. The genome is segmented into 8143 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_1.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 492080 HitCounts: 3161780.0 The genome is segmented into 8223 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 260 reads. The genome is segmented into 8165 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 192 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 252 reads. Running with 1 threads ... ============================================== 2025-02-18 16:40:30 The genome is segmented into 8068 regions for analysis. Original read count stats: _IP Bases: 1328803 HitCounts: 5194382.0 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 48 reads. The genome is segmented into 8055 regions for analysis. Running with 1 threads ... The genome is segmented into 8241 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 265 reads. ============================================== 2025-02-18 16:40:30 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 268 reads. Original read count stats: _IP Bases: 1276938 HitCounts: 5447865.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_2.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_2.SE.a.GPS The genome is segmented into 8043 regions for analysis. The genome is segmented into 8244 regions for analysis. The genome is segmented into 8326 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 162 reads. Running with 1 threads ... The genome is segmented into 8248 regions for analysis. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-18 16:40:30 Original read count stats: _IP Bases: 1209448 HitCounts: 2337412.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 146 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 301 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 347 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 302 reads. The genome is segmented into 8134 regions for analysis. Running with 1 threads ... The genome is segmented into 7978 regions for analysis. ============================================== 2025-02-18 16:40:31 Running with 1 threads ... The genome is segmented into 8137 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc.SE.a.GPS Running with 1 threads ... ============================================== 2025-02-18 16:40:31 The genome is segmented into 8619 regions for analysis. Original read count stats: Original read count stats: _IP Bases: 414734 HitCounts: 2588211.0 _IP Bases: 1351825 HitCounts: 5573370.0 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS Original read count stats: The genome is segmented into 8302 regions for analysis. _IP Bases: 59012 HitCounts: 3767043.0 Running with 1 threads ... The genome is segmented into 8291 regions for analysis. The genome is segmented into 8103 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 17 reads. ============================================== 2025-02-18 16:40:31 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_1.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_1.SE.a.GPS The genome is segmented into 8137 regions for analysis. The genome is segmented into 4607 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 119260 HitCounts: 6376516.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 64 reads. The genome is segmented into 8174 regions for analysis. ============================================== 2025-02-18 16:40:32 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 348 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 31 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 180 reads. The genome is segmented into 8282 regions for analysis. --------------------------- Events discovered Significant: 1521 Insignificant: 335 Filtered: 5 ============================================== 2025-02-18 16:40:32Finish binding event prediction: 2.6m --------------------------- Events discovered Significant: 458 Insignificant: 61 Filtered: 4 Finish binding event prediction: 2.4m Refine read distribution from 1068 binding events. Original read count stats: Running with 1 threads ... _IP Bases: 1318880 HitCounts: 6071004.0 Refine read distribution from 278 binding events. Original read count stats: _IP Bases: 549043 HitCounts: 2852730.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS ============================================== 2025-02-18 16:40:32 The genome is segmented into 8313 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS The genome is segmented into 7967 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:40:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 342 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 309 reads. Original read count stats: _IP Bases: 1006893 HitCounts: 2500403.0 Original read count stats: _IP Bases: 337150 HitCounts: 2529783.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 88 reads. ============================================== 2025-02-18 16:40:33 Original read count stats: ============================================== 2025-02-18 16:40:33_IP Bases: 464480 HitCounts: 2957006.0 ============================================== 2025-02-18 16:40:33 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 58 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS The genome is segmented into 8205 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 78 reads. The genome is segmented into 8237 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1321313 HitCounts: 2708218.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 159 reads. Original read count stats: _IP Bases: 1900000 HitCounts: 2508739.0 Original read count stats: _IP Bases: 1678388 HitCounts: 2459239.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 364 reads. ============================================== 2025-02-18 16:40:34 The genome is segmented into 8379 regions for analysis. The genome is segmented into 8338 regions for analysis. Running with 1 threads ... The genome is segmented into 8494 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS Running with 1 threads ... The genome is segmented into 8262 regions for analysis. The genome is segmented into 8447 regions for analysis. The genome is segmented into 8580 regions for analysis. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 197 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 219 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 343 reads. _IP Bases: 1750069 HitCounts: 2575882.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 234 reads. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8506 regions for analysis. Running with 1 threads ... The genome is segmented into 7944 regions for analysis. The genome is segmented into 7988 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8012 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 230 reads. The genome is segmented into 8087 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:40:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_1.SE.a.GPS Original read count stats: ============================================== 2025-02-18 16:40:42_IP Bases: 1986820 HitCounts: 1.0355888E7 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc.1x36mers.unique.GPS Original read count stats: _IP Bases: 35696 HitCounts: 3927513.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 15 reads. The genome is segmented into 2420 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:40:44 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS Original read count stats: _IP Bases: 3125560 HitCounts: 9701821.0 --------------------------- Events discovered Significant: 118 Insignificant: 0 Filtered: 11 At Poisson p-value 1.0e-03, in a 301bp window, expect 724 reads. Finish binding event prediction: 21.1s Refine read distribution from 65 binding events. Running with 1 threads ... ============================================== 2025-02-18 16:40:49 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp.SE.a.GPS The genome is segmented into 8549 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 688 reads. --------------------------- Events discovered Significant: 98 Insignificant: 0 Filtered: 18 --------------------------- Events discovered Significant: 107 Insignificant: 1 Filtered: 19 Original read count stats: Finish binding event prediction: 24.0s Finish binding event prediction: 23.7s _IP Bases: 3310667 HitCounts: 1.194029E7 Refine read distribution from 60 binding events. Running with 1 threads ... Refine read distribution from 77 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1749 Insignificant: 495 Filtered: 2 The genome is segmented into 8069 regions for analysis. Finish binding event prediction: 2.7m Refine read distribution from 1297 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 142 Insignificant: 18 Filtered: 1 Finish binding event prediction: 6.1s Refine read distribution from 106 binding events. At Poisson p-value 1.0e-03, in a 301bp window, expect 842 reads. --------------------------- Events discovered Significant: 118 Insignificant: 13 Filtered: 0 Finish binding event prediction: 10.1s Refine read distribution from 94 binding events. The genome is segmented into 8223 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 1521 Insignificant: 310 Filtered: 13 Finish binding event prediction: 3.7m Refine read distribution from 1049 binding events. --------------------------- Events discovered Significant: 159 Insignificant: 0 Filtered: 7 Finish binding event prediction: 30.1s Refine read distribution from 65 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 171 Insignificant: 14 Filtered: 35 Finish binding event prediction: 43.1s Refine read distribution from 76 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 147 Insignificant: 24 Filtered: 0 Finish binding event prediction: 23.0s Refine read distribution from 105 binding events. --------------------------- Events discovered Significant: 208 Insignificant: 11 Filtered: 31 Finish binding event prediction: 49.1s Refine read distribution from 85 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 66 Insignificant: 0 Filtered: 13 Finish binding event prediction: 1.0m Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 56 Insignificant: 0 Filtered: 15 Finish binding event prediction: 1.1m Refine read distribution from 38 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 137 Insignificant: 5 Filtered: 2 Finish binding event prediction: 16.6s Refine read distribution from 90 binding events. --------------------------- Events discovered Significant: 98 Insignificant: 61 Filtered: 42 Finish binding event prediction: 1.1m Refine read distribution from 61 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 206 Insignificant: 40 Filtered: 46 Finish binding event prediction: 1.1m Refine read distribution from 113 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 152 Insignificant: 33 Filtered: 9 Finish binding event prediction: 29.1s Refine read distribution from 117 binding events. --------------------------- Events discovered Significant: 207 Insignificant: 27 Filtered: 3 --------------------------- Events discovered Significant: 1489 Insignificant: 299 Filtered: 7 Finish binding event prediction: 29.2s Finish binding event prediction: 3.3m Refine read distribution from 137 binding events. Refine read distribution from 1048 binding events. --------------------------- Events discovered Significant: 139 Insignificant: 55 Filtered: 45 Finish binding event prediction: 1.3m Refine read distribution from 78 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 126 Insignificant: 5 Filtered: 0 Finish binding event prediction: 29.1s Refine read distribution from 111 binding events. --------------------------- Events discovered Significant: 161 Insignificant: 21 Filtered: 35 Finish binding event prediction: 1.5m Refine read distribution from 78 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1584 Insignificant: 292 Filtered: 6 Finish binding event prediction: 2.9m Refine read distribution from 1085 binding events. --------------------------- Events discovered Significant: 228 Insignificant: 90 Filtered: 6 Finish binding event prediction: 32.1s Refine read distribution from 172 binding events. --------------------------- Events discovered Significant: 157 Insignificant: 0 Filtered: 24 Finish binding event prediction: 1.7m Refine read distribution from 61 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 131 Insignificant: 37 Filtered: 52 Finish binding event prediction: 1.7m Refine read distribution from 66 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 190 Insignificant: 0 Filtered: 23 Finish binding event prediction: 1.7m Refine read distribution from 71 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 162 Insignificant: 60 Filtered: 3 Finish binding event prediction: 49.2s Refine read distribution from 128 binding events. --------------------------- Events discovered Significant: 33 Insignificant: 44 Filtered: 7 Finish binding event prediction: 1.8m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 258 Insignificant: 69 Filtered: 4 Finish binding event prediction: 31.1s Refine read distribution from 191 binding events. --------------------------- Events discovered Significant: 50 Insignificant: 50 Filtered: 11 ============================================== 2025-02-18 16:42:28Finish binding event prediction: 2.0m Refine read distribution from 21 binding events. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 06-E.coli-UvrY-GSE74810/UvrY-ChIP-exo.1x36mers.unique.bam --out 06-E.coli-UvrY-GSE74810/UvrY-ChIP-exo.1x36mers.unique.GPS Original read count stats: _IP Bases: 7535219 HitCounts: 4.4173122E7 --------------------------- Events discovered Significant: 175 Insignificant: 58 Filtered: 1 Finish binding event prediction: 45.1s Refine read distribution from 120 binding events. --------------------------- Events discovered Significant: 276 Insignificant: 0 Filtered: 31 Finish binding event prediction: 2.3m Refine read distribution from 104 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 131 Insignificant: 15 Filtered: 0 ============================================== 2025-02-18 16:42:45Finish binding event prediction: 1.3m Refine read distribution from 99 binding events. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 06-E.coli-UvrY-GSE74810/UvrY-ChIP-exo.SE.a.bam --out 06-E.coli-UvrY-GSE74810/UvrY-ChIP-exo.SE.a.GPS Original read count stats: _IP Bases: 7730863 HitCounts: 5.0298113E7 --------------------------- Events discovered Significant: 242 Insignificant: 17 Filtered: 1 Finish binding event prediction: 39.1s Refine read distribution from 181 binding events. --------------------------- Events discovered Significant: 67 Insignificant: 1 Filtered: 17 Finish binding event prediction: 2.5m Refine read distribution from 40 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 145 Insignificant: 50 Filtered: 0 Finish binding event prediction: 43.1s Refine read distribution from 123 binding events. --------------------------- Events discovered Significant: 166 Insignificant: 0 Filtered: 30 Finish binding event prediction: 2.4m Refine read distribution from 61 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 226 Insignificant: 11 Filtered: 2 Finish binding event prediction: 41.1s Refine read distribution from 169 binding events. --------------------------- Events discovered Significant: 264 Insignificant: 26 Filtered: 1 Finish binding event prediction: 16.1s Refine read distribution from 178 binding events. --------------------------- Events discovered Significant: 51 Insignificant: 33 Filtered: 17 --------------------------- Events discovered Significant: 83 Insignificant: 2 Filtered: 17 Finish binding event prediction: 2.6m --------------------------- Events discovered Significant: 142 Insignificant: 39 Filtered: 0 Finish binding event prediction: 2.5m Finish binding event prediction: 15.3s Refine read distribution from 115 binding events. Refine read distribution from 17 binding events. Refine read distribution from 55 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 72 Insignificant: 34 Filtered: 16 Finish binding event prediction: 2.7m Refine read distribution from 42 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 28 Insignificant: 44 Filtered: 5 At Poisson p-value 1.0e-03, in a 301bp window, expect 3397 reads. Finish binding event prediction: 2.6m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 87 Insignificant: 4 Filtered: 14 Finish binding event prediction: 2.7m Refine read distribution from 31 binding events. Running with 1 threads ... The genome is segmented into 8018 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 36 Insignificant: 1 Filtered: 11 Finish binding event prediction: 2.6m Refine read distribution from 25 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 208 Insignificant: 12 Filtered: 43 Finish binding event prediction: 2.9m Refine read distribution from 106 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 99 Insignificant: 34 Filtered: 1 Finish binding event prediction: 56.7s Refine read distribution from 64 binding events. --------------------------- Events discovered Significant: 222 Insignificant: 0 Filtered: 35 Finish binding event prediction: 2.8m Refine read distribution from 88 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.9m Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 1 Finish binding event prediction: 2.9m Running with 1 threads ... --------------------------- Events discovered Significant: 89 Insignificant: 60 Filtered: 14 Finish binding event prediction: 53.2s Refine read distribution from 52 binding events. --------------------------- Events discovered Significant: 253 Insignificant: 21 Filtered: 1 Finish binding event prediction: 27.1s Refine read distribution from 196 binding events. --------------------------- Events discovered Significant: 49 Insignificant: 1 Filtered: 16 Finish binding event prediction: 3.0m Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 10 Insignificant: 1 Filtered: 3 Finish binding event prediction: 2.9m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 198 Insignificant: 12 Filtered: 31 Finish binding event prediction: 2.9m Refine read distribution from 81 binding events. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 3789 reads. --------------------------- Events discovered Significant: 120 Insignificant: 5 Filtered: 18 Finish binding event prediction: 3.0m Refine read distribution from 41 binding events. Running with 1 threads ... The genome is segmented into 8177 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 65 Insignificant: 2 Filtered: 20 Finish binding event prediction: 3.2m Refine read distribution from 41 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 18 Insignificant: 0 Filtered: 6 Finish binding event prediction: 3.0m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 26 Insignificant: 0 Filtered: 7 Finish binding event prediction: 3.1m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 217 Insignificant: 5 Filtered: 61 Finish binding event prediction: 3.1m Refine read distribution from 186 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 60 Insignificant: 0 Filtered: 19 Finish binding event prediction: 3.1m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 27 Insignificant: 0 Filtered: 9 Finish binding event prediction: 3.2m Refine read distribution from 20 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 33 Insignificant: 0 Filtered: 10 Finish binding event prediction: 3.4m Refine read distribution from 24 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 208 Insignificant: 6 Filtered: 1 Finish binding event prediction: 52.1s Refine read distribution from 154 binding events. --------------------------- Events discovered Significant: 276 Insignificant: 26 Filtered: 0 Finish binding event prediction: 36.1s Refine read distribution from 221 binding events. --------------------------- Events discovered Significant: 51 Insignificant: 14 Filtered: 0 Finish binding event prediction: 32.1s Refine read distribution from 41 binding events. --------------------------- Events discovered Significant: 178 Insignificant: 43 Filtered: 0 Finish binding event prediction: 50.2s Refine read distribution from 132 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.5m Running with 1 threads ... --------------------------- Events discovered Significant: 132 Insignificant: 29 Filtered: 0 --------------------------- Events discovered Significant: 320 Insignificant: 70 Filtered: 1 --------------------------- Events discovered Significant: 154 Insignificant: 23 Filtered: 0 Finish binding event prediction: 59.4s Finish binding event prediction: 44.5s Finish binding event prediction: 51.8s Refine read distribution from 120 binding events. Refine read distribution from 104 binding events. Refine read distribution from 237 binding events. --------------------------- Events discovered Significant: 86 Insignificant: 35 Filtered: 1 Finish binding event prediction: 54.1s Refine read distribution from 48 binding events. --------------------------- Events discovered Significant: 246 Insignificant: 61 Filtered: 3 Finish binding event prediction: 39.1s Refine read distribution from 175 binding events. --------------------------- Events discovered Significant: 133 Insignificant: 37 Filtered: 0 Finish binding event prediction: 55.2s Refine read distribution from 109 binding events. --------------------------- Events discovered Significant: 150 Insignificant: 15 Filtered: 0 Finish binding event prediction: 48.1s Refine read distribution from 83 binding events. --------------------------- Events discovered Significant: 23 Insignificant: 1 Filtered: 8 Finish binding event prediction: 3.8m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 23 Insignificant: 0 Filtered: 6 --------------------------- Events discovered Significant: 202 Insignificant: 35 Filtered: 2 --------------------------- Events discovered Significant: 5 Insignificant: 0 Filtered: 0 --------------------------- Events discovered Significant: 31 Insignificant: 1 Filtered: 8 Finish binding event prediction: 52.7s Finish binding event prediction: 3.7m Finish binding event prediction: 3.9m Finish binding event prediction: 3.8m Refine read distribution from 19 binding events. Running with 1 threads ... Refine read distribution from 145 binding events. Running with 1 threads ... Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.9m Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.9m Running with 1 threads ... --------------------------- Events discovered Significant: 25 Insignificant: 0 Filtered: 6 Finish binding event prediction: 4.0m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 265 Insignificant: 0 Filtered: 70 Finish binding event prediction: 3.9m Refine read distribution from 221 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 103 Insignificant: 17 Filtered: 0 Finish binding event prediction: 55.1s Refine read distribution from 88 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 4.1m Running with 1 threads ... --------------------------- Events discovered Significant: 52 Insignificant: 0 Filtered: 14 --------------------------- Events discovered Significant: 108 Insignificant: 24 Filtered: 0 --------------------------- Events discovered Significant: 140 Insignificant: 13 Filtered: 4 Finish binding event prediction: 4.3m Finish binding event prediction: 1.0m Finish binding event prediction: 1.2m Refine read distribution from 93 binding events. Refine read distribution from 105 binding events. Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 1 Finish binding event prediction: 1.6m --------------------------- Events discovered Significant: 174 Insignificant: 3 Filtered: 37 --------------------------- Events discovered Significant: 91 Insignificant: 7 Filtered: 0 Finish binding event prediction: 34.7s Refine read distribution from 77 binding events. Finish binding event prediction: 4.3m Refine read distribution from 77 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 112 Insignificant: 19 Filtered: 0 Finish binding event prediction: 41.2s Refine read distribution from 94 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 4.5m Running with 1 threads ... --------------------------- Events discovered Significant: 68 Insignificant: 6 Filtered: 0 Finish binding event prediction: 1.4m Refine read distribution from 62 binding events. --------------------------- Events discovered Significant: 122 Insignificant: 22 Filtered: 0 Finish binding event prediction: 38.1s Refine read distribution from 103 binding events. --------------------------- Events discovered Significant: 69 Insignificant: 9 Filtered: 9 Finish binding event prediction: 1.2m Refine read distribution from 27 binding events. --------------------------- Events discovered Significant: 749 Insignificant: 137 Filtered: 2 Finish binding event prediction: 1.4m Refine read distribution from 591 binding events. --------------------------- Events discovered Significant: 54 Insignificant: 0 Filtered: 17 Finish binding event prediction: 4.6m Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 4.7m Running with 1 threads ... --------------------------- Events discovered Significant: 48 Insignificant: 1 Filtered: 16 Finish binding event prediction: 4.8m Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 598 Insignificant: 60 Filtered: 11 Finish binding event prediction: 1.7m Refine read distribution from 344 binding events. --------------------------- Events discovered Significant: 94 Insignificant: 6 Filtered: 0 Finish binding event prediction: 1.2m Refine read distribution from 90 binding events. --------------------------- Events discovered Significant: 285 Insignificant: 68 Filtered: 0 Finish binding event prediction: 44.1s Refine read distribution from 209 binding events. --------------------------- Events discovered Significant: 120 Insignificant: 2 Filtered: 0 Finish binding event prediction: 54.2s Refine read distribution from 105 binding events. --------------------------- Events discovered Significant: 103 Insignificant: 53 Filtered: 15 Finish binding event prediction: 5.0m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 1 Filtered: 1 Finish binding event prediction: 1.9m --------------------------- Events discovered Significant: 130 Insignificant: 14 Filtered: 0 Finish binding event prediction: 48.1s Refine read distribution from 107 binding events. --------------------------- Events discovered Significant: 849 Insignificant: 96 Filtered: 2 Finish binding event prediction: 1.7m Refine read distribution from 655 binding events. --------------------------- Events discovered Significant: 43 Insignificant: 2 Filtered: 11 Finish binding event prediction: 5.3m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.0m --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.1m No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 565 Insignificant: 81 Filtered: 6 Finish binding event prediction: 1.6m Refine read distribution from 324 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.3m --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 2.0m --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.6m --------------------------- Events discovered Significant: 143 Insignificant: 7 Filtered: 0 Finish binding event prediction: 1.1m Refine read distribution from 120 binding events. --------------------------- Events discovered Significant: 48 Insignificant: 0 Filtered: 12 Finish binding event prediction: 6.5m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.3m ============================================== 2025-02-18 16:47:53 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS Original read count stats: _IP Bases: 381825 HitCounts: 473216.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 52 reads. ============================================== 2025-02-18 16:47:54 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS The genome is segmented into 8333 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 443679 HitCounts: 575080.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 61 reads. ============================================== 2025-02-18 16:47:55 The genome is segmented into 8493 regions for analysis. ============================================== 2025-02-18 16:47:55 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod.SE.a.GPS ============================================== 2025-02-18 16:47:56 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1-2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1-2.1x36mers.unique.GPS ============================================== 2025-02-18 16:47:56 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1-2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1-2.SE.a.GPS Original read count stats: _IP Bases: 488308 HitCounts: 1020135.0 Original read count stats: _IP Bases: 428463 HitCounts: 805679.0 Original read count stats: _IP Bases: 79741 HitCounts: 942573.0 Original read count stats: _IP Bases: 99628 HitCounts: 1197830.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 28 reads. The genome is segmented into 2050 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:47:57 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 09-E.coli-OmpR-GSE88979/OmpR_NaCl_1.1x36mers.unique.bam --out 09-E.coli-OmpR-GSE88979/OmpR_NaCl_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 37 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 80 reads. The genome is segmented into 1972 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 95 reads. Original read count stats: _IP Bases: 619219 HitCounts: 1262962.0 The genome is segmented into 8378 regions for analysis. Running with 1 threads ... The genome is segmented into 8563 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 84 reads. ============================================== 2025-02-18 16:47:58 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc.1x36mers.unique.GPS ============================================== 2025-02-18 16:47:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif.1x36mers.unique.GPS ============================================== 2025-02-18 16:47:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 09-E.coli-OmpR-GSE88979/OmpR_NaCl_1.SE.a.bam --out 09-E.coli-OmpR-GSE88979/OmpR_NaCl_1.SE.a.GPS Original read count stats: _IP Bases: 163457 HitCounts: 1721380.0 ============================================== 2025-02-18 16:47:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod.1x36mers.unique.GPS The genome is segmented into 8224 regions for analysis. ============================================== 2025-02-18 16:47:59 At Poisson p-value 1.0e-03, in a 301bp window, expect 30 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS Original read count stats: _IP Bases: 675501 HitCounts: 1566952.0 Original read count stats: _IP Bases: 1148670 HitCounts: 2637507.0 Original read count stats: _IP Bases: 744572 HitCounts: 1598433.0 The genome is segmented into 8504 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:48:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif.SE.a.GPS ============================================== 2025-02-18 16:48:00 ============================================== 2025-02-18 16:48:00 Original read count stats: _IP Bases: 687742 HitCounts: 3202622.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1.1x36mers.unique.GPS ============================================== 2025-02-18 16:48:00 ============================================== 2025-02-18 16:48:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 108 reads. ============================================== 2025-02-18 16:48:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp.SE.a.GPS ============================================== 2025-02-18 16:48:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc.SE.a.GPS Original read count stats: _IP Bases: 231019 HitCounts: 1963578.0 ============================================== 2025-02-18 16:48:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_2.SE.a.GPS ============================================== 2025-02-18 16:48:00 Original read count stats: _IP Bases: 1179824 HitCounts: 2834809.0 Original read count stats: _IP Bases: 1009392 HitCounts: 1740862.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 175 reads. Original read count stats: _IP Bases: 1160578 HitCounts: 1729799.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 140 reads. Original read count stats: _IP Bases: 1319551 HitCounts: 2858938.0 Original read count stats: _IP Bases: 446872 HitCounts: 1845860.0 The genome is segmented into 8410 regions for analysis. ============================================== 2025-02-18 16:48:01 ============================================== 2025-02-18 16:48:01 Original read count stats: _IP Bases: 516410 HitCounts: 3209017.0 Original read count stats: _IP Bases: 188802 HitCounts: 2032736.0 Original read count stats: _IP Bases: 1477153 HitCounts: 3092701.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod.1x36mers.unique.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 134 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 78 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod.SE.a.GPS ============================================== 2025-02-18 16:48:01 ============================================== 2025-02-18 16:48:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_2.1x36mers.unique.GPS ============================================== 2025-02-18 16:48:01 The genome is segmented into 4737 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 42 reads. The genome is segmented into 8419 regions for analysis. ============================================== 2025-02-18 16:48:01 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif.SE.a.GPS ============================================== 2025-02-18 16:48:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 74 reads. Running with 1 threads ... Original read count stats: _IP Bases: 748183 HitCounts: 1823069.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_2.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_2.SE.a.GPS Original read count stats: _IP Bases: 149901 HitCounts: 2135890.0 The genome is segmented into 8416 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 134 reads. Original read count stats: _IP Bases: 1112024 HitCounts: 3337018.0 The genome is segmented into 8722 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1178616 HitCounts: 3241046.0 Running with 1 threads ... ============================================== 2025-02-18 16:48:02 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod.SE.a.GPS The genome is segmented into 8392 regions for analysis. Running with 1 threads ... Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 187 reads. _IP Bases: 806937 HitCounts: 1974463.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 152 reads. Original read count stats: _IP Bases: 1039546 HitCounts: 1878542.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 43 reads. The genome is segmented into 8084 regions for analysis. ============================================== 2025-02-18 16:48:02 Original read count stats: _IP Bases: 769277 HitCounts: 3912487.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 09-E.coli-OmpR-GSE88979/OmpR_NaCl_2.1x36mers.unique.bam --out 09-E.coli-OmpR-GSE88979/OmpR_NaCl_2.1x36mers.unique.GPS Running with 1 threads ... The genome is segmented into 8091 regions for analysis. Running with 1 threads ... The genome is segmented into 8554 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 167 reads. ============================================== 2025-02-18 16:48:02 Original read count stats: _IP Bases: 837256 HitCounts: 2062163.0 ============================================== 2025-02-18 16:48:02 ============================================== 2025-02-18 16:48:02 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod.1x36mers.unique.GPS ============================================== 2025-02-18 16:48:02 The genome is segmented into 8220 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 223 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp.1x36mers.unique.GPS ============================================== 2025-02-18 16:48:03 Original read count stats: _IP Bases: 91635 HitCounts: 2183353.0 Original read count stats: _IP Bases: 979321 HitCounts: 2037491.0 Running with 1 threads ... The genome is segmented into 8237 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod.1x36mers.unique.GPS ============================================== 2025-02-18 16:48:03 ============================================== 2025-02-18 16:48:03 Running with 1 threads ... ============================================== 2025-02-18 16:48:03 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_1.1x36mers.unique.GPS ============================================== 2025-02-18 16:48:03 The genome is segmented into 8579 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 156 reads. ============================================== 2025-02-18 16:48:03 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_2.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 834608 HitCounts: 2056572.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 144 reads. Original read count stats: _IP Bases: 735590 HitCounts: 3882562.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 40 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 255 reads. The genome is segmented into 2102 regions for analysis. The genome is segmented into 8352 regions for analysis. ============================================== 2025-02-18 16:48:03 Original read count stats: The genome is segmented into 8338 regions for analysis. Original read count stats: Original read count stats: ============================================== 2025-02-18 16:48:03 ============================================== 2025-02-18 16:48:03 At Poisson p-value 1.0e-03, in a 301bp window, expect 141 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 166 reads. ============================================== 2025-02-18 16:48:04 At Poisson p-value 1.0e-03, in a 301bp window, expect 172 reads. Original read count stats: Original read count stats: ============================================== 2025-02-18 16:48:04 Original read count stats: ============================================== 2025-02-18 16:48:04 At Poisson p-value 1.0e-03, in a 301bp window, expect 251 reads. Original read count stats: _IP Bases: 2075470 HitCounts: 3947063.0 _IP Bases: 260615 HitCounts: 2369911.0 The genome is segmented into 8334 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 214 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 249 reads. ============================================== 2025-02-18 16:48:03 ============================================== 2025-02-18 16:48:04_IP Bases: 653794 HitCounts: 4092634.0 ============================================== 2025-02-18 16:48:05_IP Bases: 1334139 HitCounts: 3793306.0 The genome is segmented into 8256 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 172 reads. ============================================== 2025-02-18 16:48:05 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 220 reads. ============================================== 2025-02-18 16:48:05 ============================================== 2025-02-18 16:48:05_IP Bases: 913929 HitCounts: 2052805.0 _IP Bases: 1924300 HitCounts: 3825109.0 _IP Bases: 1186793 HitCounts: 2178001.0 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_2.1x36mers.unique.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/Ybih_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/Ybih_glc2_ChIPexo.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_1.1x36mers.unique.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc.1x36mers.unique.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod.SE.a.GPS ============================================== 2025-02-18 16:48:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc2_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-18 16:48:05 Original read count stats: Original read count stats: _IP Bases: 75295 HitCounts: 2787467.0 _IP Bases: 200808 HitCounts: 4623573.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc2_ChIPexo.SE.a.GPS ============================================== 2025-02-18 16:48:05 Original read count stats: _IP Bases: 543195 HitCounts: 1392083.0 Original read count stats: The genome is segmented into 8280 regions for analysis. _IP Bases: 667227 HitCounts: 2443037.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_1.1x36mers.unique.GPS The genome is segmented into 8431 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 17 reads. Original read count stats: Original read count stats: The genome is segmented into 8408 regions for analysis. _IP Bases: 528315 HitCounts: 4692658.0 Running with 1 threads ... Original read count stats: _IP Bases: 834020 HitCounts: 2373223.0 _IP Bases: 1216223 HitCounts: 2066333.0 The genome is segmented into 8595 regions for analysis. Original read count stats: The genome is segmented into 8518 regions for analysis. _IP Bases: 2075470 HitCounts: 3947063.0 Running with 1 threads ... Original read count stats: The genome is segmented into 8491 regions for analysis. Original read count stats: _IP Bases: 1348584 HitCounts: 2256281.0 _IP Bases: 2059637 HitCounts: 4263014.0 Running with 1 threads ... ============================================== 2025-02-18 16:48:06 Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc1_ChIPexo.1x36mers.unique.GPS The genome is segmented into 7607 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 95 reads. Running with 1 threads ... ============================================== 2025-02-18 16:48:06 Original read count stats: _IP Bases: 2081926 HitCounts: 4844593.0 ============================================== 2025-02-18 16:48:06 Original read count stats: _IP Bases: 2134910 HitCounts: 4406669.0 ============================================== 2025-02-18 16:48:06 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_2.1x36mers.unique.GPS ============================================== 2025-02-18 16:48:06 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 09-E.coli-OmpR-GSE88979/OmpR_NaCl_2.SE.a.bam --out 09-E.coli-OmpR-GSE88979/OmpR_NaCl_2.SE.a.GPS Original read count stats: _IP Bases: 457073 HitCounts: 2595928.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_2.SE.a.GPS ============================================== 2025-02-18 16:48:06 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod.SE.a.GPS Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 82 reads. ============================================== 2025-02-18 16:48:06_IP Bases: 1618403 HitCounts: 4739985.0 The genome is segmented into 4789 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2.SE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod.1x36mers.unique.GPS Original read count stats: _IP Bases: 1622652 HitCounts: 5166553.0 The genome is segmented into 8276 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 169 reads. The genome is segmented into 8126 regions for analysis. Original read count stats: _IP Bases: 119255 HitCounts: 2908697.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 116 reads. Original read count stats: _IP Bases: 585107 HitCounts: 2539290.0 Running with 1 threads ... Original read count stats: _IP Bases: 1673120 HitCounts: 5250822.0 Running with 1 threads ... ============================================== 2025-02-18 16:48:06 At Poisson p-value 1.0e-03, in a 301bp window, expect 124 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS Original read count stats: _IP Bases: 1037999 HitCounts: 2515025.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 208 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 84 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 173 reads. Original read count stats: _IP Bases: 894720 HitCounts: 2545263.0 ============================================== 2025-02-18 16:48:07 Original read count stats: Original read count stats: _IP Bases: 1715285 HitCounts: 6130646.0 _IP Bases: 1073587 HitCounts: 2454437.0 The genome is segmented into 8310 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc.SE.a.GPS Running with 1 threads ... ============================================== 2025-02-18 16:48:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 58 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_1.1x36mers.unique.GPS ============================================== 2025-02-18 16:48:07 The genome is segmented into 8373 regions for analysis. Original read count stats: _IP Bases: 642093 HitCounts: 2835927.0 ============================================== 2025-02-18 16:48:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 187 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 180 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod.1x36mers.unique.GPS Running with 1 threads ... The genome is segmented into 2003 regions for analysis. ============================================== 2025-02-18 16:48:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 106 reads. The genome is segmented into 8519 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod.SE.a.GPS The genome is segmented into 8278 regions for analysis. Running with 1 threads ... No valid binding event was found. ============================================== 2025-02-18 16:48:07 Running with 1 threads ... The genome is segmented into 8336 regions for analysis. Original read count stats: _IP Bases: 88830 HitCounts: 3267184.0 ============================================== 2025-02-18 16:48:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_2.SE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_1.SE.a.GPS Running with 1 threads ... Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod.SE.a.GPS _IP Bases: 149880 HitCounts: 3031819.0 Running with 1 threads ... ============================================== 2025-02-18 16:48:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 22 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 218 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 191 reads. ============================================== 2025-02-18 16:48:07 ============================================== 2025-02-18 16:48:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 303 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/Ybih_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/Ybih_glc2_ChIPexo.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 276 reads. The genome is segmented into 8285 regions for analysis. Original read count stats: The genome is segmented into 8358 regions for analysis. _IP Bases: 1008992 HitCounts: 2623163.0 ============================================== 2025-02-18 16:48:08 Original read count stats: _IP Bases: 919414 HitCounts: 2624573.0 The genome is segmented into 7438 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc1_ChIPexo.SE.a.GPS Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_1.SE.a.GPS ============================================== 2025-02-18 16:48:08 The genome is segmented into 8421 regions for analysis. ============================================== 2025-02-18 16:48:08 Original read count stats: _IP Bases: 1008583 HitCounts: 2646749.0 The genome is segmented into 8174 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc1_ChIPexo.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc1_ChIPexo.SE.a.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 109 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 55 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 175 reads. Running with 1 threads ... The genome is segmented into 8521 regions for analysis. The genome is segmented into 8511 regions for analysis. Original read count stats: _IP Bases: 2237823 HitCounts: 5848235.0 Original read count stats: Original read count stats: _IP Bases: 639738 HitCounts: 2052870.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 343 reads. _IP Bases: 2118691 HitCounts: 5559372.0 Running with 1 threads ... ============================================== 2025-02-18 16:48:08 The genome is segmented into 8394 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc1_ChIPexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 2217025 HitCounts: 5965128.0 The genome is segmented into 8238 regions for analysis. ============================================== 2025-02-18 16:48:08 Original read count stats: _IP Bases: 1675720 HitCounts: 5701076.0 Running with 1 threads ... Original read count stats: _IP Bases: 2237823 HitCounts: 5848235.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc1_ChIPexo.1x36mers.unique.GPS Original read count stats: ============================================== 2025-02-18 16:48:08_IP Bases: 1875154 HitCounts: 3158304.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_2.SE.a.GPS Original read count stats: _IP Bases: 1831636 HitCounts: 2670029.0 The genome is segmented into 8324 regions for analysis. The genome is segmented into 8163 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 200 reads. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8448 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 204 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 343 reads. Original read count stats: Running with 1 threads ... _IP Bases: 369555 HitCounts: 6482466.0 ============================================== 2025-02-18 16:48:09 Original read count stats: _IP Bases: 197077 HitCounts: 3162472.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod.SE.a.GPS Original read count stats: _IP Bases: 1187546 HitCounts: 2271039.0 The genome is segmented into 8414 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 381 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 364 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 132 reads. The genome is segmented into 8455 regions for analysis. The genome is segmented into 8086 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 76 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 382 reads. --------------------------- Events discovered Significant: 271 Insignificant: 66 Filtered: 5 At Poisson p-value 1.0e-03, in a 301bp window, expect 209 reads. The genome is segmented into 8242 regions for analysis. The genome is segmented into 8500 regions for analysis. The genome is segmented into 8542 regions for analysis. ============================================== 2025-02-18 16:48:10 At Poisson p-value 1.0e-03, in a 301bp window, expect 205 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 237 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 351 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 90 reads. Finish binding event prediction: 2.4m Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 382 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 274 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 209 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 365 reads. ============================================== 2025-02-18 16:48:10_IP Bases: 1451878 HitCounts: 6223388.0 The genome is segmented into 8448 regions for analysis. The genome is segmented into 8352 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 175 reads. Running with 1 threads ... Running with 1 threads ... Refine read distribution from 215 binding events. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc2_ChIPexo.SE.a.GPS ============================================== 2025-02-18 16:48:11 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_1.SE.a.GPS Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc2_ChIPexo.1x36mers.unique.GPS The genome is segmented into 8574 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8402 regions for analysis. Running with 1 threads ... The genome is segmented into 8437 regions for analysis. The genome is segmented into 8443 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 452 reads. The genome is segmented into 8480 regions for analysis. The genome is segmented into 8188 regions for analysis. The genome is segmented into 8148 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 1205994 HitCounts: 2678812.0 Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 2266622 HitCounts: 4559295.0 Original read count stats: _IP Bases: 2298417 HitCounts: 6888464.0 ============================================== 2025-02-18 16:48:12 At Poisson p-value 1.0e-03, in a 301bp window, expect 395 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace1_ChIPexp.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace1_ChIPexp.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 484 reads. The genome is segmented into 8332 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 455 reads. The genome is segmented into 8357 regions for analysis. Running with 1 threads ... The genome is segmented into 8510 regions for analysis. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 483 reads. The genome is segmented into 8579 regions for analysis. The genome is segmented into 8027 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:48:14 ============================================== 2025-02-18 16:48:14 ============================================== 2025-02-18 16:48:14 The genome is segmented into 8652 regions for analysis. _IP Bases: 597430 HitCounts: 5335290.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 484 reads. ============================================== 2025-02-18 16:48:14 The genome is segmented into 8688 regions for analysis. The genome is segmented into 8607 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 192 reads. The genome is segmented into 8684 regions for analysis. ============================================== 2025-02-18 16:48:14 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbiH_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbiH_glc1_ChIPexo.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace2_ChIPexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_2.SE.a.GPS Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_2.1x36mers.unique.GPS Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc1_ChIPexo.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 843900 HitCounts: 5931041.0 Original read count stats: _IP Bases: 546927 HitCounts: 5781067.0 The genome is segmented into 8714 regions for analysis. The genome is segmented into 8607 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 1327092 HitCounts: 5721611.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 406 reads. Original read count stats: _IP Bases: 1872599 HitCounts: 3878171.0 Original read count stats: _IP Bases: 2029489 HitCounts: 6375548.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 369 reads. ============================================== 2025-02-18 16:48:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc2_ChIPexo.1x36mers.unique.GPS The genome is segmented into 8190 regions for analysis. The genome is segmented into 8609 regions for analysis. The genome is segmented into 8298 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 216 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 214 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 560 reads. ============================================== 2025-02-18 16:48:17 At Poisson p-value 1.0e-03, in a 301bp window, expect 180 reads. Original read count stats: ============================================== 2025-02-18 16:48:16 ============================================== 2025-02-18 16:48:17 ============================================== 2025-02-18 16:48:17 ============================================== 2025-02-18 16:48:17 ============================================== 2025-02-18 16:48:17_IP Bases: 457192 HitCounts: 9211598.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc2_ChIPexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc1_ChIPexo.1x36mers.unique.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace1_ChIPexp.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace1_ChIPexp.1x36mers.unique.GPS ============================================== 2025-02-18 16:48:18 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc1_ChIPexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace2_ChIPexo.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc1_ChIPexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc2_ChIPexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 494928 HitCounts: 3533937.0 Original read count stats: _IP Bases: 1481417 HitCounts: 3297764.0 The genome is segmented into 8518 regions for analysis. The genome is segmented into 8460 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 338 reads. Original read count stats: _IP Bases: 448563 HitCounts: 3762205.0 Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 1241813 HitCounts: 3868336.0 The genome is segmented into 8755 regions for analysis. The genome is segmented into 8235 regions for analysis. Original read count stats: _IP Bases: 1346539 HitCounts: 7092185.0 Running with 1 threads ... Original read count stats: Running with 1 threads ... _IP Bases: 458281 HitCounts: 1.0303767E7 Original read count stats: _IP Bases: 1628172 HitCounts: 7375457.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 104 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 428 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 98 reads. The genome is segmented into 8310 regions for analysis. The genome is segmented into 8530 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 223 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 90 reads. The genome is segmented into 8327 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 244 reads. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 265 reads. ============================================== 2025-02-18 16:48:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_1_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-18 16:48:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc2_ChIPexo.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 518 reads. The genome is segmented into 8573 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1356204 HitCounts: 3389580.0 The genome is segmented into 8310 regions for analysis. The genome is segmented into 8352 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8200 regions for analysis. Original read count stats: _IP Bases: 1380503 HitCounts: 7734162.0 The genome is segmented into 8173 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8714 regions for analysis. ============================================== 2025-02-18 16:48:22 ============================================== 2025-02-18 16:48:22 At Poisson p-value 1.0e-03, in a 301bp window, expect 516 reads. ============================================== 2025-02-18 16:48:23 At Poisson p-value 1.0e-03, in a 301bp window, expect 235 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 505 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbiH_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbiH_glc1_ChIPexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc2_ChIPexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 362514 HitCounts: 1.2193127E7 The genome is segmented into 8325 regions for analysis. The genome is segmented into 8365 regions for analysis. Original read count stats: _IP Bases: 963221 HitCounts: 8703987.0 Original read count stats: _IP Bases: 2106195 HitCounts: 3620796.0 Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 479 reads. The genome is segmented into 8190 regions for analysis. Running with 1 threads ... The genome is segmented into 8357 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:48:27 At Poisson p-value 1.0e-03, in a 301bp window, expect 232 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc2_ChIPexo.SE.a.GPS The genome is segmented into 6077 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 300 reads. Running with 1 threads ... Original read count stats: _IP Bases: 554652 HitCounts: 1.4257693E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 348 reads. --------------------------- Events discovered Significant: 135 Insignificant: 0 Filtered: 2 Finish binding event prediction: 22.1s Refine read distribution from 46 binding events. Running with 1 threads ... The genome is segmented into 8389 regions for analysis. The genome is segmented into 8119 regions for analysis. ============================================== 2025-02-18 16:48:29 ============================================== 2025-02-18 16:48:29 ============================================== 2025-02-18 16:48:30 Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_1_ChIPexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_2_ChIPexo.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 356 reads. Original read count stats: _IP Bases: 408312 HitCounts: 1.520003E7 The genome is segmented into 8485 regions for analysis. ============================================== 2025-02-18 16:48:31 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1501320 HitCounts: 1.0192229E7 Original read count stats: _IP Bases: 1209739 HitCounts: 1.0516335E7 Original read count stats: _IP Bases: 202055 HitCounts: 1.5130991E7 ============================================== 2025-02-18 16:48:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 228210 HitCounts: 1.5836484E7 ============================================== 2025-02-18 16:48:33 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2-2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2-2.1x36mers.unique.GPS Original read count stats: _IP Bases: 177241 HitCounts: 1.6325999E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 303 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 205 reads. The genome is segmented into 4754 regions for analysis. The genome is segmented into 6084 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-18 16:48:35 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_1.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 328674 HitCounts: 1.7509608E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 271 reads. The genome is segmented into 4255 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 206 reads. The genome is segmented into 2998 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 645 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 668 reads. Running with 1 threads ... The genome is segmented into 8350 regions for analysis. Running with 1 threads ... The genome is segmented into 8352 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 320 reads. The genome is segmented into 7740 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:48:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_2.SE.a.GPS Original read count stats: _IP Bases: 221557 HitCounts: 1.8350328E7 ============================================== 2025-02-18 16:48:42 ============================================== 2025-02-18 16:48:42 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2-2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2-2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1.SE.a.GPS Original read count stats: _IP Bases: 196735 HitCounts: 1.8967515E7 Original read count stats: _IP Bases: 255148 HitCounts: 1.8840967E7 --------------------------- Events discovered Significant: 107 Insignificant: 16 Filtered: 0 At Poisson p-value 1.0e-03, in a 301bp window, expect 270 reads. Finish binding event prediction: 17.2s Refine read distribution from 82 binding events. The genome is segmented into 4785 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 250 reads. The genome is segmented into 3086 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 338 reads. The genome is segmented into 4252 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:48:49 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_1.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_1.SE.a.GPS Original read count stats: _IP Bases: 358181 HitCounts: 2.1232522E7 --------------------------- Events discovered Significant: 152 Insignificant: 0 Filtered: 9 Finish binding event prediction: 51.9s Refine read distribution from 47 binding events. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 410 reads. The genome is segmented into 7998 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 142 Insignificant: 5 Filtered: 0 Finish binding event prediction: 1.8m Refine read distribution from 127 binding events. --------------------------- Events discovered Significant: 137 Insignificant: 10 Filtered: 0 Finish binding event prediction: 23.1s Refine read distribution from 108 binding events. --------------------------- Events discovered Significant: 168 Insignificant: 26 Filtered: 45 Finish binding event prediction: 1.2m Refine read distribution from 56 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 110 Insignificant: 0 Filtered: 15 Finish binding event prediction: 1.6m Refine read distribution from 59 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1260 Insignificant: 0 Filtered: 214 Finish binding event prediction: 1.5m Refine read distribution from 625 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 170 Insignificant: 37 Filtered: 1 Finish binding event prediction: 16.1s Refine read distribution from 113 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 854 Insignificant: 1 Filtered: 77 Finish binding event prediction: 1.7m Refine read distribution from 344 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 155 Insignificant: 41 Filtered: 31 Finish binding event prediction: 1.7m Refine read distribution from 63 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 223 Insignificant: 1 Filtered: 35 Finish binding event prediction: 1.7m Refine read distribution from 62 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 174 Insignificant: 65 Filtered: 5 Finish binding event prediction: 9.3s Refine read distribution from 130 binding events. --------------------------- Events discovered Significant: 221 Insignificant: 1 Filtered: 20 Finish binding event prediction: 1.9m Refine read distribution from 71 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 173 Insignificant: 7 Filtered: 0 Finish binding event prediction: 29.1s Refine read distribution from 151 binding events. --------------------------- Events discovered Significant: 1137 Insignificant: 237 Filtered: 19 --------------------------- Events discovered Significant: 56 Insignificant: 28 Filtered: 21 --------------------------- Events discovered Significant: 40 Insignificant: 0 Filtered: 6 Finish binding event prediction: 1.8m Finish binding event prediction: 26.8s Finish binding event prediction: 2.0m Refine read distribution from 29 binding events. Refine read distribution from 24 binding events. Running with 1 threads ... Running with 1 threads ... Refine read distribution from 739 binding events. --------------------------- Events discovered Significant: 260 Insignificant: 2 Filtered: 19 Finish binding event prediction: 1.9m Refine read distribution from 61 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 127 Insignificant: 54 Filtered: 25 Finish binding event prediction: 1.8m Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 24 Insignificant: 0 Filtered: 3 Finish binding event prediction: 2.1m Refine read distribution from 21 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 285 Insignificant: 2 Filtered: 36 Finish binding event prediction: 2.0m Refine read distribution from 86 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 994 Insignificant: 0 Filtered: 106 Finish binding event prediction: 2.2m Refine read distribution from 626 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 308 Insignificant: 32 Filtered: 1 Finish binding event prediction: 33.4s Refine read distribution from 151 binding events. --------------------------- Events discovered Significant: 198 Insignificant: 2 Filtered: 29 Finish binding event prediction: 2.3m Refine read distribution from 68 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 188 Insignificant: 0 Filtered: 36 Finish binding event prediction: 2.4m Refine read distribution from 74 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 117 Insignificant: 49 Filtered: 28 Finish binding event prediction: 2.2m Refine read distribution from 37 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 841 Insignificant: 2 Filtered: 91 Finish binding event prediction: 2.5m Refine read distribution from 555 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 53 Insignificant: 0 Filtered: 15 --------------------------- Events discovered Significant: 85 Insignificant: 58 Filtered: 23 --------------------------- Events discovered Significant: 62 Insignificant: 0 Filtered: 14 Finish binding event prediction: 2.4m Finish binding event prediction: 2.5m Finish binding event prediction: 2.5m Refine read distribution from 34 binding events. Running with 1 threads ... Refine read distribution from 42 binding events. Running with 1 threads ... Refine read distribution from 44 binding events. Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 111 Insignificant: 15 Filtered: 2 Finish binding event prediction: 32.1s Refine read distribution from 103 binding events. --------------------------- Events discovered Significant: 1324 Insignificant: 0 Filtered: 81 Finish binding event prediction: 2.0m Refine read distribution from 509 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 74 Insignificant: 17 Filtered: 18 Finish binding event prediction: 2.5m Refine read distribution from 52 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 63 Insignificant: 17 Filtered: 18 Finish binding event prediction: 2.5m Refine read distribution from 42 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 18 Insignificant: 33 Filtered: 6 Finish binding event prediction: 2.3m Refine read distribution from 6 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 70 Insignificant: 43 Filtered: 18 --------------------------- Events discovered Significant: 170 Insignificant: 60 Filtered: 2 --------------------------- Events discovered Significant: 72 Insignificant: 6 Filtered: 17 Finish binding event prediction: 34.8s Finish binding event prediction: 2.5m Finish binding event prediction: 2.5m Refine read distribution from 22 binding events. Running with 1 threads ... Refine read distribution from 117 binding events. Refine read distribution from 57 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 674 Insignificant: 82 Filtered: 8 Finish binding event prediction: 1.1m Refine read distribution from 469 binding events. --------------------------- Events discovered Significant: 94 Insignificant: 46 Filtered: 23 Finish binding event prediction: 2.2m --------------------------- Events discovered Significant: 197 Insignificant: 29 Filtered: 3 Finish binding event prediction: 46.1s Refine read distribution from 27 binding events. Refine read distribution from 109 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 23 Insignificant: 18 Filtered: 6 --------------------------- Events discovered Significant: 1378 Insignificant: 0 Filtered: 72 Finish binding event prediction: 2.7m Finish binding event prediction: 2.1m Refine read distribution from 554 binding events. Refine read distribution from 14 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 116 Insignificant: 18 Filtered: 0 Finish binding event prediction: 36.1s Refine read distribution from 113 binding events. --------------------------- Events discovered Significant: 187 Insignificant: 2 Filtered: 41 Finish binding event prediction: 2.9m Refine read distribution from 96 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 789 Insignificant: 174 Filtered: 26 --------------------------- Events discovered Significant: 1086 Insignificant: 0 Filtered: 107 Finish binding event prediction: 24.1s Finish binding event prediction: 2.4m Refine read distribution from 470 binding events. Running with 1 threads ... Refine read distribution from 529 binding events. --------------------------- Events discovered Significant: 8 Insignificant: 20 Filtered: 9 Finish binding event prediction: 2.6m Running with 1 threads ... --------------------------- Events discovered Significant: 259 Insignificant: 33 Filtered: 3 Finish binding event prediction: 33.1s Refine read distribution from 142 binding events. --------------------------- Events discovered Significant: 90 Insignificant: 58 Filtered: 17 Finish binding event prediction: 3.0m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 817 Insignificant: 6 Filtered: 96 Finish binding event prediction: 3.1m Refine read distribution from 319 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 878 Insignificant: 0 Filtered: 84 Finish binding event prediction: 3.1m Refine read distribution from 604 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 328 Insignificant: 37 Filtered: 3 --------------------------- Events discovered Significant: 36 Insignificant: 14 Filtered: 9 Finish binding event prediction: 53.1s Finish binding event prediction: 3.0m Refine read distribution from 26 binding events. Refine read distribution from 172 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 193 Insignificant: 26 Filtered: 0 Finish binding event prediction: 35.1s Refine read distribution from 175 binding events. --------------------------- Events discovered Significant: 1390 Insignificant: 0 Filtered: 286 Finish binding event prediction: 2.7m Refine read distribution from 668 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 255 Insignificant: 31 Filtered: 4 Finish binding event prediction: 43.7s Refine read distribution from 140 binding events. --------------------------- Events discovered Significant: 1169 Insignificant: 0 Filtered: 126 Finish binding event prediction: 2.6m Refine read distribution from 457 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 158 Insignificant: 48 Filtered: 4 Finish binding event prediction: 41.2s --------------------------- Events discovered Significant: 18 Insignificant: 0 Filtered: 6 Finish binding event prediction: 3.2m Refine read distribution from 110 binding events. Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 172 Insignificant: 0 Filtered: 57 --------------------------- Events discovered Significant: 172 Insignificant: 68 Filtered: 48 --------------------------- Events discovered Significant: 173 Insignificant: 25 Filtered: 0 Finish binding event prediction: 3.0m Finish binding event prediction: 3.1m Finish binding event prediction: 37.4s Refine read distribution from 36 binding events. Running with 1 threads ... Refine read distribution from 148 binding events. Refine read distribution from 147 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 166 Insignificant: 62 Filtered: 1 Finish binding event prediction: 43.1s Refine read distribution from 123 binding events. --------------------------- Events discovered Significant: 187 Insignificant: 8 Filtered: 0 Finish binding event prediction: 44.2s Refine read distribution from 163 binding events. --------------------------- Events discovered Significant: 188 Insignificant: 65 Filtered: 2 Finish binding event prediction: 1.3m Refine read distribution from 133 binding events. --------------------------- Events discovered Significant: 30 Insignificant: 44 Filtered: 10 Finish binding event prediction: 2.7m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 943 Insignificant: 2 Filtered: 90 Finish binding event prediction: 3.2m Refine read distribution from 618 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 822 Insignificant: 189 Filtered: 22 Finish binding event prediction: 31.2s Refine read distribution from 572 binding events. --------------------------- Events discovered Significant: 190 Insignificant: 32 Filtered: 2 Finish binding event prediction: 1.3m Refine read distribution from 116 binding events. --------------------------- Events discovered Significant: 185 Insignificant: 31 Filtered: 0 Finish binding event prediction: 44.1s Refine read distribution from 140 binding events. --------------------------- Events discovered Significant: 77 Insignificant: 16 Filtered: 0 Finish binding event prediction: 34.1s Refine read distribution from 58 binding events. --------------------------- Events discovered Significant: 1293 Insignificant: 2 Filtered: 92 Finish binding event prediction: 2.6m Refine read distribution from 476 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 158 Insignificant: 47 Filtered: 0 Finish binding event prediction: 45.1s Refine read distribution from 114 binding events. --------------------------- Events discovered Significant: 176 Insignificant: 0 Filtered: 58 Finish binding event prediction: 3.3m Refine read distribution from 143 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 68 Insignificant: 0 Filtered: 14 Finish binding event prediction: 3.3m Refine read distribution from 44 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 178 Insignificant: 84 Filtered: 52 Finish binding event prediction: 3.4m Refine read distribution from 42 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 19 Insignificant: 0 Filtered: 5 --------------------------- Events discovered Significant: 974 Insignificant: 237 Filtered: 3 --------------------------- Events discovered Significant: 90 Insignificant: 7 Filtered: 19 Finish binding event prediction: 1.0m Finish binding event prediction: 3.4m Finish binding event prediction: 3.6m Refine read distribution from 12 binding events. Running with 1 threads ... Refine read distribution from 673 binding events. Refine read distribution from 62 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 44 Insignificant: 34 Filtered: 2 Finish binding event prediction: 58.1s Refine read distribution from 13 binding events. --------------------------- Events discovered Significant: 644 Insignificant: 115 Filtered: 11 Finish binding event prediction: 31.1s Refine read distribution from 397 binding events. --------------------------- Events discovered Significant: 33 Insignificant: 54 Filtered: 12 --------------------------- Events discovered Significant: 108 Insignificant: 87 Filtered: 27 Finish binding event prediction: 3.0m Finish binding event prediction: 3.3m Refine read distribution from 17 binding events. Refine read distribution from 19 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 231 Insignificant: 0 Filtered: 31 --------------------------- Events discovered Significant: 139 Insignificant: 66 Filtered: 23 Finish binding event prediction: 3.3m Finish binding event prediction: 3.2m Refine read distribution from 36 binding events. Refine read distribution from 92 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 13 Insignificant: 0 Filtered: 4 Finish binding event prediction: 3.5m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 803 Insignificant: 2 Filtered: 112 Finish binding event prediction: 3.6m Refine read distribution from 507 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 90 Insignificant: 6 Filtered: 1 Finish binding event prediction: 32.1s Refine read distribution from 90 binding events. --------------------------- Events discovered Significant: 693 Insignificant: 154 Filtered: 49 Finish binding event prediction: 35.1s Refine read distribution from 473 binding events. --------------------------- Events discovered Significant: 92 Insignificant: 69 Filtered: 15 --------------------------- Events discovered Significant: 228 Insignificant: 0 Filtered: 36 --------------------------- Events discovered Significant: 1127 Insignificant: 289 Filtered: 4 --------------------------- Events discovered Significant: 9 Insignificant: 4 Filtered: 4 --------------------------- Events discovered Significant: 677 Insignificant: 148 Filtered: 51 Finish binding event prediction: 3.7m Finish binding event prediction: 3.7m Finish binding event prediction: 1.5m Finish binding event prediction: 3.6m Finish binding event prediction: 50.6s --------------------------- Events discovered Significant: 12 Insignificant: 26 Filtered: 4 Finish binding event prediction: 3.4m Running with 1 threads ... Refine read distribution from 20 binding events. Refine read distribution from 87 binding events. Running with 1 threads ... Running with 1 threads ... Refine read distribution from 475 binding events. Refine read distribution from 7 binding events. Running with 1 threads ... Refine read distribution from 814 binding events. --------------------------- Events discovered Significant: 261 Insignificant: 78 Filtered: 2 Finish binding event prediction: 1.1m --------------------------- Events discovered Significant: 989 Insignificant: 1 Filtered: 119 Finish binding event prediction: 3.7m Refine read distribution from 184 binding events. Refine read distribution from 651 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 803 Insignificant: 2 Filtered: 87 Finish binding event prediction: 3.8m Refine read distribution from 549 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 182 Insignificant: 27 Filtered: 0 Finish binding event prediction: 20.1s Refine read distribution from 155 binding events. --------------------------- Events discovered Significant: 118 Insignificant: 44 Filtered: 0 Finish binding event prediction: 47.2s Refine read distribution from 96 binding events. --------------------------- Events discovered Significant: 991 Insignificant: 0 Filtered: 83 Finish binding event prediction: 3.7m Refine read distribution from 654 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 21 Filtered: 9 Finish binding event prediction: 3.6m Running with 1 threads ... --------------------------- Events discovered Significant: 867 Insignificant: 13 Filtered: 120 Finish binding event prediction: 3.8m Refine read distribution from 343 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 28 Insignificant: 0 Filtered: 3 Finish binding event prediction: 3.8m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 31 Insignificant: 1 Filtered: 10 --------------------------- Events discovered Significant: 32 Insignificant: 2 Filtered: 10 Finish binding event prediction: 3.8m Finish binding event prediction: 3.7m Refine read distribution from 19 binding events. Refine read distribution from 18 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 75 Insignificant: 0 Filtered: 17 Finish binding event prediction: 3.8m Refine read distribution from 37 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 90 Insignificant: 0 Filtered: 25 Finish binding event prediction: 3.5m Refine read distribution from 35 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 185 Insignificant: 72 Filtered: 1 Finish binding event prediction: 1.5m Refine read distribution from 117 binding events. --------------------------- Events discovered Significant: 93 Insignificant: 0 Filtered: 15 Finish binding event prediction: 3.9m Refine read distribution from 70 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 493 Insignificant: 0 Filtered: 149 Finish binding event prediction: 3.8m Refine read distribution from 383 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 826 Insignificant: 0 Filtered: 84 Finish binding event prediction: 4.0m Refine read distribution from 584 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1077 Insignificant: 243 Filtered: 65 Finish binding event prediction: 53.2s Refine read distribution from 690 binding events. --------------------------- Events discovered Significant: 801 Insignificant: 142 Filtered: 33 Finish binding event prediction: 48.1s Refine read distribution from 530 binding events. --------------------------- Events discovered Significant: 16 Insignificant: 28 Filtered: 4 --------------------------- Events discovered Significant: 1025 Insignificant: 0 Filtered: 106 Finish binding event prediction: 3.8m Finish binding event prediction: 3.5m Refine read distribution from 7 binding events. Refine read distribution from 466 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 156 Insignificant: 44 Filtered: 35 Finish binding event prediction: 45.1s Refine read distribution from 79 binding events. --------------------------- Events discovered Significant: 174 Insignificant: 0 Filtered: 29 Finish binding event prediction: 4.1m Refine read distribution from 67 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 151 Insignificant: 0 Filtered: 35 --------------------------- Events discovered Significant: 310 Insignificant: 16 Filtered: 2 Finish binding event prediction: 4.0m Finish binding event prediction: 28.1s Refine read distribution from 69 binding events. Running with 1 threads ... Refine read distribution from 221 binding events. --------------------------- Events discovered Significant: 59 Insignificant: 14 Filtered: 20 Finish binding event prediction: 4.0m Refine read distribution from 34 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 56 Insignificant: 0 Filtered: 0 Finish binding event prediction: 45.1s Refine read distribution from 54 binding events. --------------------------- Events discovered Significant: 20 Insignificant: 33 Filtered: 6 --------------------------- Events discovered Significant: 937 Insignificant: 0 Filtered: 77 Finish binding event prediction: 3.9m Finish binding event prediction: 4.2m Refine read distribution from 369 binding events. Running with 1 threads ... Refine read distribution from 6 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1269 Insignificant: 5 Filtered: 195 Finish binding event prediction: 4.2m --------------------------- Events discovered Significant: 21 Insignificant: 0 Filtered: 7 Finish binding event prediction: 4.1m Refine read distribution from 605 binding events. Running with 1 threads ... Refine read distribution from 17 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 32 Insignificant: 21 Filtered: 17 Finish binding event prediction: 4.0m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 631 Insignificant: 2 Filtered: 98 --------------------------- Events discovered Significant: 146 Insignificant: 66 Filtered: 3 Finish binding event prediction: 4.2m --------------------------- Events discovered Significant: 132 Insignificant: 52 Filtered: 20 Finish binding event prediction: 1.3m Finish binding event prediction: 4.3m Refine read distribution from 39 binding events. Running with 1 threads ... Refine read distribution from 96 binding events. Refine read distribution from 432 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 36 Insignificant: 15 Filtered: 0 Finish binding event prediction: 35.1s Refine read distribution from 21 binding events. --------------------------- Events discovered Significant: 614 Insignificant: 109 Filtered: 25 Finish binding event prediction: 28.1s Refine read distribution from 386 binding events. --------------------------- Events discovered Significant: 100 Insignificant: 34 Filtered: 3 Finish binding event prediction: 1.1m Refine read distribution from 63 binding events. --------------------------- Events discovered Significant: 8 Insignificant: 20 Filtered: 9 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 82 Insignificant: 4 Filtered: 0 Finish binding event prediction: 33.1s Refine read distribution from 61 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 4 Filtered: 3 Finish binding event prediction: 4.2m Running with 1 threads ... --------------------------- Events discovered Significant: 279 Insignificant: 65 Filtered: 2 Finish binding event prediction: 48.1s Refine read distribution from 164 binding events. --------------------------- Events discovered Significant: 1155 Insignificant: 0 Filtered: 139 Finish binding event prediction: 3.7m Refine read distribution from 462 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 946 Insignificant: 2 Filtered: 103 --------------------------- Events discovered Significant: 41 Insignificant: 3 Filtered: 1 --------------------------- Events discovered Significant: 52 Insignificant: 0 Filtered: 15 Finish binding event prediction: 4.4m Finish binding event prediction: 47.3s Finish binding event prediction: 4.2m Refine read distribution from 37 binding events. Refine read distribution from 31 binding events. Running with 1 threads ... Refine read distribution from 599 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 661 Insignificant: 113 Filtered: 13 Finish binding event prediction: 13.1s Refine read distribution from 415 binding events. --------------------------- Events discovered Significant: 111 Insignificant: 44 Filtered: 0 Finish binding event prediction: 58.2s Refine read distribution from 74 binding events. --------------------------- Events discovered Significant: 149 Insignificant: 61 Filtered: 6 Finish binding event prediction: 1.4m Refine read distribution from 98 binding events. --------------------------- Events discovered Significant: 46 Insignificant: 22 Filtered: 14 --------------------------- Events discovered Significant: 163 Insignificant: 1 Filtered: 53 Finish binding event prediction: 4.5m Finish binding event prediction: 44.3s Refine read distribution from 14 binding events. Refine read distribution from 134 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 968 Insignificant: 1 Filtered: 120 Finish binding event prediction: 4.6m Refine read distribution from 608 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 659 Insignificant: 147 Filtered: 49 Finish binding event prediction: 31.1s Refine read distribution from 456 binding events. --------------------------- Events discovered Significant: 321 Insignificant: 2 Filtered: 28 Finish binding event prediction: 4.4m Refine read distribution from 89 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 336 Insignificant: 5 Filtered: 38 Finish binding event prediction: 4.5m Refine read distribution from 178 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 158 Insignificant: 1 Filtered: 1 Finish binding event prediction: 46.1s Refine read distribution from 135 binding events. --------------------------- Events discovered Significant: 147 Insignificant: 48 Filtered: 0 --------------------------- Events discovered Significant: 317 Insignificant: 53 Filtered: 3 Finish binding event prediction: 59.8s Finish binding event prediction: 1.9m Refine read distribution from 88 binding events. Refine read distribution from 234 binding events. --------------------------- Events discovered Significant: 150 Insignificant: 3 Filtered: 11 Finish binding event prediction: 51.1s Refine read distribution from 55 binding events. --------------------------- Events discovered Significant: 698 Insignificant: 143 Filtered: 51 Finish binding event prediction: 21.1s Refine read distribution from 490 binding events. --------------------------- Events discovered Significant: 47 Insignificant: 36 Filtered: 19 Finish binding event prediction: 4.5m Refine read distribution from 18 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 171 Insignificant: 1 Filtered: 0 --------------------------- Events discovered Significant: 175 Insignificant: 70 Filtered: 9 --------------------------- Events discovered Significant: 33 Insignificant: 17 Filtered: 0 Finish binding event prediction: 1.5m Finish binding event prediction: 1.2m Finish binding event prediction: 41.4s Refine read distribution from 99 binding events. Refine read distribution from 15 binding events. Refine read distribution from 125 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 2 Filtered: 2 Finish binding event prediction: 4.7m Running with 1 threads ... --------------------------- Events discovered Significant: 166 Insignificant: 0 Filtered: 52 Finish binding event prediction: 4.7m Refine read distribution from 145 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 233 Insignificant: 30 Filtered: 5 --------------------------- Events discovered Significant: 1042 Insignificant: 238 Filtered: 1 Finish binding event prediction: 43.6s Finish binding event prediction: 1.9m Refine read distribution from 138 binding events. Refine read distribution from 747 binding events. --------------------------- Events discovered Significant: 97 Insignificant: 0 Filtered: 18 Finish binding event prediction: 4.8m Refine read distribution from 53 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 48 Insignificant: 13 Filtered: 20 --------------------------- Events discovered Significant: 251 Insignificant: 25 Filtered: 3 Finish binding event prediction: 4.8m Finish binding event prediction: 1.1m Refine read distribution from 193 binding events. Refine read distribution from 30 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 42 Insignificant: 19 Filtered: 11 Finish binding event prediction: 1.1m Refine read distribution from 13 binding events. --------------------------- Events discovered Significant: 1105 Insignificant: 218 Filtered: 19 Finish binding event prediction: 42.1s Refine read distribution from 680 binding events. --------------------------- Events discovered Significant: 17 Insignificant: 9 Filtered: 8 Finish binding event prediction: 4.8m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1267 Insignificant: 0 Filtered: 71 --------------------------- Events discovered Significant: 1079 Insignificant: 244 Filtered: 2 Finish binding event prediction: 4.2m Finish binding event prediction: 1.1m Refine read distribution from 782 binding events. Refine read distribution from 532 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 81 Insignificant: 6 Filtered: 16 Finish binding event prediction: 5.0m Refine read distribution from 53 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 2 Filtered: 2 Finish binding event prediction: 5.1m Running with 1 threads ... --------------------------- Events discovered Significant: 50 Insignificant: 51 Filtered: 4 Finish binding event prediction: 58.1s Refine read distribution from 17 binding events. --------------------------- Events discovered Significant: 17 Insignificant: 9 Filtered: 8 Finish binding event prediction: 5.1m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 366 Insignificant: 51 Filtered: 3 Finish binding event prediction: 1.1m Refine read distribution from 259 binding events. --------------------------- Events discovered Significant: 1309 Insignificant: 6 Filtered: 262 Finish binding event prediction: 4.8m Refine read distribution from 600 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 32 Insignificant: 1 Filtered: 11 Finish binding event prediction: 5.3m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 21 Filtered: 9 Finish binding event prediction: 1.6m --------------------------- Events discovered Significant: 185 Insignificant: 56 Filtered: 1 --------------------------- Events discovered Significant: 253 Insignificant: 1 Filtered: 28 --------------------------- Events discovered Significant: 112 Insignificant: 4 Filtered: 0 Finish binding event prediction: 5.2m Finish binding event prediction: 1.2m Finish binding event prediction: 1.2m Refine read distribution from 136 binding events. Refine read distribution from 91 binding events. Refine read distribution from 85 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 4 Filtered: 4 Finish binding event prediction: 1.8m --------------------------- Events discovered Significant: 992 Insignificant: 3 Filtered: 118 Finish binding event prediction: 5.4m Refine read distribution from 619 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 967 Insignificant: 246 Filtered: 3 Finish binding event prediction: 1.9m Refine read distribution from 690 binding events. --------------------------- Events discovered Significant: 795 Insignificant: 183 Filtered: 22 Finish binding event prediction: 32.2s Refine read distribution from 549 binding events. --------------------------- Events discovered Significant: 124 Insignificant: 21 Filtered: 1 --------------------------- Events discovered Significant: 1087 Insignificant: 300 Filtered: 2 Finish binding event prediction: 1.3m Finish binding event prediction: 2.4m Refine read distribution from 82 binding events. Refine read distribution from 751 binding events. --------------------------- Events discovered Significant: 1168 Insignificant: 295 Filtered: 6 Finish binding event prediction: 1.8m Refine read distribution from 819 binding events. --------------------------- Events discovered Significant: 146 Insignificant: 73 Filtered: 4 Finish binding event prediction: 2.1m Refine read distribution from 62 binding events. --------------------------- Events discovered Significant: 383 Insignificant: 59 Filtered: 5 Finish binding event prediction: 1.0m Refine read distribution from 222 binding events. --------------------------- Events discovered Significant: 1008 Insignificant: 0 Filtered: 124 Finish binding event prediction: 5.8m Refine read distribution from 645 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 197 Insignificant: 34 Filtered: 1 Finish binding event prediction: 46.1s Refine read distribution from 156 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 5.4m Running with 1 threads ... --------------------------- Events discovered Significant: 201 Insignificant: 3 Filtered: 0 Finish binding event prediction: 55.1s Refine read distribution from 157 binding events. --------------------------- Events discovered Significant: 361 Insignificant: 0 Filtered: 75 Finish binding event prediction: 5.9m Refine read distribution from 223 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 996 Insignificant: 217 Filtered: 2 Finish binding event prediction: 2.3m Refine read distribution from 696 binding events. --------------------------- Events discovered Significant: 990 Insignificant: 182 Filtered: 2 Finish binding event prediction: 1.8m Refine read distribution from 728 binding events. --------------------------- Events discovered Significant: 1010 Insignificant: 218 Filtered: 68 Finish binding event prediction: 48.2s Refine read distribution from 649 binding events. --------------------------- Events discovered Significant: 255 Insignificant: 16 Filtered: 0 Finish binding event prediction: 1.7m Refine read distribution from 194 binding events. --------------------------- Events discovered Significant: 1154 Insignificant: 287 Filtered: 2 Finish binding event prediction: 2.5m Refine read distribution from 844 binding events. --------------------------- Events discovered Significant: 1015 Insignificant: 271 Filtered: 1 Finish binding event prediction: 1.7m Refine read distribution from 750 binding events. --------------------------- Events discovered Significant: 59 Insignificant: 15 Filtered: 1 Finish binding event prediction: 1.2m Refine read distribution from 46 binding events. --------------------------- Events discovered Significant: 1341 Insignificant: 200 Filtered: 10 Finish binding event prediction: 3.0m Refine read distribution from 959 binding events. --------------------------- Events discovered Significant: 1069 Insignificant: 285 Filtered: 2 Finish binding event prediction: 1.7m Refine read distribution from 776 binding events. --------------------------- Events discovered Significant: 59 Insignificant: 15 Filtered: 1 Finish binding event prediction: 1.1m Refine read distribution from 46 binding events. --------------------------- Events discovered Significant: 1532 Insignificant: 319 Filtered: 4 Finish binding event prediction: 2.5m Refine read distribution from 1087 binding events. --------------------------- Events discovered Significant: 320 Insignificant: 36 Filtered: 1 Finish binding event prediction: 2.3m Refine read distribution from 237 binding events. --------------------------- Events discovered Significant: 831 Insignificant: 0 Filtered: 103 Finish binding event prediction: 6.5m Refine read distribution from 546 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 601 Insignificant: 95 Filtered: 0 Finish binding event prediction: 1.9m Refine read distribution from 452 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 4 Filtered: 3 Finish binding event prediction: 2.3m --------------------------- Events discovered Significant: 242 Insignificant: 39 Filtered: 0 Finish binding event prediction: 2.0m Refine read distribution from 175 binding events. --------------------------- Events discovered Significant: 639 Insignificant: 1 Filtered: 89 Finish binding event prediction: 7.2m Refine read distribution from 413 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 272 Insignificant: 10 Filtered: 2 Finish binding event prediction: 2.0m Refine read distribution from 209 binding events. --------------------------- Events discovered Significant: 1109 Insignificant: 302 Filtered: 2 Finish binding event prediction: 1.9m Refine read distribution from 797 binding events. --------------------------- Events discovered Significant: 1373 Insignificant: 212 Filtered: 5 Finish binding event prediction: 4.0m Refine read distribution from 967 binding events. --------------------------- Events discovered Significant: 292 Insignificant: 40 Filtered: 1 Finish binding event prediction: 2.5m Refine read distribution from 229 binding events. --------------------------- Events discovered Significant: 278 Insignificant: 40 Filtered: 1 Finish binding event prediction: 2.0m Refine read distribution from 168 binding events. --------------------------- Events discovered Significant: 731 Insignificant: 85 Filtered: 2 Finish binding event prediction: 1.5m Refine read distribution from 560 binding events. --------------------------- Events discovered Significant: 1332 Insignificant: 224 Filtered: 8 Finish binding event prediction: 2.9m Refine read distribution from 962 binding events. --------------------------- Events discovered Significant: 1299 Insignificant: 217 Filtered: 8 Finish binding event prediction: 2.8m Refine read distribution from 954 binding events. --------------------------- Events discovered Significant: 1179 Insignificant: 297 Filtered: 3 Finish binding event prediction: 1.9m Refine read distribution from 852 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 2 Filtered: 2 Finish binding event prediction: 3.2m --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 2.8m --------------------------- Events discovered Significant: 1076 Insignificant: 208 Filtered: 1 Finish binding event prediction: 2.1m Refine read distribution from 778 binding events. --------------------------- Events discovered Significant: 917 Insignificant: 209 Filtered: 4 Finish binding event prediction: 1.9m Refine read distribution from 666 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 2 Filtered: 2 Finish binding event prediction: 4.4m ============================================== 2025-02-18 16:58:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_30C_rep2.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/SigH_30C_rep2.1x36mers.unique.GPS Original read count stats: _IP Bases: 209881 HitCounts: 783247.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 41 reads. ============================================== 2025-02-18 16:58:06 The genome is segmented into 8198 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_30C_rep2.SE.a.bam --out 13-E.coli-SigH-GSE60667/SigH_30C_rep2.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 241297 HitCounts: 972770.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 53 reads. The genome is segmented into 8376 regions for analysis. ============================================== 2025-02-18 16:58:07 Running with 1 threads ... ============================================== 2025-02-18 16:58:08 ============================================== 2025-02-18 16:58:07 ============================================== 2025-02-18 16:58:08 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_42C_rep2.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/SigH_42C_rep2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_30C_rep1.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/SigH_30C_rep1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_42C_rep1.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/SigH_42C_rep1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_30C_rep1.SE.a.bam --out 13-E.coli-SigH-GSE60667/SigH_30C_rep1.SE.a.GPS ============================================== 2025-02-18 16:58:09 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_42C_rep2.SE.a.bam --out 13-E.coli-SigH-GSE60667/SigH_42C_rep2.SE.a.GPS Original read count stats: _IP Bases: 292571 HitCounts: 1028084.0 Original read count stats: _IP Bases: 518443 HitCounts: 1165275.0 Original read count stats: _IP Bases: 559314 HitCounts: 1408673.0 Original read count stats: _IP Bases: 502630 HitCounts: 1164140.0 ============================================== 2025-02-18 16:58:09 Original read count stats: _IP Bases: 330253 HitCounts: 1253451.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_42C_rep1.SE.a.bam --out 13-E.coli-SigH-GSE60667/SigH_42C_rep1.SE.a.GPS ============================================== 2025-02-18 16:58:09 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc1_ChIPexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 63 reads. ============================================== 2025-02-18 16:58:09 ============================================== 2025-02-18 16:58:09 Original read count stats: _IP Bases: 572078 HitCounts: 1386680.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 93 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc2_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-18 16:58:10 At Poisson p-value 1.0e-03, in a 301bp window, expect 90 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc1_ChIPexo.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc1_ChIPexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 109 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 77 reads. Original read count stats: Original read count stats: ============================================== 2025-02-18 16:58:11 The genome is segmented into 8121 regions for analysis. The genome is segmented into 8245 regions for analysis. _IP Bases: 1282628 HitCounts: 3060253.0 _IP Bases: 1047968 HitCounts: 2265185.0 ============================================== 2025-02-18 16:58:11 The genome is segmented into 8165 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 110 reads. Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc1_ChIPexo.SE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc2_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 1656846 HitCounts: 3399376.0 The genome is segmented into 8427 regions for analysis. Running with 1 threads ... The genome is segmented into 8325 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1790537 HitCounts: 4585003.0 Original read count stats: _IP Bases: 1746897 HitCounts: 3892383.0 Original read count stats: _IP Bases: 1752821 HitCounts: 4369271.0 The genome is segmented into 8286 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 164 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 211 reads. ============================================== 2025-02-18 16:58:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc1_ChIPexo.SE.a.GPS ============================================== 2025-02-18 16:58:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_2_ChIPexo.1x36mers.unique.GPS The genome is segmented into 8067 regions for analysis. ============================================== 2025-02-18 16:58:13 ============================================== 2025-02-18 16:58:13 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 261 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR1_Chipexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc2_ChIPexo.SE.a.GPS ============================================== 2025-02-18 16:58:14 The genome is segmented into 8063 regions for analysis. ============================================== 2025-02-18 16:58:14 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep1.SE.a.bam --out 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep1.SE.a.GPS Original read count stats: Running with 1 threads ... Original read count stats: _IP Bases: 990904 HitCounts: 4627757.0 _IP Bases: 1709302 HitCounts: 4724037.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR2_Chipexo.1x36mers.unique.GPS ============================================== 2025-02-18 16:58:14 At Poisson p-value 1.0e-03, in a 301bp window, expect 286 reads. Original read count stats: _IP Bases: 1211564 HitCounts: 4834683.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_2.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 214243 HitCounts: 2296872.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 334 reads. The genome is segmented into 8115 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2374561 HitCounts: 4213036.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 318 reads. Original read count stats: _IP Bases: 1425613 HitCounts: 4612456.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 35 reads. ============================================== 2025-02-18 16:58:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR1_Chipexo.1x36mers.unique.GPS The genome is segmented into 8138 regions for analysis. Running with 1 threads ... The genome is segmented into 8508 regions for analysis. Original read count stats: _IP Bases: 2660419 HitCounts: 3886369.0 Running with 1 threads ... The genome is segmented into 8215 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:58:15 ============================================== 2025-02-18 16:58:15 Original read count stats: _IP Bases: 1482104 HitCounts: 3904373.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE1_Chipexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc1_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-18 16:58:15 At Poisson p-value 1.0e-03, in a 301bp window, expect 210 reads. ============================================== 2025-02-18 16:58:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc2_ChIPexo.1x36mers.unique.GPS The genome is segmented into 7998 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc2_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-18 16:58:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_1.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_1.1x36mers.unique.GPS ============================================== 2025-02-18 16:58:16 ============================================== 2025-02-18 16:58:16 Original read count stats: Original read count stats: Original read count stats: Original read count stats: ============================================== 2025-02-18 16:58:17 ============================================== 2025-02-18 16:58:17 At Poisson p-value 1.0e-03, in a 301bp window, expect 272 reads. ============================================== 2025-02-18 16:58:17 ============================================== 2025-02-18 16:58:16 At Poisson p-value 1.0e-03, in a 301bp window, expect 336 reads. The genome is segmented into 8261 regions for analysis. _IP Bases: 1610631 HitCounts: 3491921.0 ============================================== 2025-02-18 16:58:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc2_ChIPexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 1075222 HitCounts: 2515621.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 352 reads. ============================================== 2025-02-18 16:58:17 ============================================== 2025-02-18 16:58:17 ============================================== 2025-02-18 16:58:17_IP Bases: 827343 HitCounts: 4985011.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 357 reads. _IP Bases: 1978188 HitCounts: 5553881.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR2_Chipexo.SE.a.GPS _IP Bases: 2182657 HitCounts: 3924083.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep1.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep2.SE.a.bam --out 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB1_Chipexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_1.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR2_Chipexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_2.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_2_ChIPexo.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE2_Chipexo.SE.a.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 351 reads. Original read count stats: _IP Bases: 239441 HitCounts: 2626261.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 385 reads. ============================================== 2025-02-18 16:58:18 Original read count stats: _IP Bases: 1074920 HitCounts: 3305175.0 Original read count stats: _IP Bases: 1309542 HitCounts: 2446813.0 The genome is segmented into 8244 regions for analysis. Original read count stats: _IP Bases: 2350672 HitCounts: 3947684.0 The genome is segmented into 8252 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc2_ChIPexo.SE.a.GPS The genome is segmented into 8263 regions for analysis. ============================================== 2025-02-18 16:58:18 ============================================== 2025-02-18 16:58:19 Running with 1 threads ... Original read count stats: _IP Bases: 1521678 HitCounts: 5489183.0 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc2_ChIPexo.SE.a.GPS Original read count stats: Original read count stats: _IP Bases: 2357226 HitCounts: 4201743.0 _IP Bases: 2205925 HitCounts: 6047454.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_2.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_2.SE.a.GPS ============================================== 2025-02-18 16:58:19 Original read count stats: _IP Bases: 2280649 HitCounts: 5093285.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 42 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc1_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 2175771 HitCounts: 4272864.0 Original read count stats: _IP Bases: 2820191 HitCounts: 5038373.0 The genome is segmented into 8212 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 165 reads. Running with 1 threads ... Original read count stats: _IP Bases: 1175323 HitCounts: 3446599.0 The genome is segmented into 8310 regions for analysis. Running with 1 threads ... The genome is segmented into 8236 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 168 reads. The genome is segmented into 8716 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 848694 HitCounts: 6029784.0 Original read count stats: _IP Bases: 2361437 HitCounts: 6990153.0 Original read count stats: _IP Bases: 2122957 HitCounts: 6414530.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 254 reads. ============================================== 2025-02-18 16:58:20 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB2_Chipexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 195 reads. ============================================== 2025-02-18 16:58:20 The genome is segmented into 8228 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_1.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_1.SE.a.GPS The genome is segmented into 8050 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8177 regions for analysis. The genome is segmented into 8093 regions for analysis. Original read count stats: _IP Bases: 2864798 HitCounts: 4836427.0 Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 229 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 337 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 354 reads. Original read count stats: _IP Bases: 937867 HitCounts: 6864887.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 250 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 250 reads. ============================================== 2025-02-18 16:58:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR1_Chipexo.SE.a.GPS The genome is segmented into 8308 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 352 reads. The genome is segmented into 8405 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 346 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 397 reads. The genome is segmented into 8265 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 355 reads. Original read count stats: _IP Bases: 1614636 HitCounts: 7034704.0 ============================================== 2025-02-18 16:58:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR2_Chipexo.SE.a.GPS ============================================== 2025-02-18 16:58:22 The genome is segmented into 8288 regions for analysis. The genome is segmented into 8056 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_1_ChIPexo.SE.a.GPS The genome is segmented into 8074 regions for analysis. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8248 regions for analysis. The genome is segmented into 8254 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 438 reads. Running with 1 threads ... Original read count stats: _IP Bases: 1145536 HitCounts: 7296145.0 Original read count stats: _IP Bases: 1044243 HitCounts: 9439826.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 447 reads. ============================================== 2025-02-18 16:58:23 At Poisson p-value 1.0e-03, in a 301bp window, expect 437 reads. The genome is segmented into 7998 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR2_Chipexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 462 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 285 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 412 reads. Running with 1 threads ... ============================================== 2025-02-18 16:58:23 The genome is segmented into 8429 regions for analysis. ============================================== 2025-02-18 16:58:23 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_1.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_2_ChIPexo.SE.a.GPS Running with 1 threads ... ============================================== 2025-02-18 16:58:23 ============================================== 2025-02-18 16:58:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB2_Chipexo.SE.a.GPS ============================================== 2025-02-18 16:58:24 Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB1_Chipexo.1x36mers.unique.GPS _IP Bases: 1025804 HitCounts: 3892202.0 The genome is segmented into 8170 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_1.1x36mers.unique.GPS The genome is segmented into 8396 regions for analysis. Running with 1 threads ... The genome is segmented into 8235 regions for analysis. Running with 1 threads ... The genome is segmented into 8372 regions for analysis. The genome is segmented into 8220 regions for analysis. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 2127751 HitCounts: 3349430.0 Original read count stats: _IP Bases: 1122985 HitCounts: 1.0082213E7 ============================================== 2025-02-18 16:58:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_2.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 420 reads. ============================================== 2025-02-18 16:58:24 Original read count stats: _IP Bases: 2216015 HitCounts: 3387230.0 Original read count stats: _IP Bases: 1962927 HitCounts: 3916062.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR1_Chipexo.1x36mers.unique.GPS ============================================== 2025-02-18 16:58:24 Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR2_Chipexo.1x36mers.unique.GPS _IP Bases: 3031212 HitCounts: 5725144.0 ============================================== 2025-02-18 16:58:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_1.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 463610 HitCounts: 8799722.0 ============================================== 2025-02-18 16:58:25 ============================================== 2025-02-18 16:58:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_1_ChIPexo.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR1_Chipexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 201 reads. Original read count stats: Original read count stats: The genome is segmented into 8211 regions for analysis. ============================================== 2025-02-18 16:58:26 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 501 reads. ============================================== 2025-02-18 16:58:25_IP Bases: 917095 HitCounts: 4325586.0 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 443 reads. ============================================== 2025-02-18 16:58:26_IP Bases: 1683890 HitCounts: 3491565.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 295 reads. _IP Bases: 2217182 HitCounts: 3606084.0 _IP Bases: 453159 HitCounts: 4051920.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 306 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc2_ChIPexo.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_1.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_1.SE.a.GPS ============================================== 2025-02-18 16:58:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_2.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep2.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep2.1x36mers.unique.GPS The genome is segmented into 8452 regions for analysis. The genome is segmented into 8474 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 507 reads. Running with 1 threads ... Original read count stats: _IP Bases: 377374 HitCounts: 3987404.0 Running with 1 threads ... Original read count stats: _IP Bases: 2233352 HitCounts: 3617240.0 ============================================== 2025-02-18 16:58:28 Original read count stats: Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE1_Chipexo.1x36mers.unique.GPS Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 338 reads. _IP Bases: 1404555 HitCounts: 2834972.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 107 reads. _IP Bases: 1068257 HitCounts: 9824664.0 _IP Bases: 545227 HitCounts: 8969180.0 The genome is segmented into 8450 regions for analysis. The genome is segmented into 8270 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 16:58:28 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 374 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR1_Chipexo.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 195 reads. The genome is segmented into 8440 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 90 reads. Running with 1 threads ... The genome is segmented into 8144 regions for analysis. Original read count stats: _IP Bases: 2067892 HitCounts: 3442736.0 Running with 1 threads ... The genome is segmented into 8267 regions for analysis. The genome is segmented into 8549 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 1799002 HitCounts: 3924880.0 ============================================== 2025-02-18 16:58:29 At Poisson p-value 1.0e-03, in a 301bp window, expect 273 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 568 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE2_Chipexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 488 reads. The genome is segmented into 8712 regions for analysis. ============================================== 2025-02-18 16:58:29 The genome is segmented into 8525 regions for analysis. The genome is segmented into 8303 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc1_ChIPexo.1x36mers.unique.GPS Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 310 reads. The genome is segmented into 8421 regions for analysis. The genome is segmented into 8233 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 251 reads. Original read count stats: _IP Bases: 2037009 HitCounts: 3677942.0 The genome is segmented into 8368 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8108 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 311 reads. Running with 1 threads ... Original read count stats: _IP Bases: 1563229 HitCounts: 1.1097442E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 257 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 297 reads. ============================================== 2025-02-18 16:58:31 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_2.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_2.1x36mers.unique.GPS The genome is segmented into 8081 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 307 reads. Running with 1 threads ... Original read count stats: The genome is segmented into 8400 regions for analysis. The genome is segmented into 8065 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 398 reads. The genome is segmented into 8087 regions for analysis. _IP Bases: 743251 HitCounts: 4363490.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 301 reads. The genome is segmented into 8163 regions for analysis. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 406 reads. The genome is segmented into 8592 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 142 reads. The genome is segmented into 8089 regions for analysis. The genome is segmented into 8073 regions for analysis. The genome is segmented into 8251 regions for analysis. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-18 16:58:36 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 12-E.coli-cysB-metJ-GSE122320/cysB_taur_2_ChIPexo.PE.a.bam --out 12-E.coli-cysB-metJ-GSE122320/cysB_taur_2_ChIPexo.PE.a.GPS Original read count stats: _IP Bases: 2054929 HitCounts: 1.273821E7 ============================================== 2025-02-18 16:58:41 ============================================== 2025-02-18 16:58:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc2_ChIPexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 12-E.coli-cysB-metJ-GSE122320/metJ_meio_2_ChIPexo.PE.a.bam --out 12-E.coli-cysB-metJ-GSE122320/metJ_meio_2_ChIPexo.PE.a.GPS Original read count stats: _IP Bases: 1202264 HitCounts: 1.5698825E7 Original read count stats: _IP Bases: 4000280 HitCounts: 1.3723754E7 ============================================== 2025-02-18 16:58:44 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 12-E.coli-cysB-metJ-GSE122320/metJ_meio_1_ChIPexo.PE.a.bam --out 12-E.coli-cysB-metJ-GSE122320/metJ_meio_1_ChIPexo.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 845 reads. Original read count stats: _IP Bases: 4211725 HitCounts: 1.5186838E7 ============================================== 2025-02-18 16:58:46 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 12-E.coli-cysB-metJ-GSE122320/cysB_taur_1_ChIPexo.PE.a.bam --out 12-E.coli-cysB-metJ-GSE122320/cysB_taur_1_ChIPexo.PE.a.GPS The genome is segmented into 8717 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2202941 HitCounts: 1.6697324E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 597 reads. ============================================== 2025-02-18 16:58:49 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc1_ChIPexo.SE.a.GPS The genome is segmented into 8231 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1714830 HitCounts: 1.8162704E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 1087 reads. The genome is segmented into 8653 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 1060 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 819 reads. The genome is segmented into 8728 regions for analysis. Running with 1 threads ... The genome is segmented into 8245 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 1193 reads. The genome is segmented into 8681 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 847 Insignificant: 1 Filtered: 103 Finish binding event prediction: 1.2m Refine read distribution from 524 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 72 Insignificant: 0 Filtered: 10 Finish binding event prediction: 1.3m Refine read distribution from 26 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 996 Insignificant: 206 Filtered: 6 Finish binding event prediction: 24.1s Refine read distribution from 804 binding events. --------------------------- Events discovered Significant: 126 Insignificant: 9 Filtered: 2 Finish binding event prediction: 16.1s Refine read distribution from 87 binding events. --------------------------- Events discovered Significant: 64 Insignificant: 3 Filtered: 16 Finish binding event prediction: 1.6m Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 960 Insignificant: 0 Filtered: 192 Finish binding event prediction: 1.9m Refine read distribution from 674 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1023 Insignificant: 0 Filtered: 140 Finish binding event prediction: 2.1m Refine read distribution from 681 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 26 Insignificant: 41 Filtered: 9 Finish binding event prediction: 2.0m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 77 Insignificant: 49 Filtered: 10 Finish binding event prediction: 1.7m Refine read distribution from 25 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 756 Insignificant: 13 Filtered: 155 Finish binding event prediction: 2.3m Refine read distribution from 520 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1379 Insignificant: 439 Filtered: 4 Finish binding event prediction: 33.2s Refine read distribution from 1082 binding events. --------------------------- Events discovered Significant: 275 Insignificant: 10 Filtered: 40 Finish binding event prediction: 2.1m Refine read distribution from 101 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1090 Insignificant: 313 Filtered: 6 Finish binding event prediction: 25.1s Refine read distribution from 825 binding events. --------------------------- Events discovered Significant: 150 Insignificant: 18 Filtered: 1 Finish binding event prediction: 51.1s Refine read distribution from 103 binding events. --------------------------- Events discovered Significant: 91 Insignificant: 33 Filtered: 17 Finish binding event prediction: 2.4m Refine read distribution from 26 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 52 Insignificant: 45 Filtered: 10 Finish binding event prediction: 2.4m Refine read distribution from 17 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 919 Insignificant: 11 Filtered: 202 Finish binding event prediction: 2.7m Refine read distribution from 666 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 844 Insignificant: 263 Filtered: 6 Finish binding event prediction: 34.5s Refine read distribution from 641 binding events. --------------------------- Events discovered Significant: 6 Insignificant: 37 Filtered: 5 Finish binding event prediction: 2.5m Running with 1 threads ... --------------------------- Events discovered Significant: 432 Insignificant: 1 Filtered: 129 --------------------------- Events discovered Significant: 33 Insignificant: 0 Filtered: 11 Finish binding event prediction: 2.5m Finish binding event prediction: 2.6m --------------------------- Events discovered Significant: 117 Insignificant: 3 Filtered: 29 Finish binding event prediction: 2.7m Refine read distribution from 19 binding events. Running with 1 threads ... Refine read distribution from 299 binding events. Refine read distribution from 28 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 60 Insignificant: 55 Filtered: 16 Finish binding event prediction: 2.3m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 855 Insignificant: 7 Filtered: 213 Finish binding event prediction: 3.1m --------------------------- Events discovered Significant: 69 Insignificant: 2 Filtered: 8 Finish binding event prediction: 3.0m Refine read distribution from 37 binding events. Running with 1 threads ... Refine read distribution from 652 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 391 Insignificant: 2 Filtered: 119 Finish binding event prediction: 2.9m Refine read distribution from 248 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 935 Insignificant: 2 Filtered: 175 Finish binding event prediction: 3.1m Refine read distribution from 606 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 13 Insignificant: 0 Filtered: 4 Finish binding event prediction: 3.2m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 74 Insignificant: 55 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 32 binding events. --------------------------- Events discovered Significant: 133 Insignificant: 2 Filtered: 32 --------------------------- Events discovered Significant: 919 Insignificant: 1 Filtered: 197 Finish binding event prediction: 3.1m Finish binding event prediction: 3.3m Refine read distribution from 47 binding events. Running with 1 threads ... Refine read distribution from 641 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 46 Insignificant: 2 Filtered: 11 Finish binding event prediction: 3.1m Refine read distribution from 28 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 57 Insignificant: 51 Filtered: 13 Finish binding event prediction: 3.0m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 12 Insignificant: 4 Filtered: 5 Finish binding event prediction: 3.2m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 155 Insignificant: 64 Filtered: 2 Finish binding event prediction: 1.2m Refine read distribution from 91 binding events. --------------------------- Events discovered Significant: 14 Insignificant: 0 Filtered: 4 --------------------------- Events discovered Significant: 25 Insignificant: 12 Filtered: 8 --------------------------- Events discovered Significant: 14 Insignificant: 0 Filtered: 4 Finish binding event prediction: 3.2m Finish binding event prediction: 3.3m Refine read distribution from 11 binding events. Finish binding event prediction: 3.3m Running with 1 threads ... Refine read distribution from 12 binding events. Running with 1 threads ... Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 409 Insignificant: 59 Filtered: 5 Finish binding event prediction: 1.1m Refine read distribution from 210 binding events. --------------------------- Events discovered Significant: 122 Insignificant: 1 Filtered: 25 Finish binding event prediction: 3.2m Refine read distribution from 42 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1170 Insignificant: 448 Filtered: 51 Finish binding event prediction: 44.2s Refine read distribution from 909 binding events. --------------------------- Events discovered Significant: 14 Insignificant: 12 Filtered: 8 Finish binding event prediction: 3.4m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 370 Insignificant: 11 Filtered: 124 Finish binding event prediction: 3.4m Refine read distribution from 201 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 215 Insignificant: 46 Filtered: 10 Finish binding event prediction: 58.0s Refine read distribution from 142 binding events. --------------------------- Events discovered Significant: 17 Insignificant: 17 Filtered: 6 Finish binding event prediction: 3.5m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 68 Insignificant: 6 Filtered: 17 Finish binding event prediction: 47.1s Refine read distribution from 18 binding events. --------------------------- Events discovered Significant: 10 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.5m Refine read distribution from 4 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 84 Insignificant: 66 Filtered: 9 Finish binding event prediction: 3.4m Refine read distribution from 27 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 24 Filtered: 3 Finish binding event prediction: 3.5m Running with 1 threads ... --------------------------- Events discovered Significant: 46 Insignificant: 41 Filtered: 14 Finish binding event prediction: 3.0m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 154 Insignificant: 3 Filtered: 38 Finish binding event prediction: 3.5m Refine read distribution from 57 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 93 Insignificant: 32 Filtered: 21 Finish binding event prediction: 3.6m --------------------------- Events discovered Significant: 43 Insignificant: 1 Filtered: 10 Refine read distribution from 22 binding events. Finish binding event prediction: 3.6m Running with 1 threads ... Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 39 Insignificant: 2 Filtered: 6 Finish binding event prediction: 3.6m Refine read distribution from 18 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 20 Insignificant: 0 Filtered: 5 Finish binding event prediction: 3.7m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 73 Insignificant: 14 Filtered: 0 Finish binding event prediction: 34.5s Refine read distribution from 67 binding events. --------------------------- Events discovered Significant: 8 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.6m Running with 1 threads ... --------------------------- Events discovered Significant: 39 Insignificant: 0 Filtered: 9 Finish binding event prediction: 3.9m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 42 Insignificant: 7 Filtered: 0 Finish binding event prediction: 39.2s Refine read distribution from 42 binding events. --------------------------- Events discovered Significant: 72 Insignificant: 3 Filtered: 21 Finish binding event prediction: 3.7m Refine read distribution from 32 binding events. Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 101 Insignificant: 17 Filtered: 7 --------------------------- Events discovered Significant: 6 Insignificant: 37 Filtered: 5 Finish binding event prediction: 1.1m Finish binding event prediction: 1.4m Refine read distribution from 53 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 128 Insignificant: 45 Filtered: 0 Finish binding event prediction: 1.2m Refine read distribution from 83 binding events. --------------------------- Events discovered Significant: 193 Insignificant: 7 Filtered: 6 Finish binding event prediction: 1.3m Refine read distribution from 61 binding events. --------------------------- Events discovered Significant: 1173 Insignificant: 440 Filtered: 7 Finish binding event prediction: 1.1m Refine read distribution from 926 binding events. --------------------------- Events discovered Significant: 311 Insignificant: 8 Filtered: 35 Finish binding event prediction: 3.9m Refine read distribution from 104 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 4.1m Running with 1 threads ... --------------------------- Events discovered Significant: 135 Insignificant: 35 Filtered: 1 --------------------------- Events discovered Significant: 46 Insignificant: 30 Filtered: 0 Finish binding event prediction: 1.6m Finish binding event prediction: 52.9s Refine read distribution from 42 binding events. Refine read distribution from 94 binding events. --------------------------- Events discovered Significant: 38 Insignificant: 7 Filtered: 0 Finish binding event prediction: 39.1s Refine read distribution from 32 binding events. --------------------------- Events discovered Significant: 384 Insignificant: 22 Filtered: 128 Finish binding event prediction: 4.1m Refine read distribution from 219 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 130 Insignificant: 1 Filtered: 35 Finish binding event prediction: 4.2m Refine read distribution from 61 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 938 Insignificant: 358 Filtered: 29 Finish binding event prediction: 1.3m Refine read distribution from 690 binding events. --------------------------- Events discovered Significant: 1349 Insignificant: 417 Filtered: 2 Finish binding event prediction: 1.2m Refine read distribution from 1092 binding events. --------------------------- Events discovered Significant: 226 Insignificant: 13 Filtered: 10 --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.3m Finish binding event prediction: 4.3m Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 20 Filtered: 5 Finish binding event prediction: 40.2s Refine read distribution from 99 binding events. --------------------------- Events discovered Significant: 11 Insignificant: 0 Filtered: 3 Finish binding event prediction: 4.5m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 20 Filtered: 0 Finish binding event prediction: 4.0m Running with 1 threads ... --------------------------- Events discovered Significant: 121 Insignificant: 3 Filtered: 37 Finish binding event prediction: 4.2m Refine read distribution from 58 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 208 Insignificant: 21 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 100 binding events. --------------------------- Events discovered Significant: 81 Insignificant: 18 Filtered: 15 --------------------------- Events discovered Significant: 199 Insignificant: 55 Filtered: 7 --------------------------- Events discovered Significant: 140 Insignificant: 50 Filtered: 0 Finish binding event prediction: 1.4m Finish binding event prediction: 49.4s Finish binding event prediction: 1.4m Refine read distribution from 37 binding events. Refine read distribution from 79 binding events. Refine read distribution from 124 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 9 Filtered: 4 Finish binding event prediction: 4.4m Running with 1 threads ... --------------------------- Events discovered Significant: 59 Insignificant: 22 Filtered: 0 --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 1 Finish binding event prediction: 1.1m Finish binding event prediction: 4.4m Running with 1 threads ... Refine read distribution from 39 binding events. --------------------------- Events discovered Significant: 108 Insignificant: 102 Filtered: 1 Finish binding event prediction: 1.5m Refine read distribution from 98 binding events. --------------------------- Events discovered Significant: 71 Insignificant: 36 Filtered: 0 Finish binding event prediction: 1.3m Refine read distribution from 51 binding events. --------------------------- Events discovered Significant: 134 Insignificant: 68 Filtered: 4 Finish binding event prediction: 1.2m Refine read distribution from 76 binding events. --------------------------- Events discovered Significant: 112 Insignificant: 32 Filtered: 2 --------------------------- Events discovered Significant: 426 Insignificant: 45 Filtered: 3 Finish binding event prediction: 1.1m --------------------------- Events discovered Significant: 3 Insignificant: 4 Filtered: 2 Finish binding event prediction: 39.7s Finish binding event prediction: 4.7m Running with 1 threads ... Refine read distribution from 60 binding events. Refine read distribution from 220 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.6m Running with 1 threads ... --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 4.9m Running with 1 threads ... --------------------------- Events discovered Significant: 199 Insignificant: 14 Filtered: 3 Finish binding event prediction: 1.2m Refine read distribution from 181 binding events. --------------------------- Events discovered Significant: 10 Insignificant: 0 Filtered: 3 Finish binding event prediction: 4.7m Refine read distribution from 2 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 199 Insignificant: 18 Filtered: 1 Finish binding event prediction: 1.2m Refine read distribution from 184 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 315 Insignificant: 51 Filtered: 1 Running with 1 threads ... Finish binding event prediction: 43.3s Refine read distribution from 208 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 24 Filtered: 3 Finish binding event prediction: 1.4m --------------------------- Events discovered Significant: 200 Insignificant: 0 Filtered: 3 Finish binding event prediction: 1.1m Refine read distribution from 187 binding events. --------------------------- Events discovered Significant: 122 Insignificant: 81 Filtered: 0 Finish binding event prediction: 1.8m Refine read distribution from 91 binding events. --------------------------- Events discovered Significant: 985 Insignificant: 317 Filtered: 30 Finish binding event prediction: 2.1m Refine read distribution from 689 binding events. --------------------------- Events discovered Significant: 143 Insignificant: 8 Filtered: 3 Finish binding event prediction: 1.1m Refine read distribution from 68 binding events. --------------------------- Events discovered Significant: 310 Insignificant: 33 Filtered: 1 Finish binding event prediction: 41.2s Refine read distribution from 195 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 2 Filtered: 1 Finish binding event prediction: 5.0m Running with 1 threads ... --------------------------- Events discovered Significant: 268 Insignificant: 21 Filtered: 4 Finish binding event prediction: 1.7m Refine read distribution from 119 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 51 Insignificant: 26 Filtered: 1 Finish binding event prediction: 56.1s Refine read distribution from 45 binding events. --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 2 Finish binding event prediction: 5.3m Running with 1 threads ... --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 5.4m Running with 1 threads ... --------------------------- Events discovered Significant: 46 Insignificant: 1 Filtered: 15 Finish binding event prediction: 5.5m Refine read distribution from 31 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 39 Insignificant: 0 Filtered: 10 Finish binding event prediction: 5.7m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 707 Insignificant: 277 Filtered: 45 Finish binding event prediction: 2.4m Refine read distribution from 491 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 20 Filtered: 0 Finish binding event prediction: 1.5m No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 6 Filtered: 1 Finish binding event prediction: 5.3m Running with 1 threads ... --------------------------- Events discovered Significant: 42 Insignificant: 5 Filtered: 8 Finish binding event prediction: 1.0m Refine read distribution from 17 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 9 Filtered: 4 Finish binding event prediction: 1.6m --------------------------- Events discovered Significant: 8 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.3m --------------------------- Events discovered Significant: 986 Insignificant: 330 Filtered: 43 Finish binding event prediction: 3.6m Refine read distribution from 706 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 15 Filtered: 1 Finish binding event prediction: 5.7m Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.1m --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 2.4m --------------------------- Events discovered Significant: 4 Insignificant: 2 Filtered: 2 Finish binding event prediction: 5.9m Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 199 Insignificant: 0 Filtered: 1 Finish binding event prediction: 1.1m Refine read distribution from 191 binding events. --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.4m --------------------------- Events discovered Significant: 3 Insignificant: 4 Filtered: 2 Finish binding event prediction: 2.4m --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 2.6m --------------------------- Events discovered Significant: 1 Insignificant: 15 Filtered: 1 Finish binding event prediction: 1.3m --------------------------- Events discovered Significant: 2 Insignificant: 6 Filtered: 1 Finish binding event prediction: 1.8m --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 2 Finish binding event prediction: 2.4m --------------------------- Events discovered Significant: 4 Insignificant: 2 Filtered: 1 Finish binding event prediction: 2.7m No valid binding event was found. --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 2.5m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.3m --------------------------- Events discovered Significant: 323 Insignificant: 15 Filtered: 0 Finish binding event prediction: 2.5m Refine read distribution from 262 binding events. --------------------------- Events discovered Significant: 661 Insignificant: 281 Filtered: 56 Finish binding event prediction: 4.0m Refine read distribution from 473 binding events. No valid binding event was found. No valid binding event was found. No valid binding event was found. --------------------------- Events discovered Significant: 4 Insignificant: 2 Filtered: 2 Finish binding event prediction: 4.1m ============================================== 2025-02-18 17:10:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 727246 HitCounts: 1330197.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 96 reads. The genome is segmented into 8235 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 17:11:01 ============================================== 2025-02-18 17:11:01 ============================================== 2025-02-18 17:11:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 469734 HitCounts: 1519851.0 Original read count stats: ============================================== 2025-02-18 17:11:01_IP Bases: 582502 HitCounts: 1410081.0 Original read count stats: _IP Bases: 1283146 HitCounts: 1530907.0 ============================================== 2025-02-18 17:11:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_2.1x36mers.unique.GPS ============================================== 2025-02-18 17:11:02 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_2.1x36mers.unique.GPS ============================================== 2025-02-18 17:11:02 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 74 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 89 reads. ============================================== 2025-02-18 17:11:02 Original read count stats: _IP Bases: 1332088 HitCounts: 1740661.0 Original read count stats: _IP Bases: 1268950 HitCounts: 1516292.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1836371 HitCounts: 2756191.0 The genome is segmented into 8411 regions for analysis. Original read count stats: Running with 1 threads ... _IP Bases: 1317068 HitCounts: 1723711.0 The genome is segmented into 8298 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 151 reads. Original read count stats: _IP Bases: 520730 HitCounts: 1775756.0 ============================================== 2025-02-18 17:11:03 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_2.1x36mers.unique.GPS ============================================== 2025-02-18 17:11:03 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_1.SE.a.GPS ============================================== 2025-02-18 17:11:03 ============================================== 2025-02-18 17:11:03 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 150 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 84 reads. Original read count stats: _IP Bases: 1093038 HitCounts: 1752582.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 168 reads. Original read count stats: _IP Bases: 792223 HitCounts: 1838681.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 166 reads. ============================================== 2025-02-18 17:11:04 The genome is segmented into 8374 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 17:11:04 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_2.SE.a.GPS The genome is segmented into 8177 regions for analysis. Original read count stats: The genome is segmented into 8165 regions for analysis. _IP Bases: 2370720 HitCounts: 4318058.0 Original read count stats: _IP Bases: 1981907 HitCounts: 3289556.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 242 reads. ============================================== 2025-02-18 17:11:04 Running with 1 threads ... ============================================== 2025-02-18 17:11:04 Running with 1 threads ... The genome is segmented into 8345 regions for analysis. ============================================== 2025-02-18 17:11:04 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_2.1x36mers.unique.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-18 17:11:04 At Poisson p-value 1.0e-03, in a 301bp window, expect 143 reads. The genome is segmented into 8356 regions for analysis. ============================================== 2025-02-18 17:11:04 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_1.SE.a.GPS ============================================== 2025-02-18 17:11:04 Original read count stats: _IP Bases: 1193361 HitCounts: 3816542.0 ============================================== 2025-02-18 17:11:04 ============================================== 2025-02-18 17:11:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_2.1x36mers.unique.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 136 reads. Original read count stats: _IP Bases: 837761 HitCounts: 3203985.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_2.1x36mers.unique.GPS ============================================== 2025-02-18 17:11:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-18 17:11:05 Original read count stats: _IP Bases: 961923 HitCounts: 1955313.0 Original read count stats: _IP Bases: 1953471 HitCounts: 3998354.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 646953 HitCounts: 1921735.0 ============================================== 2025-02-18 17:11:05 ============================================== 2025-02-18 17:11:05 ============================================== 2025-02-18 17:11:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_2.SE.a.GPS ============================================== 2025-02-18 17:11:05 Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_1.1x36mers.unique.GPS _IP Bases: 2663537 HitCounts: 3892301.0 Original read count stats: _IP Bases: 1341389 HitCounts: 3672629.0 ============================================== 2025-02-18 17:11:05 ============================================== 2025-02-18 17:11:05 ============================================== 2025-02-18 17:11:05 Original read count stats: _IP Bases: 1170828 HitCounts: 4037353.0 The genome is segmented into 8045 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_1.1x36mers.unique.GPS The genome is segmented into 8418 regions for analysis. ============================================== 2025-02-18 17:11:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_2.1x36mers.unique.GPS Running with 1 threads ... ============================================== 2025-02-18 17:11:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_2.1x36mers.unique.GPS ============================================== 2025-02-18 17:11:05 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_1.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_1.1x36mers.unique.GPS Original read count stats: Original read count stats: _IP Bases: 925178 HitCounts: 3599521.0 _IP Bases: 909271 HitCounts: 4239459.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_2.1x36mers.unique.GPS ============================================== 2025-02-18 17:11:05 ============================================== 2025-02-18 17:11:05 Original read count stats: _IP Bases: 2227898 HitCounts: 4296963.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_2.SE.a.GPS Original read count stats: _IP Bases: 1147001 HitCounts: 2041145.0 ============================================== 2025-02-18 17:11:06 Original read count stats: _IP Bases: 905381 HitCounts: 4213645.0 Original read count stats: _IP Bases: 894308 HitCounts: 4740332.0 Original read count stats: _IP Bases: 1080795 HitCounts: 3678513.0 Original read count stats: _IP Bases: 1019615 HitCounts: 4679799.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_2.SE.a.GPS The genome is segmented into 8065 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 966395 HitCounts: 3758165.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 137 reads. Original read count stats: _IP Bases: 928922 HitCounts: 4267421.0 ============================================== 2025-02-18 17:11:06 Original read count stats: _IP Bases: 1401694 HitCounts: 4048408.0 ============================================== 2025-02-18 17:11:06 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 130 reads. _IP Bases: 1336599 HitCounts: 4197429.0 Original read count stats: _IP Bases: 536739 HitCounts: 2343485.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1632857 HitCounts: 4020316.0 ============================================== 2025-02-18 17:11:06 Original read count stats: _IP Bases: 2513342 HitCounts: 3912182.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1352124 HitCounts: 4315258.0 ============================================== 2025-02-18 17:11:06 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 188 reads. ============================================== 2025-02-18 17:11:06 ============================================== 2025-02-18 17:11:06 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_2.1x36mers.unique.GPS ============================================== 2025-02-18 17:11:06 At Poisson p-value 1.0e-03, in a 301bp window, expect 208 reads. ============================================== 2025-02-18 17:11:06 The genome is segmented into 8465 regions for analysis. ============================================== 2025-02-18 17:11:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 322 reads. ============================================== 2025-02-18 17:11:07 Original read count stats: ============================================== 2025-02-18 17:11:06 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 275 reads. The genome is segmented into 8419 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 365 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 356 reads. ============================================== 2025-02-18 17:11:07 Original read count stats: Original read count stats: Original read count stats: ============================================== 2025-02-18 17:11:08 ============================================== 2025-02-18 17:11:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 192 reads. ============================================== 2025-02-18 17:11:08 ============================================== 2025-02-18 17:11:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 165 reads. ============================================== 2025-02-18 17:11:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 215 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 262 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 284 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 133 reads. ============================================== 2025-02-18 17:11:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 352 reads. ============================================== 2025-02-18 17:11:08_IP Bases: 2498372 HitCounts: 4169448.0 The genome is segmented into 8104 regions for analysis. ============================================== 2025-02-18 17:11:08_IP Bases: 542365 HitCounts: 4668361.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 218 reads. _IP Bases: 1552810 HitCounts: 4896400.0 ============================================== 2025-02-18 17:11:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 197 reads. ============================================== 2025-02-18 17:11:08 ============================================== 2025-02-18 17:11:08 ============================================== 2025-02-18 17:11:08_IP Bases: 1240141 HitCounts: 2065973.0 _IP Bases: 1290184 HitCounts: 4201094.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 291 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 286 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 19-E.coli-ZraR-GSE181993/ZraR_1.1x36mers.unique.bam --out 19-E.coli-ZraR-GSE181993/ZraR_1.1x36mers.unique.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 267 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_1.SE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/narL_2.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/narL_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 16-E.coli-ydhB-GSE166465/ydhB_1.1x36mers.unique.bam --out 16-E.coli-ydhB-GSE166465/ydhB_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 295 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 317 reads. ============================================== 2025-02-18 17:11:09 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/narL_1.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/narL_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 310 reads. ============================================== 2025-02-18 17:11:09 The genome is segmented into 8289 regions for analysis. The genome is segmented into 8164 regions for analysis. Original read count stats: _IP Bases: 585682 HitCounts: 2697824.0 ============================================== 2025-02-18 17:11:09 ============================================== 2025-02-18 17:11:09 Running with 1 threads ... Original read count stats: _IP Bases: 772560 HitCounts: 2410847.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 75 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 297 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_2.1x36mers.unique.GPS The genome is segmented into 8594 regions for analysis. Original read count stats: Original read count stats: The genome is segmented into 8308 regions for analysis. Original read count stats: _IP Bases: 1622652 HitCounts: 5166553.0 _IP Bases: 924610 HitCounts: 4241004.0 Original read count stats: _IP Bases: 1292688 HitCounts: 2397527.0 Running with 1 threads ... _IP Bases: 1052195 HitCounts: 4563536.0 The genome is segmented into 8311 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc1_ChIPexo.SE.a.GPS The genome is segmented into 8259 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_2.1x36mers.unique.GPS Original read count stats: Original read count stats: Original read count stats: _IP Bases: 1531665 HitCounts: 4243110.0 Original read count stats: Running with 1 threads ... Running with 1 threads ... Original read count stats: Original read count stats: The genome is segmented into 8201 regions for analysis. The genome is segmented into 8517 regions for analysis. The genome is segmented into 8529 regions for analysis. _IP Bases: 464470 HitCounts: 5526371.0 The genome is segmented into 8262 regions for analysis. Running with 1 threads ... Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 321 reads. _IP Bases: 1537564 HitCounts: 4758369.0 Original read count stats: Running with 1 threads ... Original read count stats: _IP Bases: 1101243 HitCounts: 4769684.0 Original read count stats: Original read count stats: ============================================== 2025-02-18 17:11:09 Original read count stats: _IP Bases: 2835132 HitCounts: 5104303.0 _IP Bases: 2116429 HitCounts: 4703088.0 The genome is segmented into 8479 regions for analysis. _IP Bases: 581095 HitCounts: 5254679.0 The genome is segmented into 8192 regions for analysis. Original read count stats: _IP Bases: 2293136 HitCounts: 5165780.0 ============================================== 2025-02-18 17:11:09 Original read count stats: The genome is segmented into 8167 regions for analysis. _IP Bases: 1393698 HitCounts: 5157484.0 The genome is segmented into 8491 regions for analysis. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 357 reads. _IP Bases: 760697 HitCounts: 5506418.0 Running with 1 threads ... _IP Bases: 1604927 HitCounts: 2432215.0 _IP Bases: 2203293 HitCounts: 4934203.0 _IP Bases: 2479530 HitCounts: 4435047.0 Running with 1 threads ... ============================================== 2025-02-18 17:11:09 Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Original read count stats: ============================================== 2025-02-18 17:11:09 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_1.SE.a.GPS _IP Bases: 1473906 HitCounts: 2033900.0 Running with 1 threads ... _IP Bases: 592410 HitCounts: 5673812.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 168 reads. _IP Bases: 2472536 HitCounts: 4060551.0 Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_2.SE.a.GPS The genome is segmented into 8557 regions for analysis. Running with 1 threads ... The genome is segmented into 8344 regions for analysis. The genome is segmented into 8212 regions for analysis. The genome is segmented into 8322 regions for analysis. Original read count stats: _IP Bases: 1347668 HitCounts: 5571014.0 The genome is segmented into 8211 regions for analysis. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 2092940 HitCounts: 4913782.0 ============================================== 2025-02-18 17:11:10 ============================================== 2025-02-18 17:11:10 At Poisson p-value 1.0e-03, in a 301bp window, expect 130 reads. ============================================== 2025-02-18 17:11:10 ============================================== 2025-02-18 17:11:10 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 99 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/narL_2.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/narL_2.SE.a.GPS The genome is segmented into 8335 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 146 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_2.SE.a.GPS ============================================== 2025-02-18 17:11:10 Running with 1 threads ... The genome is segmented into 8258 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 98 reads. Running with 1 threads ... ============================================== 2025-02-18 17:11:10 ============================================== 2025-02-18 17:11:10 The genome is segmented into 8335 regions for analysis. ============================================== 2025-02-18 17:11:10 The genome is segmented into 8473 regions for analysis. ============================================== 2025-02-18 17:11:10 Original read count stats: Original read count stats: _IP Bases: 2129793 HitCounts: 3353120.0 _IP Bases: 1451407 HitCounts: 5629371.0 The genome is segmented into 8241 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_2.SE.a.GPS Running with 1 threads ... Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 90 reads. _IP Bases: 2049853 HitCounts: 4877443.0 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/narL_1.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/narL_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 2100328 HitCounts: 5349698.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 192 reads. The genome is segmented into 8565 regions for analysis. Original read count stats: _IP Bases: 1031055 HitCounts: 2704001.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 231 reads. The genome is segmented into 8113 regions for analysis. ============================================== 2025-02-18 17:11:11 At Poisson p-value 1.0e-03, in a 301bp window, expect 170 reads. Original read count stats: _IP Bases: 2254669 HitCounts: 5293574.0 The genome is segmented into 8374 regions for analysis. Running with 1 threads ... The genome is segmented into 8353 regions for analysis. Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_1.1x36mers.unique.GPS Running with 1 threads ... _IP Bases: 2136191 HitCounts: 5341767.0 Original read count stats: _IP Bases: 2540585 HitCounts: 6814164.0 Running with 1 threads ... Original read count stats: _IP Bases: 3222569 HitCounts: 5322203.0 Original read count stats: _IP Bases: 633966 HitCounts: 6405331.0 Original read count stats: _IP Bases: 401373 HitCounts: 6455486.0 The genome is segmented into 8035 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 17:11:11 At Poisson p-value 1.0e-03, in a 301bp window, expect 184 reads. The genome is segmented into 8258 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 307 reads. Original read count stats: _IP Bases: 2344058 HitCounts: 5548944.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_1.1x36mers.unique.GPS ============================================== 2025-02-18 17:11:11 The genome is segmented into 8227 regions for analysis. Running with 1 threads ... The genome is segmented into 8340 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 2759347 HitCounts: 5546316.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 216 reads. Running with 1 threads ... ============================================== 2025-02-18 17:11:11 The genome is segmented into 8493 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 286 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 16-E.coli-ydhB-GSE166465/ydhB_2.1x36mers.unique.bam --out 16-E.coli-ydhB-GSE166465/ydhB_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 95 reads. ============================================== 2025-02-18 17:11:12 The genome is segmented into 8402 regions for analysis. Original read count stats: _IP Bases: 1673120 HitCounts: 5250822.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 122 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_1.1x36mers.unique.GPS The genome is segmented into 8198 regions for analysis. The genome is segmented into 8030 regions for analysis. Original read count stats: _IP Bases: 2136906 HitCounts: 5574342.0 Original read count stats: _IP Bases: 1675720 HitCounts: 5701076.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 193 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 374 reads. The genome is segmented into 8437 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 347 reads. Original read count stats: _IP Bases: 817565 HitCounts: 6981979.0 Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 301 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 314 reads. ============================================== 2025-02-18 17:11:12 At Poisson p-value 1.0e-03, in a 301bp window, expect 365 reads. ============================================== 2025-02-18 17:11:12 The genome is segmented into 8315 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 365 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_2.SE.a.GPS The genome is segmented into 8183 regions for analysis. Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_2.SE.a.GPS ============================================== 2025-02-18 17:11:12 At Poisson p-value 1.0e-03, in a 301bp window, expect 357 reads. Original read count stats: _IP Bases: 2095222 HitCounts: 4989098.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_1.SE.a.GPS The genome is segmented into 8408 regions for analysis. The genome is segmented into 8303 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 296 reads. The genome is segmented into 8242 regions for analysis. Original read count stats: The genome is segmented into 8716 regions for analysis. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 360 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 351 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 384 reads. The genome is segmented into 8535 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 443 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 383 reads. _IP Bases: 2113095 HitCounts: 7206027.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 378 reads. ============================================== 2025-02-18 17:11:13 ============================================== 2025-02-18 17:11:14 Running with 1 threads ... The genome is segmented into 7968 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 356 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 451 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 203 reads. ============================================== 2025-02-18 17:11:14 ============================================== 2025-02-18 17:11:14 At Poisson p-value 1.0e-03, in a 301bp window, expect 365 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 377 reads. The genome is segmented into 8688 regions for analysis. _IP Bases: 2008676 HitCounts: 5379932.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 384 reads. ============================================== 2025-02-18 17:11:14 ============================================== 2025-02-18 17:11:14 At Poisson p-value 1.0e-03, in a 301bp window, expect 390 reads. Running with 1 threads ... The genome is segmented into 7991 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 408 reads. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 410 reads. _IP Bases: 2143412 HitCounts: 6061388.0 Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-18 17:11:15 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_2.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_1.SE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 19-E.coli-ZraR-GSE181993/ZraR_2.SE.a.bam --out 19-E.coli-ZraR-GSE181993/ZraR_2.SE.a.GPS ============================================== 2025-02-18 17:11:15 The genome is segmented into 8432 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 19-E.coli-ZraR-GSE181993/ZraR_2.1x36mers.unique.bam --out 19-E.coli-ZraR-GSE181993/ZraR_2.1x36mers.unique.GPS ============================================== 2025-02-18 17:11:15 At Poisson p-value 1.0e-03, in a 301bp window, expect 445 reads. The genome is segmented into 8189 regions for analysis. The genome is segmented into 8254 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 565 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_2.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_2.1x36mers.unique.GPS The genome is segmented into 8152 regions for analysis. Running with 1 threads ... The genome is segmented into 8122 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 1182488 HitCounts: 6724907.0 The genome is segmented into 8678 regions for analysis. The genome is segmented into 8315 regions for analysis. The genome is segmented into 8176 regions for analysis. The genome is segmented into 8382 regions for analysis. The genome is segmented into 8097 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1019855 HitCounts: 8412773.0 Running with 1 threads ... Original read count stats: Running with 1 threads ... _IP Bases: 1191078 HitCounts: 8059265.0 Running with 1 threads ... Original read count stats: _IP Bases: 2079380 HitCounts: 6185748.0 Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 1859952 HitCounts: 7174248.0 Original read count stats: The genome is segmented into 8265 regions for analysis. _IP Bases: 2253826 HitCounts: 5543604.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 370 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 468 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 418 reads. Original read count stats: Original read count stats: _IP Bases: 1063480 HitCounts: 4219336.0 _IP Bases: 2932537 HitCounts: 6611735.0 ============================================== 2025-02-18 17:11:16 ============================================== 2025-02-18 17:11:16 The genome is segmented into 8427 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_1.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_1.SE.a.GPS The genome is segmented into 8396 regions for analysis. The genome is segmented into 8245 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 382 reads. The genome is segmented into 7998 regions for analysis. ============================================== 2025-02-18 17:11:16 ============================================== 2025-02-18 17:11:16 The genome is segmented into 8015 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 19-E.coli-ZraR-GSE181993/ZraR_1.SE.a.bam --out 19-E.coli-ZraR-GSE181993/ZraR_1.SE.a.GPS The genome is segmented into 8683 regions for analysis. ============================================== 2025-02-18 17:11:16 At Poisson p-value 1.0e-03, in a 301bp window, expect 395 reads. ============================================== 2025-02-18 17:11:17 The genome is segmented into 7962 regions for analysis. Original read count stats: ============================================== 2025-02-18 17:11:16 ============================================== 2025-02-18 17:11:16 The genome is segmented into 8255 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 210 reads. The genome is segmented into 8068 regions for analysis. _IP Bases: 1713126 HitCounts: 3726589.0 Running with 1 threads ... ============================================== 2025-02-18 17:11:18 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_2.SE.a.GPS ============================================== 2025-02-18 17:11:18 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_1.SE.a.GPS Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_2.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_2.SE.a.GPS Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_2.1x36mers.unique.GPS Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 297 reads. The genome is segmented into 8187 regions for analysis. Running with 1 threads ... The genome is segmented into 8652 regions for analysis. Original read count stats: _IP Bases: 626797 HitCounts: 8303695.0 Original read count stats: _IP Bases: 1150465 HitCounts: 8393367.0 The genome is segmented into 8480 regions for analysis. Original read count stats: _IP Bases: 1849788 HitCounts: 3660778.0 Original read count stats: _IP Bases: 2251947 HitCounts: 7703728.0 Original read count stats: _IP Bases: 1779004 HitCounts: 7842874.0 Running with 1 threads ... Original read count stats: _IP Bases: 1674295 HitCounts: 7791351.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 433 reads. Original read count stats: _IP Bases: 2205187 HitCounts: 7654432.0 Running with 1 threads ... Original read count stats: _IP Bases: 2300274 HitCounts: 7324153.0 Original read count stats: _IP Bases: 2393964 HitCounts: 7516732.0 Original read count stats: _IP Bases: 3404983 HitCounts: 7271123.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 410 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 444 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 426 reads. The genome is segmented into 8209 regions for analysis. The genome is segmented into 8122 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 567 reads. ============================================== 2025-02-18 17:11:19 ============================================== 2025-02-18 17:11:19 The genome is segmented into 8478 regions for analysis. The genome is segmented into 8440 regions for analysis. ============================================== 2025-02-18 17:11:20 At Poisson p-value 1.0e-03, in a 301bp window, expect 522 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 467 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 111 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 459 reads. ============================================== 2025-02-18 17:11:21 At Poisson p-value 1.0e-03, in a 301bp window, expect 287 reads. The genome is segmented into 8251 regions for analysis. The genome is segmented into 7973 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 534 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_1.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 295 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_1.SE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_1.1x36mers.unique.GPS Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8513 regions for analysis. Running with 1 threads ... The genome is segmented into 8370 regions for analysis. Original read count stats: _IP Bases: 290754 HitCounts: 9938906.0 Running with 1 threads ... The genome is segmented into 8325 regions for analysis. Original read count stats: The genome is segmented into 8489 regions for analysis. _IP Bases: 2089370 HitCounts: 3870081.0 The genome is segmented into 8110 regions for analysis. Running with 1 threads ... The genome is segmented into 8341 regions for analysis. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 1886937 HitCounts: 1.021139E7 Original read count stats: _IP Bases: 2241350 HitCounts: 8518481.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 458 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 49 reads. The genome is segmented into 8210 regions for analysis. Running with 1 threads ... The genome is segmented into 8434 regions for analysis. Running with 1 threads ... The genome is segmented into 8425 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 524 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 530 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 555 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 605 reads. The genome is segmented into 8211 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 548 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 563 reads. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-18 17:11:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 16-E.coli-ydhB-GSE166465/ydhB_1.SE.a.bam --out 16-E.coli-ydhB-GSE166465/ydhB_1.SE.a.GPS ============================================== 2025-02-18 17:11:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_2.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_2.SE.a.GPS ============================================== 2025-02-18 17:11:24 At Poisson p-value 1.0e-03, in a 301bp window, expect 323 reads. The genome is segmented into 8456 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_2.SE.a.GPS The genome is segmented into 8410 regions for analysis. Running with 1 threads ... The genome is segmented into 8168 regions for analysis. The genome is segmented into 8345 regions for analysis. The genome is segmented into 8407 regions for analysis. The genome is segmented into 8355 regions for analysis. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 874000 HitCounts: 1.2217449E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 625 reads. Original read count stats: _IP Bases: 567869 HitCounts: 1.3596035E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 459 reads. Original read count stats: _IP Bases: 731902 HitCounts: 1.2111681E7 The genome is segmented into 8364 regions for analysis. The genome is segmented into 7982 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 569 reads. The genome is segmented into 8318 regions for analysis. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-18 17:11:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_1.SE.a.GPS The genome is segmented into 8118 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2028079 HitCounts: 1.182491E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 317 reads. The genome is segmented into 8358 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 555 reads. ============================================== 2025-02-18 17:11:30 The genome is segmented into 8504 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_1.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_1.SE.a.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 577 reads. Original read count stats: _IP Bases: 363734 HitCounts: 1.432915E7 The genome is segmented into 8491 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 17:11:31 At Poisson p-value 1.0e-03, in a 301bp window, expect 554 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 206 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_1.SE.a.GPS The genome is segmented into 8599 regions for analysis. Running with 1 threads ... The genome is segmented into 8157 regions for analysis. ============================================== 2025-02-18 17:11:34 Original read count stats: _IP Bases: 500913 HitCounts: 1.6479901E7 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 16-E.coli-ydhB-GSE166465/ydhB_2.SE.a.bam --out 16-E.coli-ydhB-GSE166465/ydhB_2.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 934058 HitCounts: 1.5781896E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 637 reads. The genome is segmented into 8590 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 727 reads. The genome is segmented into 8456 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 19 Insignificant: 1 Filtered: 6 Finish binding event prediction: 1.7m Refine read distribution from 19 binding events. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 28 Insignificant: 64 Filtered: 13 Finish binding event prediction: 1.3m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 116 Insignificant: 1 Filtered: 23 Finish binding event prediction: 1.4m Refine read distribution from 58 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 191 Insignificant: 1 Filtered: 32 Finish binding event prediction: 1.6m Refine read distribution from 47 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 31 Insignificant: 13 Filtered: 6 Finish binding event prediction: 1.7m --------------------------- Events discovered Significant: 39 Insignificant: 13 Filtered: 13 Finish binding event prediction: 1.7m Refine read distribution from 23 binding events. Running with 1 threads ... Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 37 Insignificant: 51 Filtered: 13 Finish binding event prediction: 1.3m Refine read distribution from 17 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 50 Insignificant: 46 Filtered: 10 Finish binding event prediction: 1.9m Refine read distribution from 26 binding events. Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 13 Insignificant: 5 Filtered: 5 Finish binding event prediction: 2.0m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 11 Insignificant: 4 Filtered: 4 Finish binding event prediction: 2.0m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 78 Insignificant: 3 Filtered: 0 Finish binding event prediction: 33.1s Refine read distribution from 62 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 29 Insignificant: 35 Filtered: 9 Finish binding event prediction: 1.9m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 32 Insignificant: 20 Filtered: 8 Finish binding event prediction: 2.3m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 83 Insignificant: 50 Filtered: 10 Finish binding event prediction: 33.1s Refine read distribution from 56 binding events. --------------------------- Events discovered Significant: 200 Insignificant: 48 Filtered: 0 --------------------------- Events discovered Significant: 88 Insignificant: 43 Filtered: 1 Finish binding event prediction: 38.8s Finish binding event prediction: 35.0s Refine read distribution from 49 binding events. Refine read distribution from 105 binding events. --------------------------- Events discovered Significant: 246 Insignificant: 1 Filtered: 27 Finish binding event prediction: 2.3m Refine read distribution from 43 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 27 Insignificant: 27 Filtered: 9 Finish binding event prediction: 2.3m Refine read distribution from 11 binding events. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 47 Insignificant: 32 Filtered: 7 Finish binding event prediction: 2.2m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 75 Insignificant: 0 Filtered: 17 Finish binding event prediction: 2.3m --------------------------- Events discovered Significant: 52 Insignificant: 0 Filtered: 17 Finish binding event prediction: 2.6m Refine read distribution from 31 binding events. Refine read distribution from 42 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 44 Insignificant: 55 Filtered: 11 --------------------------- Events discovered Significant: 206 Insignificant: 15 Filtered: 6 Finish binding event prediction: 2.2m Finish binding event prediction: 50.9s Refine read distribution from 61 binding events. Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 8 Filtered: 5 Finish binding event prediction: 2.5m Running with 1 threads ... --------------------------- Events discovered Significant: 117 Insignificant: 0 Filtered: 14 Finish binding event prediction: 2.5m Refine read distribution from 32 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 121 Insignificant: 1 Filtered: 14 Finish binding event prediction: 2.7m Refine read distribution from 26 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 167 Insignificant: 2 Filtered: 39 Finish binding event prediction: 2.6m Refine read distribution from 57 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 12 Insignificant: 9 Filtered: 6 Finish binding event prediction: 2.6m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 278 Insignificant: 1 Filtered: 90 Finish binding event prediction: 2.7m Refine read distribution from 267 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 14 Insignificant: 7 Filtered: 6 --------------------------- Events discovered Significant: 299 Insignificant: 1 Filtered: 96 Finish binding event prediction: 2.8m Finish binding event prediction: 2.8m Refine read distribution from 14 binding events. Running with 1 threads ... Refine read distribution from 285 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 117 Insignificant: 34 Filtered: 0 --------------------------- Events discovered Significant: 36 Insignificant: 58 Filtered: 14 Finish binding event prediction: 41.2s Finish binding event prediction: 2.7m Refine read distribution from 14 binding events. Refine read distribution from 87 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 63 Insignificant: 1 Filtered: 21 Finish binding event prediction: 2.8m Refine read distribution from 31 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 95 Insignificant: 37 Filtered: 21 Finish binding event prediction: 2.9m Refine read distribution from 31 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 7 Filtered: 4 Finish binding event prediction: 2.8m Running with 1 threads ... --------------------------- Events discovered Significant: 37 Insignificant: 56 Filtered: 16 Finish binding event prediction: 2.6m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 78 Insignificant: 26 Filtered: 0 Finish binding event prediction: 35.4s Refine read distribution from 48 binding events. --------------------------- Events discovered Significant: 108 Insignificant: 48 Filtered: 6 Finish binding event prediction: 1.0m Refine read distribution from 71 binding events. --------------------------- Events discovered Significant: 162 Insignificant: 0 Filtered: 34 --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.9m Finish binding event prediction: 2.9m Running with 1 threads ... Refine read distribution from 50 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 39 Filtered: 1 Finish binding event prediction: 2.8m Running with 1 threads ... --------------------------- Events discovered Significant: 22 Insignificant: 25 Filtered: 11 Finish binding event prediction: 2.7m Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.1m Running with 1 threads ... --------------------------- Events discovered Significant: 55 Insignificant: 0 Filtered: 18 --------------------------- Events discovered Significant: 65 Insignificant: 73 Filtered: 28 Finish binding event prediction: 3.1m Finish binding event prediction: 2.6m Refine read distribution from 17 binding events. Running with 1 threads ... Refine read distribution from 49 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 38 Insignificant: 43 Filtered: 15 Finish binding event prediction: 2.5m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 73 Insignificant: 39 Filtered: 0 Finish binding event prediction: 1.4m Refine read distribution from 37 binding events. --------------------------- Events discovered Significant: 69 Insignificant: 36 Filtered: 0 Finish binding event prediction: 1.2m Refine read distribution from 41 binding events. --------------------------- Events discovered Significant: 138 Insignificant: 17 Filtered: 3 --------------------------- Events discovered Significant: 16 Insignificant: 12 Filtered: 7 Finish binding event prediction: 36.8s Finish binding event prediction: 2.9m Refine read distribution from 8 binding events. Running with 1 threads ... Refine read distribution from 95 binding events. --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.2m Running with 1 threads ... --------------------------- Events discovered Significant: 96 Insignificant: 1 Filtered: 22 Finish binding event prediction: 2.9m Refine read distribution from 37 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 170 Insignificant: 24 Filtered: 2 Finish binding event prediction: 34.1s Refine read distribution from 121 binding events. --------------------------- Events discovered Significant: 81 Insignificant: 7 Filtered: 8 Finish binding event prediction: 3.1m Refine read distribution from 30 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 --------------------------- Events discovered Significant: 58 Insignificant: 1 Filtered: 19 Finish binding event prediction: 3.2m Finish binding event prediction: 3.1m Running with 1 threads ... Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 27 Insignificant: 35 Filtered: 10 Finish binding event prediction: 2.9m Refine read distribution from 9 binding events. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 89 Insignificant: 24 Filtered: 2 --------------------------- Events discovered Significant: 105 Insignificant: 44 Filtered: 0 Finish binding event prediction: 48.2s Finish binding event prediction: 45.1s Refine read distribution from 66 binding events. Refine read distribution from 61 binding events. --------------------------- Events discovered Significant: 165 Insignificant: 8 Filtered: 2 --------------------------- Events discovered Significant: 91 Insignificant: 32 Filtered: 1 Finish binding event prediction: 44.5s No valid binding event was found. Finish binding event prediction: 1.0m Refine read distribution from 63 binding events. Refine read distribution from 120 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 385 Insignificant: 1 Filtered: 83 Finish binding event prediction: 3.3m Refine read distribution from 309 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.3m Running with 1 threads ... --------------------------- Events discovered Significant: 82 Insignificant: 34 Filtered: 18 Finish binding event prediction: 3.4m Refine read distribution from 27 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 47 Insignificant: 1 Filtered: 16 Finish binding event prediction: 3.4m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 180 Insignificant: 13 Filtered: 2 Finish binding event prediction: 55.1s Refine read distribution from 104 binding events. --------------------------- Events discovered Significant: 61 Insignificant: 5 Filtered: 5 Finish binding event prediction: 3.4m Refine read distribution from 27 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 13 Filtered: 2 Finish binding event prediction: 3.3m Running with 1 threads ... --------------------------- Events discovered Significant: 149 Insignificant: 16 Filtered: 0 Finish binding event prediction: 26.1s Refine read distribution from 97 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.6m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 13 Filtered: 4 --------------------------- Events discovered Significant: 20 Insignificant: 6 Filtered: 7 --------------------------- Events discovered Significant: 4 Insignificant: 2 Filtered: 2 --------------------------- Events discovered Significant: 5 Insignificant: 2 Filtered: 0 Finish binding event prediction: 3.3m Finish binding event prediction: 3.5m Finish binding event prediction: 3.6m Finish binding event prediction: 3.5m Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 36 Insignificant: 31 Filtered: 9 Finish binding event prediction: 3.3m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 64 Insignificant: 51 Filtered: 11 Finish binding event prediction: 3.6m Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 297 Insignificant: 22 Filtered: 2 Finish binding event prediction: 55.5s Refine read distribution from 144 binding events. --------------------------- Events discovered Significant: 19 Insignificant: 0 Filtered: 4 --------------------------- Events discovered Significant: 50 Insignificant: 1 Filtered: 15 Finish binding event prediction: 3.7m Finish binding event prediction: 3.6m Refine read distribution from 15 binding events. Refine read distribution from 30 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 83 Insignificant: 36 Filtered: 1 Finish binding event prediction: 55.1s Refine read distribution from 55 binding events. --------------------------- Events discovered Significant: 174 Insignificant: 18 Filtered: 2 Finish binding event prediction: 38.1s Refine read distribution from 86 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 12 Filtered: 4 Finish binding event prediction: 3.6m Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 45 Insignificant: 0 Filtered: 10 Finish binding event prediction: 3.7m Refine read distribution from 24 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 21 Filtered: 2 Finish binding event prediction: 3.7m Running with 1 threads ... --------------------------- Events discovered Significant: 166 Insignificant: 0 Filtered: 52 Finish binding event prediction: 3.7m Refine read distribution from 145 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 1 Filtered: 0 Finish binding event prediction: 3.8m Running with 1 threads ... --------------------------- Events discovered Significant: 124 Insignificant: 44 Filtered: 0 Finish binding event prediction: 57.1s Refine read distribution from 68 binding events. --------------------------- Events discovered Significant: 18 Insignificant: 3 Filtered: 6 Finish binding event prediction: 3.9m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 153 Insignificant: 65 Filtered: 2 Finish binding event prediction: 1.0m Refine read distribution from 106 binding events. --------------------------- Events discovered Significant: 16 Insignificant: 20 Filtered: 8 Finish binding event prediction: 3.7m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.7m Running with 1 threads ... --------------------------- Events discovered Significant: 93 Insignificant: 68 Filtered: 26 Finish binding event prediction: 1.0m Refine read distribution from 38 binding events. --------------------------- Events discovered Significant: 1079 Insignificant: 231 Filtered: 5 Finish binding event prediction: 1.3m Refine read distribution from 935 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 53.1s --------------------------- Events discovered Significant: 156 Insignificant: 52 Filtered: 1 Finish binding event prediction: 44.1s Refine read distribution from 112 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 1 Filtered: 1 --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 --------------------------- Events discovered Significant: 123 Insignificant: 21 Filtered: 3 --------------------------- Events discovered Significant: 306 Insignificant: 19 Filtered: 0 Finish binding event prediction: 4.0m Finish binding event prediction: 1.2m Finish binding event prediction: 58.8s Finish binding event prediction: 1.2m Running with 1 threads ... Refine read distribution from 86 binding events. Refine read distribution from 166 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 --------------------------- Events discovered Significant: 79 Insignificant: 2 Filtered: 1 Finish binding event prediction: 4.1m Finish binding event prediction: 31.1s Running with 1 threads ... Refine read distribution from 58 binding events. --------------------------- Events discovered Significant: 100 Insignificant: 23 Filtered: 4 Finish binding event prediction: 1.2m Refine read distribution from 55 binding events. --------------------------- Events discovered Significant: 294 Insignificant: 0 Filtered: 94 --------------------------- Events discovered Significant: 176 Insignificant: 0 Filtered: 58 Finish binding event prediction: 4.2m Finish binding event prediction: 4.1m Refine read distribution from 143 binding events. Refine read distribution from 286 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 39 Filtered: 1 Finish binding event prediction: 1.3m --------------------------- Events discovered Significant: 112 Insignificant: 50 Filtered: 2 --------------------------- Events discovered Significant: 58 Insignificant: 0 Filtered: 11 Finish binding event prediction: 43.0s Finish binding event prediction: 4.2m Refine read distribution from 76 binding events. Refine read distribution from 55 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 36 Insignificant: 0 Filtered: 11 --------------------------- Events discovered Significant: 40 Insignificant: 1 Filtered: 12 --------------------------- Events discovered Significant: 98 Insignificant: 20 Filtered: 3 --------------------------- Events discovered Significant: 80 Insignificant: 34 Filtered: 1 Finish binding event prediction: 4.2m Finish binding event prediction: 53.9s Finish binding event prediction: 4.1m Finish binding event prediction: 1.1m Refine read distribution from 40 binding events. Refine read distribution from 44 binding events. Running with 1 threads ... Refine read distribution from 79 binding events. Refine read distribution from 25 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 203 Insignificant: 25 Filtered: 6 Finish binding event prediction: 2.0m Refine read distribution from 69 binding events. --------------------------- Events discovered Significant: 1051 Insignificant: 228 Filtered: 6 Finish binding event prediction: 1.6m Refine read distribution from 908 binding events. --------------------------- Events discovered Significant: 25 Insignificant: 22 Filtered: 10 Finish binding event prediction: 4.2m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 8 Filtered: 5 Finish binding event prediction: 1.9m --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 104 Insignificant: 59 Filtered: 2 Finish binding event prediction: 1.4m Refine read distribution from 59 binding events. --------------------------- Events discovered Significant: 22 Insignificant: 11 Filtered: 8 Finish binding event prediction: 35.2s Refine read distribution from 16 binding events. --------------------------- Events discovered Significant: 84 Insignificant: 21 Filtered: 1 Finish binding event prediction: 56.1s Refine read distribution from 55 binding events. --------------------------- Events discovered Significant: 594 Insignificant: 95 Filtered: 7 Finish binding event prediction: 1.7m Refine read distribution from 470 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.4m Running with 1 threads ... --------------------------- Events discovered Significant: 456 Insignificant: 66 Filtered: 1 Finish binding event prediction: 2.6m Refine read distribution from 296 binding events. --------------------------- Events discovered Significant: 18 Insignificant: 21 Filtered: 6 Finish binding event prediction: 4.3m Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 98 Insignificant: 13 Filtered: 13 Finish binding event prediction: 48.2s Refine read distribution from 51 binding events. --------------------------- Events discovered Significant: 308 Insignificant: 0 Filtered: 98 Finish binding event prediction: 4.6m Refine read distribution from 298 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.5m Running with 1 threads ... --------------------------- Events discovered Significant: 8 Insignificant: 2 Filtered: 3 Finish binding event prediction: 4.2m Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.6m Running with 1 threads ... --------------------------- Events discovered Significant: 801 Insignificant: 107 Filtered: 1 Finish binding event prediction: 1.4m Refine read distribution from 649 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 1 --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 2 --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 1 Finish binding event prediction: 4.6m Finish binding event prediction: 4.6m Finish binding event prediction: 1.6m Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 7 Filtered: 4 Finish binding event prediction: 1.9m --------------------------- Events discovered Significant: 468 Insignificant: 62 Filtered: 1 --------------------------- Events discovered Significant: 14 Insignificant: 22 Filtered: 3 --------------------------- Events discovered Significant: 47 Insignificant: 2 Filtered: 14 Finish binding event prediction: 2.8m Finish binding event prediction: 4.5m Finish binding event prediction: 4.8m Refine read distribution from 29 binding events. Refine read distribution from 7 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.5m Refine read distribution from 318 binding events. --------------------------- Events discovered Significant: 6 Insignificant: 1 Filtered: 0 Finish binding event prediction: 56.1s --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 --------------------------- Events discovered Significant: 4 Insignificant: 2 Filtered: 2 --------------------------- Events discovered Significant: 2 Insignificant: 13 Filtered: 2 --------------------------- Events discovered Significant: 44 Insignificant: 19 Filtered: 0 No valid binding event was found. Finish binding event prediction: 4.8m Finish binding event prediction: 1.3m Finish binding event prediction: 1.4m Finish binding event prediction: 53.4s --------------------------- Events discovered Significant: 6 Insignificant: 2 Filtered: 2 Finish binding event prediction: 4.8m Running with 1 threads ... Running with 1 threads ... Refine read distribution from 23 binding events. --------------------------- Events discovered Significant: 570 Insignificant: 59 Filtered: 4 Finish binding event prediction: 1.7m Refine read distribution from 470 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 5 Filtered: 2 Finish binding event prediction: 4.6m Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 2 Filtered: 3 --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 2 Finish binding event prediction: 4.9m Finish binding event prediction: 4.8m Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 52 Insignificant: 0 Filtered: 10 Finish binding event prediction: 4.8m Refine read distribution from 49 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 1 Finish binding event prediction: 4.7m Running with 1 threads ... --------------------------- Events discovered Significant: 18 Insignificant: 22 Filtered: 5 Finish binding event prediction: 4.8m Refine read distribution from 6 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 552 Insignificant: 89 Filtered: 6 Finish binding event prediction: 1.4m Refine read distribution from 451 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 13 Filtered: 4 Finish binding event prediction: 1.6m --------------------------- Events discovered Significant: 92 Insignificant: 11 Filtered: 5 --------------------------- Events discovered Significant: 12 Insignificant: 0 Filtered: 4 Finish binding event prediction: 50.0s Finish binding event prediction: 5.1m Refine read distribution from 51 binding events. Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 18 Filtered: 3 Finish binding event prediction: 5.0m Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 5.0m Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 2 Filtered: 0 Finish binding event prediction: 1.7m --------------------------- Events discovered Significant: 33 Insignificant: 0 Filtered: 10 Finish binding event prediction: 5.0m Refine read distribution from 30 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 333 Insignificant: 18 Filtered: 66 Finish binding event prediction: 5.2m Refine read distribution from 223 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 341 Insignificant: 14 Filtered: 51 Finish binding event prediction: 5.2m Refine read distribution from 202 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 474 Insignificant: 60 Filtered: 6 Finish binding event prediction: 2.5m Refine read distribution from 289 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 5.1m Running with 1 threads ... --------------------------- Events discovered Significant: 78 Insignificant: 24 Filtered: 0 Finish binding event prediction: 59.6s Refine read distribution from 49 binding events. --------------------------- Events discovered Significant: 576 Insignificant: 64 Filtered: 8 Finish binding event prediction: 2.1m Refine read distribution from 471 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.0m --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 2 Finish binding event prediction: 5.3m Running with 1 threads ... --------------------------- Events discovered Significant: 478 Insignificant: 63 Filtered: 7 Finish binding event prediction: 2.8m Refine read distribution from 284 binding events. --------------------------- Events discovered Significant: 381 Insignificant: 1 Filtered: 89 Finish binding event prediction: 5.5m Refine read distribution from 313 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 12 Filtered: 4 Finish binding event prediction: 1.8m No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 1101 Insignificant: 203 Filtered: 3 --------------------------- Events discovered Significant: 46 Insignificant: 15 Filtered: 0 Finish binding event prediction: 1.4m Finish binding event prediction: 1.0m --------------------------- Events discovered Significant: 248 Insignificant: 94 Filtered: 2 Finish binding event prediction: 1.3m Refine read distribution from 29 binding events. Refine read distribution from 227 binding events. Refine read distribution from 951 binding events. --------------------------- Events discovered Significant: 215 Insignificant: 107 Filtered: 1 Finish binding event prediction: 1.3m Refine read distribution from 197 binding events. --------------------------- Events discovered Significant: 1130 Insignificant: 229 Filtered: 5 Finish binding event prediction: 1.0m Refine read distribution from 969 binding events. --------------------------- Events discovered Significant: 86 Insignificant: 0 Filtered: 16 No valid binding event was found. Finish binding event prediction: 5.6m Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 21 Filtered: 2 Finish binding event prediction: 2.1m --------------------------- Events discovered Significant: 52 Insignificant: 16 Filtered: 0 Finish binding event prediction: 1.1m Refine read distribution from 32 binding events. --------------------------- Events discovered Significant: 45 Insignificant: 14 Filtered: 0 Finish binding event prediction: 52.2s Refine read distribution from 26 binding events. --------------------------- Events discovered Significant: 498 Insignificant: 75 Filtered: 12 Finish binding event prediction: 2.9m Refine read distribution from 272 binding events. --------------------------- Events discovered Significant: 109 Insignificant: 13 Filtered: 3 Finish binding event prediction: 1.3m Refine read distribution from 65 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 6.2m Running with 1 threads ... --------------------------- Events discovered Significant: 218 Insignificant: 115 Filtered: 2 Finish binding event prediction: 1.3m Refine read distribution from 202 binding events. --------------------------- Events discovered Significant: 529 Insignificant: 76 Filtered: 4 Finish binding event prediction: 2.7m Refine read distribution from 311 binding events. --------------------------- Events discovered Significant: 0 Insignificant: 2 Filtered: 0 Finish binding event prediction: 6.1m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.8m --------------------------- Events discovered Significant: 5 Insignificant: 5 Filtered: 3 Finish binding event prediction: 6.3m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.4m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.5m --------------------------- Events discovered Significant: 7 Insignificant: 18 Filtered: 3 Finish binding event prediction: 1.4m --------------------------- Events discovered Significant: 218 Insignificant: 108 Filtered: 0 --------------------------- Events discovered Significant: 8 Insignificant: 2 Filtered: 3 Finish binding event prediction: 2.1m Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 163 Insignificant: 1 Filtered: 53 Finish binding event prediction: 6.5m Refine read distribution from 186 binding events. Refine read distribution from 134 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 204 Insignificant: 109 Filtered: 1 Finish binding event prediction: 1.5m Refine read distribution from 183 binding events. --------------------------- Events discovered Significant: 1299 Insignificant: 217 Filtered: 8 Finish binding event prediction: 3.1m Refine read distribution from 954 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 1 Filtered: 1 Finish binding event prediction: 2.9m --------------------------- Events discovered Significant: 696 Insignificant: 134 Filtered: 1 Finish binding event prediction: 1.8m Refine read distribution from 547 binding events. --------------------------- Events discovered Significant: 182 Insignificant: 5 Filtered: 2 Finish binding event prediction: 1.4m Refine read distribution from 169 binding events. --------------------------- Events discovered Significant: 788 Insignificant: 119 Filtered: 3 Finish binding event prediction: 1.7m Refine read distribution from 639 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.6m --------------------------- Events discovered Significant: 679 Insignificant: 124 Filtered: 2 Finish binding event prediction: 2.0m Refine read distribution from 531 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.7m --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 2 --------------------------- Events discovered Significant: 9 Insignificant: 2 Filtered: 3 --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.7m Finish binding event prediction: 2.9m Finish binding event prediction: 3.0m --------------------------- Events discovered Significant: 2 Insignificant: 5 Filtered: 2 Finish binding event prediction: 2.8m --------------------------- Events discovered Significant: 6 Insignificant: 2 Filtered: 2 Finish binding event prediction: 3.0m --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 1 --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.9m Finish binding event prediction: 2.7m --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.4m --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.0m --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 2 Finish binding event prediction: 3.0m --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 2 Finish binding event prediction: 3.6m --------------------------- Events discovered Significant: 1373 Insignificant: 212 Filtered: 5 Finish binding event prediction: 4.3m Refine read distribution from 967 binding events. --------------------------- Events discovered Significant: 0 Insignificant: 2 Filtered: 0 Finish binding event prediction: 2.6m No valid binding event was found. --------------------------- Events discovered Significant: 5 Insignificant: 5 Filtered: 3 Finish binding event prediction: 3.1m --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.7m No valid binding event was found. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 10.0m Running with 1 threads ... --------------------------- Events discovered Significant: 1332 Insignificant: 224 Filtered: 8 Finish binding event prediction: 4.3m Refine read distribution from 962 binding events. ============================================== 2025-02-18 17:27:02 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1618403 HitCounts: 4739985.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 351 reads. The genome is segmented into 8510 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 17:27:09 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 1312431 HitCounts: 8135169.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 392 reads. The genome is segmented into 8280 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 8.7m --------------------------- Events discovered Significant: 172 Insignificant: 0 Filtered: 57 Finish binding event prediction: 2.9m Refine read distribution from 147 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 87 Insignificant: 12 Filtered: 20 Finish binding event prediction: 3.9m Refine read distribution from 30 binding events. Running with 1 threads ... ============================================== 2025-02-18 17:31:47 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1122680 HitCounts: 5692719.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 262 reads. ============================================== 2025-02-18 17:31:49 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_2.SE.a.GPS The genome is segmented into 8180 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1248816 HitCounts: 6954058.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 347 reads. The genome is segmented into 8330 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 179 Insignificant: 29 Filtered: 2 Finish binding event prediction: 53.1s Refine read distribution from 155 binding events. --------------------------- Events discovered Significant: 1341 Insignificant: 200 Filtered: 10 Finish binding event prediction: 2.7m Refine read distribution from 959 binding events. --------------------------- Events discovered Significant: 81 Insignificant: 16 Filtered: 18 Finish binding event prediction: 4.8m Refine read distribution from 34 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 88 Insignificant: 0 Filtered: 16 Finish binding event prediction: 5.3m Refine read distribution from 32 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 192 Insignificant: 31 Filtered: 3 Finish binding event prediction: 1.1m Refine read distribution from 159 binding events. --------------------------- Events discovered Significant: 193 Insignificant: 9 Filtered: 3 Finish binding event prediction: 1.1m Refine read distribution from 168 binding events. ============================================== 2025-02-18 17:41:29 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 790657 HitCounts: 4969791.0 ============================================== 2025-02-18 17:41:30 At Poisson p-value 1.0e-03, in a 301bp window, expect 175 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_1.SE.a.GPS The genome is segmented into 8261 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 910217 HitCounts: 1.0653228E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 520 reads. The genome is segmented into 8412 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 54 Insignificant: 50 Filtered: 13 Finish binding event prediction: 1.8m Refine read distribution from 25 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 140 Insignificant: 53 Filtered: 1 Finish binding event prediction: 50.1s Refine read distribution from 100 binding events. --------------------------- Events discovered Significant: 155 Insignificant: 1 Filtered: 27 Finish binding event prediction: 3.5m Refine read distribution from 75 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 289 Insignificant: 63 Filtered: 1 Finish binding event prediction: 1.8m Refine read distribution from 191 binding events. ============================================== 2025-02-18 17:53:55 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1443196 HitCounts: 2513089.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 204 reads. ============================================== 2025-02-18 17:53:58 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_2.SE.a.GPS ============================================== 2025-02-18 17:53:59 ============================================== 2025-02-18 17:53:59 The genome is segmented into 8187 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_2.1x36mers.unique.GPS Running with 1 threads ... Original read count stats: Original read count stats: ============================================== 2025-02-18 17:54:01 Original read count stats: _IP Bases: 3219770 HitCounts: 5865320.0 _IP Bases: 905254 HitCounts: 4704325.0 _IP Bases: 1030186 HitCounts: 1.0224687E7 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-18 17:54:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 3473831 HitCounts: 6371262.0 Original read count stats: _IP Bases: 3667827 HitCounts: 7765399.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 195 reads. The genome is segmented into 8245 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 538 reads. The genome is segmented into 8396 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 513 reads. The genome is segmented into 8408 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 551 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 664 reads. The genome is segmented into 8525 regions for analysis. Running with 1 threads ... The genome is segmented into 8350 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 17:54:11 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 384684 HitCounts: 5110523.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 79 reads. The genome is segmented into 8450 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 17:54:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 482037 HitCounts: 1.3523404E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 527 reads. The genome is segmented into 8608 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 142 Insignificant: 16 Filtered: 32 Finish binding event prediction: 1.7m Refine read distribution from 35 binding events. Running with 1 threads ... ============================================== 2025-02-18 17:56:12 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 3031451 HitCounts: 4745234.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 424 reads. The genome is segmented into 8235 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 46 Insignificant: 34 Filtered: 9 Finish binding event prediction: 2.3m Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 123 Insignificant: 4 Filtered: 23 Finish binding event prediction: 2.4m Refine read distribution from 55 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 27 Insignificant: 60 Filtered: 6 Finish binding event prediction: 2.6m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 135 Insignificant: 56 Filtered: 1 Finish binding event prediction: 37.1s Refine read distribution from 103 binding events. --------------------------- Events discovered Significant: 184 Insignificant: 29 Filtered: 1 Finish binding event prediction: 1.2m Refine read distribution from 78 binding events. --------------------------- Events discovered Significant: 273 Insignificant: 38 Filtered: 2 Finish binding event prediction: 42.3s Refine read distribution from 202 binding events. --------------------------- Events discovered Significant: 56 Insignificant: 37 Filtered: 1 Finish binding event prediction: 44.3s Refine read distribution from 30 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 4.0m Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 4.3m Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.2m --------------------------- Events discovered Significant: 11 Insignificant: 0 Filtered: 3 Finish binding event prediction: 6.4m Refine read distribution from 2 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 3 Finish binding event prediction: 6.6m Running with 1 threads ... --------------------------- Events discovered Significant: 28 Insignificant: 0 Filtered: 6 Finish binding event prediction: 55.1s Refine read distribution from 13 binding events. ============================================== 2025-02-18 18:02:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 759418 HitCounts: 5492266.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 169 reads. The genome is segmented into 8333 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 18:02:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 877187 HitCounts: 1.2400471E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 586 reads. The genome is segmented into 8484 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 12 Insignificant: 0 Filtered: 4 Finish binding event prediction: 6.4m Refine read distribution from 1 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 4.9m --------------------------- Events discovered Significant: 14 Insignificant: 2 Filtered: 5 Finish binding event prediction: 1.3m Refine read distribution from 6 binding events. --------------------------- Events discovered Significant: 164 Insignificant: 2 Filtered: 38 Finish binding event prediction: 1.8m Refine read distribution from 59 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 45 Insignificant: 52 Filtered: 15 Finish binding event prediction: 1.8m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 294 Insignificant: 20 Filtered: 2 Finish binding event prediction: 51.1s Refine read distribution from 158 binding events. --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 3 Finish binding event prediction: 4.3m --------------------------- Events discovered Significant: 129 Insignificant: 46 Filtered: 0 Finish binding event prediction: 1.1m Refine read distribution from 84 binding events. ============================================== 2025-02-18 18:05:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-18 18:06:00 ============================================== 2025-02-18 18:06:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 2394079 HitCounts: 3904971.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-18 18:06:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1924569 HitCounts: 4353424.0 Original read count stats: _IP Bases: 2069035 HitCounts: 2805746.0 Original read count stats: _IP Bases: 1907290 HitCounts: 2544961.0 ============================================== 2025-02-18 18:06:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-18 18:06:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-18 18:06:02 ============================================== 2025-02-18 18:06:02 Original read count stats: ============================================== 2025-02-18 18:06:02 ============================================== 2025-02-18 18:06:02 ============================================== 2025-02-18 18:06:03 ============================================== 2025-02-18 18:06:03 ============================================== 2025-02-18 18:06:03 ============================================== 2025-02-18 18:06:03 ============================================== 2025-02-18 18:06:03 Original read count stats: _IP Bases: 2988974 HitCounts: 5401419.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 237 reads. _IP Bases: 2590001 HitCounts: 4858536.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 260 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 343 reads. Original read count stats: _IP Bases: 291911 HitCounts: 4967131.0 ============================================== 2025-02-18 18:06:04 The genome is segmented into 8235 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_1.SE.a.GPS The genome is segmented into 8228 regions for analysis. Original read count stats: _IP Bases: 954794 HitCounts: 5465371.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 64 reads. Running with 1 threads ... Original read count stats: _IP Bases: 975537 HitCounts: 5416839.0 ============================================== 2025-02-18 18:06:04 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 368 reads. _IP Bases: 816155 HitCounts: 6963095.0 Original read count stats: _IP Bases: 2606664 HitCounts: 5174404.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_1.SE.a.GPS The genome is segmented into 8521 regions for analysis. Original read count stats: _IP Bases: 3014736 HitCounts: 5177269.0 Running with 1 threads ... Original read count stats: Original read count stats: _IP Bases: 2993521 HitCounts: 6148374.0 _IP Bases: 3146596 HitCounts: 5352823.0 ============================================== 2025-02-18 18:06:04 Original read count stats: _IP Bases: 2809979 HitCounts: 4913559.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-18 18:06:05 ============================================== 2025-02-18 18:06:05 The genome is segmented into 8511 regions for analysis. ============================================== 2025-02-18 18:06:05 ============================================== 2025-02-18 18:06:05 At Poisson p-value 1.0e-03, in a 301bp window, expect 201 reads. Original read count stats: ============================================== 2025-02-18 18:06:06 At Poisson p-value 1.0e-03, in a 301bp window, expect 250 reads. Original read count stats: The genome is segmented into 8316 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 251 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_2.1x36mers.unique.GPS _IP Bases: 2562485 HitCounts: 5263361.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_1.SE.a.GPS _IP Bases: 2239255 HitCounts: 5980687.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_1.SE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 2760577 HitCounts: 5952426.0 ============================================== 2025-02-18 18:06:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 403 reads. ============================================== 2025-02-18 18:06:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_1.SE.a.GPS The genome is segmented into 8291 regions for analysis. Original read count stats: Original read count stats: _IP Bases: 843802 HitCounts: 6263812.0 _IP Bases: 1591466 HitCounts: 3768693.0 ============================================== 2025-02-18 18:06:07 ============================================== 2025-02-18 18:06:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 2227173 HitCounts: 3657724.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_1.1x36mers.unique.GPS The genome is segmented into 8320 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 18:06:07 Original read count stats: _IP Bases: 2334074 HitCounts: 6252928.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 461 reads. Original read count stats: _IP Bases: 2689013 HitCounts: 5582365.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_2.1x36mers.unique.GPS The genome is segmented into 8190 regions for analysis. Original read count stats: _IP Bases: 918381 HitCounts: 7226287.0 Running with 1 threads ... The genome is segmented into 8265 regions for analysis. Original read count stats: The genome is segmented into 8222 regions for analysis. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 420 reads. ============================================== 2025-02-18 18:06:08 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 522 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 420 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 467 reads. _IP Bases: 2770337 HitCounts: 6765117.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 307 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 207 reads. _IP Bases: 2069132 HitCounts: 6881702.0 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 460 reads. Running with 1 threads ... ============================================== 2025-02-18 18:06:09_IP Bases: 2786318 HitCounts: 6977195.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 239 reads. _IP Bases: 2064319 HitCounts: 6642853.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 332 reads. The genome is segmented into 8358 regions for analysis. ============================================== 2025-02-18 18:06:10 ============================================== 2025-02-18 18:06:10 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_2.1x36mers.unique.GPS The genome is segmented into 8324 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_2.SE.a.GPS The genome is segmented into 8147 regions for analysis. Running with 1 threads ... The genome is segmented into 8380 regions for analysis. The genome is segmented into 8336 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 472 reads. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-18 18:06:10 Running with 1 threads ... Original read count stats: The genome is segmented into 8135 regions for analysis. _IP Bases: 3175337 HitCounts: 7639307.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 465 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 454 reads. Original read count stats: _IP Bases: 2942618 HitCounts: 6832102.0 The genome is segmented into 8289 regions for analysis. The genome is segmented into 8304 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-18 18:06:11 Original read count stats: _IP Bases: 1771424 HitCounts: 3016404.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_2.SE.a.GPS The genome is segmented into 8332 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2864072 HitCounts: 8042448.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 451 reads. The genome is segmented into 8159 regions for analysis. The genome is segmented into 8483 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2930579 HitCounts: 7459665.0 ============================================== 2025-02-18 18:06:12 Running with 1 threads ... Original read count stats: _IP Bases: 2060339 HitCounts: 3326636.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_1.SE.a.GPS ============================================== 2025-02-18 18:06:12 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 517 reads. The genome is segmented into 8190 regions for analysis. Running with 1 threads ... The genome is segmented into 8070 regions for analysis. Original read count stats: _IP Bases: 2831975 HitCounts: 4249272.0 Running with 1 threads ... The genome is segmented into 8492 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 436 reads. Running with 1 threads ... Original read count stats: _IP Bases: 3114941 HitCounts: 8580558.0 ============================================== 2025-02-18 18:06:13 At Poisson p-value 1.0e-03, in a 301bp window, expect 446 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 259 reads. ============================================== 2025-02-18 18:06:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 1100564 HitCounts: 9593307.0 ============================================== 2025-02-18 18:06:14 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 565 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 303 reads. The genome is segmented into 8246 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 559 reads. The genome is segmented into 8346 regions for analysis. The genome is segmented into 8246 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 522 reads. _IP Bases: 1079615 HitCounts: 9875080.0 Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_1.1x36mers.unique.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 382 reads. The genome is segmented into 8389 regions for analysis. The genome is segmented into 8304 regions for analysis. The genome is segmented into 8357 regions for analysis. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 2164640 HitCounts: 4016475.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 639 reads. ============================================== 2025-02-18 18:06:17 At Poisson p-value 1.0e-03, in a 301bp window, expect 574 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 641 reads. ============================================== 2025-02-18 18:06:17 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_1.SE.a.GPS The genome is segmented into 8404 regions for analysis. Running with 1 threads ... The genome is segmented into 8211 regions for analysis. The genome is segmented into 8352 regions for analysis. Original read count stats: _IP Bases: 2072892 HitCounts: 4188854.0 Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8088 regions for analysis. Running with 1 threads ... The genome is segmented into 8151 regions for analysis. ============================================== 2025-02-18 18:06:19 Running with 1 threads ... Original read count stats: _IP Bases: 2224842 HitCounts: 1.0968279E7 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 524 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 645 reads. The genome is segmented into 8418 regions for analysis. The genome is segmented into 8261 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 335 reads. Running with 1 threads ... Original read count stats: _IP Bases: 2230983 HitCounts: 1.1508791E7 The genome is segmented into 8315 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 331 reads. ============================================== 2025-02-18 18:06:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 542 reads. Original read count stats: _IP Bases: 937554 HitCounts: 1.6021871E7 The genome is segmented into 8187 regions for analysis. Running with 1 threads ... The genome is segmented into 8427 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 714 reads. The genome is segmented into 8390 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 746 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 738 reads. The genome is segmented into 8402 regions for analysis. The genome is segmented into 8458 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-18 18:06:37 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 968170 HitCounts: 1.8594108E7 ============================================== 2025-02-18 18:06:46 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 933 reads. Original read count stats: _IP Bases: 1045667 HitCounts: 2.176312E7 The genome is segmented into 8449 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 1075 reads. The genome is segmented into 8441 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 208 Insignificant: 7 Filtered: 25 Finish binding event prediction: 1.2m Refine read distribution from 43 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 186 Insignificant: 30 Filtered: 5 Finish binding event prediction: 30.0s Refine read distribution from 59 binding events. --------------------------- Events discovered Significant: 157 Insignificant: 2 Filtered: 33 Finish binding event prediction: 1.9m Refine read distribution from 57 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 80 Insignificant: 16 Filtered: 21 Finish binding event prediction: 2.4m Refine read distribution from 52 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 49 Insignificant: 54 Filtered: 13 Finish binding event prediction: 2.2m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 88 Insignificant: 4 Filtered: 15 Finish binding event prediction: 2.6m Refine read distribution from 39 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 174 Insignificant: 3 Filtered: 38 Finish binding event prediction: 2.6m Refine read distribution from 35 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 3 Filtered: 2 Finish binding event prediction: 2.7m Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 15 Filtered: 2 Finish binding event prediction: 3.1m Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 4 Filtered: 3 Finish binding event prediction: 3.1m Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.2m Running with 1 threads ... --------------------------- Events discovered Significant: 147 Insignificant: 25 Filtered: 5 Finish binding event prediction: 52.1s Refine read distribution from 115 binding events. --------------------------- Events discovered Significant: 19 Insignificant: 24 Filtered: 7 Finish binding event prediction: 3.0m Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 286 Insignificant: 24 Filtered: 2 Finish binding event prediction: 1.5m Refine read distribution from 163 binding events. --------------------------- Events discovered Significant: 44 Insignificant: 60 Filtered: 8 Finish binding event prediction: 2.6m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 113 Insignificant: 50 Filtered: 2 Finish binding event prediction: 57.1s Refine read distribution from 62 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 23 Filtered: 1 Finish binding event prediction: 3.5m Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 16 Filtered: 5 Finish binding event prediction: 3.7m Running with 1 threads ... --------------------------- Events discovered Significant: 171 Insignificant: 2 Filtered: 33 Finish binding event prediction: 3.7m Refine read distribution from 40 binding events. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 47 Insignificant: 38 Filtered: 18 Finish binding event prediction: 3.6m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 228 Insignificant: 11 Filtered: 8 Finish binding event prediction: 1.3m Refine read distribution from 73 binding events. --------------------------- Events discovered Significant: 142 Insignificant: 20 Filtered: 3 Finish binding event prediction: 1.4m Refine read distribution from 111 binding events. --------------------------- Events discovered Significant: 47 Insignificant: 53 Filtered: 5 Finish binding event prediction: 3.4m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 49 Insignificant: 17 Filtered: 0 Finish binding event prediction: 50.2s Refine read distribution from 26 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 2 Finish binding event prediction: 4.1m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 23 Filtered: 1 Finish binding event prediction: 58.1s --------------------------- Events discovered Significant: 43 Insignificant: 35 Filtered: 16 Finish binding event prediction: 4.3m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 4.5m Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 11 Filtered: 3 Finish binding event prediction: 4.4m Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 4 Filtered: 3 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 9 Insignificant: 1 Filtered: 3 Finish binding event prediction: 4.5m Running with 1 threads ... --------------------------- Events discovered Significant: 20 Insignificant: 26 Filtered: 6 Finish binding event prediction: 4.4m Refine read distribution from 6 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 11 Filtered: 1 --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 --------------------------- Events discovered Significant: 91 Insignificant: 38 Filtered: 1 Finish binding event prediction: 4.6m Finish binding event prediction: 1.5m Finish binding event prediction: 1.3m Running with 1 threads ... Refine read distribution from 45 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 3 Filtered: 2 Finish binding event prediction: 1.9m --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 4.8m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 1 Filtered: 1 Finish binding event prediction: 4.7m Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 2 Filtered: 1 Finish binding event prediction: 4.9m Running with 1 threads ... --------------------------- Events discovered Significant: 246 Insignificant: 11 Filtered: 5 Finish binding event prediction: 1.3m Refine read distribution from 98 binding events. --------------------------- Events discovered Significant: 103 Insignificant: 28 Filtered: 2 Finish binding event prediction: 1.2m Refine read distribution from 74 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 --------------------------- Events discovered Significant: 3 Insignificant: 15 Filtered: 2 Finish binding event prediction: 5.1m Finish binding event prediction: 1.9m Running with 1 threads ... --------------------------- Events discovered Significant: 0 Insignificant: 12 Filtered: 0 No valid binding event was found. Finish binding event prediction: 5.0m Running with 1 threads ... --------------------------- Events discovered Significant: 11 Insignificant: 1 Filtered: 4 Finish binding event prediction: 5.1m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 16 Filtered: 5 Finish binding event prediction: 1.6m --------------------------- Events discovered Significant: 88 Insignificant: 39 Filtered: 0 Finish binding event prediction: 1.3m Refine read distribution from 52 binding events. --------------------------- Events discovered Significant: 50 Insignificant: 15 Filtered: 1 Finish binding event prediction: 49.1s Refine read distribution from 26 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 5.5m Running with 1 threads ... --------------------------- Events discovered Significant: 97 Insignificant: 29 Filtered: 1 Finish binding event prediction: 1.1m Refine read distribution from 68 binding events. --------------------------- Events discovered Significant: 6 Insignificant: 3 Filtered: 2 Finish binding event prediction: 5.8m Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 2 Finish binding event prediction: 2.0m --------------------------- Events discovered Significant: 31 Insignificant: 7 Filtered: 1 Finish binding event prediction: 57.4s Refine read distribution from 27 binding events. --------------------------- Events discovered Significant: 11 Insignificant: 1 Filtered: 4 --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 6.1m Finish binding event prediction: 6.3m Refine read distribution from 9 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 6.2m Running with 1 threads ... --------------------------- Events discovered Significant: 10 Insignificant: 6 Filtered: 3 Finish binding event prediction: 6.2m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 6.3m Running with 1 threads ... --------------------------- Events discovered Significant: 10 Insignificant: 1 Filtered: 3 Finish binding event prediction: 6.6m Refine read distribution from 6 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 11 Filtered: 3 Finish binding event prediction: 2.2m --------------------------- Events discovered Significant: 5 Insignificant: 0 Filtered: 1 Finish binding event prediction: 6.7m Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 2.3m --------------------------- Events discovered Significant: 5 Insignificant: 4 Filtered: 3 Finish binding event prediction: 6.8m Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 3 Filtered: 2 Finish binding event prediction: 24.1s --------------------------- Events discovered Significant: 49 Insignificant: 2 Filtered: 1 Finish binding event prediction: 49.1s Refine read distribution from 35 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 11 Filtered: 1 Finish binding event prediction: 2.4m --------------------------- Events discovered Significant: 9 Insignificant: 1 Filtered: 3 Finish binding event prediction: 2.5m No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 32 Insignificant: 6 Filtered: 0 Finish binding event prediction: 55.2s Refine read distribution from 26 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 2 Filtered: 1 Finish binding event prediction: 2.3m --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 7.3m Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 2.6m --------------------------- Events discovered Significant: 11 Insignificant: 0 Filtered: 3 Finish binding event prediction: 7.6m --------------------------- Events discovered Significant: 0 Insignificant: 12 Filtered: 0 Finish binding event prediction: 2.5m --------------------------- Events discovered Significant: 2 Insignificant: 1 Filtered: 1 Finish binding event prediction: 2.9m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.6m --------------------------- Events discovered Significant: 6 Insignificant: 3 Filtered: 2 Finish binding event prediction: 3.3m --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.2m --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.0m --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.9m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.7m --------------------------- Events discovered Significant: 5 Insignificant: 0 Filtered: 1 Finish binding event prediction: 4.4m --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.9m --------------------------- Events discovered Significant: 5 Insignificant: 4 Filtered: 3 Finish binding event prediction: 4.7m ============================================== 2025-02-18 18:18:33 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 147695 HitCounts: 1063562.0 ============================================== 2025-02-18 18:18:33 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 33 reads. ============================================== 2025-02-18 18:18:33 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_1.SE.a.GPS Original read count stats: _IP Bases: 519057 HitCounts: 1193050.0 The genome is segmented into 8087 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 550114 HitCounts: 1244085.0 ============================================== 2025-02-18 18:18:34 At Poisson p-value 1.0e-03, in a 301bp window, expect 84 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_2.1x36mers.unique.GPS ============================================== 2025-02-18 18:18:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_1.1x36mers.unique.GPS The genome is segmented into 8462 regions for analysis. Original read count stats: _IP Bases: 210564 HitCounts: 1555994.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 88 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 45 reads. Original read count stats: _IP Bases: 725823 HitCounts: 1052672.0 ============================================== 2025-02-18 18:18:35 The genome is segmented into 8652 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_1.SE.a.GPS The genome is segmented into 8545 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 96 reads. Original read count stats: ============================================== 2025-02-18 18:18:36 ============================================== 2025-02-18 18:18:36 ============================================== 2025-02-18 18:18:36 ============================================== 2025-02-18 18:18:36 ============================================== 2025-02-18 18:18:36 ============================================== 2025-02-18 18:18:37 ============================================== 2025-02-18 18:18:37_IP Bases: 751154 HitCounts: 1107032.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_2.SE.a.GPS Original read count stats: _IP Bases: 567995 HitCounts: 1288140.0 The genome is segmented into 8494 regions for analysis. Original read count stats: _IP Bases: 755863 HitCounts: 1575242.0 Original read count stats: _IP Bases: 742110 HitCounts: 1542286.0 Original read count stats: _IP Bases: 864902 HitCounts: 1334816.0 Running with 1 threads ... Original read count stats: _IP Bases: 712384 HitCounts: 1494591.0 Original read count stats: _IP Bases: 724829 HitCounts: 1523511.0 Original read count stats: _IP Bases: 892240 HitCounts: 1403363.0 ============================================== 2025-02-18 18:18:38 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-18 18:18:38 At Poisson p-value 1.0e-03, in a 301bp window, expect 100 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_1.SE.a.GPS Original read count stats: _IP Bases: 208032 HitCounts: 2470496.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 91 reads. Original read count stats: _IP Bases: 1666235 HitCounts: 2067685.0 The genome is segmented into 8639 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 107 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 113 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 111 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 115 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 108 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 120 reads. ============================================== 2025-02-18 18:18:39 ============================================== 2025-02-18 18:18:39 ============================================== 2025-02-18 18:18:39 ============================================== 2025-02-18 18:18:39 At Poisson p-value 1.0e-03, in a 301bp window, expect 126 reads. ============================================== 2025-02-18 18:18:39 ============================================== 2025-02-18 18:18:40 ============================================== 2025-02-18 18:18:39 At Poisson p-value 1.0e-03, in a 301bp window, expect 198 reads. The genome is segmented into 8671 regions for analysis. ============================================== 2025-02-18 18:18:39 ============================================== 2025-02-18 18:18:40 The genome is segmented into 8389 regions for analysis. ============================================== 2025-02-18 18:18:40 ============================================== 2025-02-18 18:18:40 The genome is segmented into 8395 regions for analysis. ============================================== 2025-02-18 18:18:40 The genome is segmented into 8544 regions for analysis. The genome is segmented into 8539 regions for analysis. The genome is segmented into 8650 regions for analysis. The genome is segmented into 8464 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_2.SE.a.GPS Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_1.1x36mers.unique.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5A10.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5A10.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_1.1x36mers.unique.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_2.1x36mers.unique.GPS Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-18 18:18:40 ============================================== 2025-02-18 18:18:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_1.1x36mers.unique.GPS The genome is segmented into 7480 regions for analysis. ============================================== 2025-02-18 18:18:40 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-18 18:18:41 Original read count stats: Original read count stats: Original read count stats: _IP Bases: 465352 HitCounts: 2004733.0 Original read count stats: Original read count stats: _IP Bases: 169142 HitCounts: 2585054.0 _IP Bases: 89026 HitCounts: 2127757.0 _IP Bases: 114803 HitCounts: 2511340.0 _IP Bases: 404037 HitCounts: 3533324.0 Original read count stats: _IP Bases: 103598 HitCounts: 2497958.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 384213 HitCounts: 2231588.0 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 20 reads. _IP Bases: 456732 HitCounts: 2239488.0 ============================================== 2025-02-18 18:18:41 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 22 reads. _IP Bases: 826342 HitCounts: 4979790.0 ============================================== 2025-02-18 18:18:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5A10.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5A10.SE.a.GPS ============================================== 2025-02-18 18:18:41 Original read count stats: _IP Bases: 740577 HitCounts: 5151060.0 The genome is segmented into 8645 regions for analysis. The genome is segmented into 7884 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_1.SE.a.GPS Running with 1 threads ... ============================================== 2025-02-18 18:18:41 Original read count stats: _IP Bases: 2289635 HitCounts: 4841273.0 Original read count stats: _IP Bases: 1806230 HitCounts: 2487884.0 Running with 1 threads ... Original read count stats: _IP Bases: 2961705 HitCounts: 5101014.0 Original read count stats: Original read count stats: _IP Bases: 2725026 HitCounts: 4851740.0 _IP Bases: 1184791 HitCounts: 4300293.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_M2.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_M2.1x36mers.unique.GPS Original read count stats: _IP Bases: 3056511 HitCounts: 4795808.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 61 reads. Original read count stats: _IP Bases: 131625 HitCounts: 2622151.0 Original read count stats: _IP Bases: 127720 HitCounts: 2786283.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 60 reads. Original read count stats: _IP Bases: 52887 HitCounts: 4643043.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 92 reads. ============================================== 2025-02-18 18:18:41 ============================================== 2025-02-18 18:18:41 ============================================== 2025-02-18 18:18:41 ============================================== 2025-02-18 18:18:41 At Poisson p-value 1.0e-03, in a 301bp window, expect 85 reads. ============================================== 2025-02-18 18:18:42 The genome is segmented into 8611 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 22 reads. The genome is segmented into 7487 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-18 18:18:42 At Poisson p-value 1.0e-03, in a 301bp window, expect 96 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_2.1x36mers.unique.GPS Running with 1 threads ... Original read count stats: ============================================== 2025-02-18 18:18:42 At Poisson p-value 1.0e-03, in a 301bp window, expect 35 reads. The genome is segmented into 8858 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 65 reads. ============================================== 2025-02-18 18:18:42 ============================================== 2025-02-18 18:18:43 The genome is segmented into 8188 regions for analysis. The genome is segmented into 8421 regions for analysis. Running with 1 threads ... _IP Bases: 1813453 HitCounts: 2919876.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 165 reads. Original read count stats: ============================================== 2025-02-18 18:18:43 ============================================== 2025-02-18 18:18:42 Original read count stats: ============================================== 2025-02-18 18:18:43 ============================================== 2025-02-18 18:18:42 At Poisson p-value 1.0e-03, in a 301bp window, expect 115 reads. ============================================== 2025-02-18 18:18:43_IP Bases: 32839 HitCounts: 2500185.0 ============================================== 2025-02-18 18:18:42 ============================================== 2025-02-18 18:18:43 At Poisson p-value 1.0e-03, in a 301bp window, expect 157 reads. ============================================== 2025-02-18 18:18:42 Running with 1 threads ... ============================================== 2025-02-18 18:18:43 ============================================== 2025-02-18 18:18:43 ============================================== 2025-02-18 18:18:43 Original read count stats: ============================================== 2025-02-18 18:18:42 At Poisson p-value 1.0e-03, in a 301bp window, expect 290 reads. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 235 reads. The genome is segmented into 8375 regions for analysis. _IP Bases: 471979 HitCounts: 5915317.0 ============================================== 2025-02-18 18:18:43 ============================================== 2025-02-18 18:18:44_IP Bases: 2572737 HitCounts: 5632376.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_1.1x36mers.unique.GPS Running with 1 threads ... ============================================== 2025-02-18 18:18:43_IP Bases: 1980889 HitCounts: 2555030.0 The genome is segmented into 8418 regions for analysis. ============================================== 2025-02-18 18:18:44 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2C4.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2C4.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4A3.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4A3.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_2.1x36mers.unique.GPS Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_1.1x36mers.unique.GPS The genome is segmented into 1050 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_1.1x36mers.unique.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_2.SE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_2.SE.a.GPS ============================================== 2025-02-18 18:18:44 ============================================== 2025-02-18 18:18:44 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 13 reads. The genome is segmented into 8380 regions for analysis. ============================================== 2025-02-18 18:18:44 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_2.1x36mers.unique.GPS The genome is segmented into 2284 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_2.SE.a.GPS Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_M2.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_M2.SE.a.GPS Original read count stats: _IP Bases: 1403600 HitCounts: 4123570.0 ============================================== 2025-02-18 18:18:44 Original read count stats: _IP Bases: 152727 HitCounts: 2812355.0 The genome is segmented into 8585 regions for analysis. Original read count stats: _IP Bases: 122017 HitCounts: 2669570.0 ============================================== 2025-02-18 18:18:44 Original read count stats: Running with 1 threads ... _IP Bases: 160531 HitCounts: 2977178.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_2.1x36mers.unique.GPS The genome is segmented into 8316 regions for analysis. Original read count stats: _IP Bases: 275088 HitCounts: 3541908.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_2.SE.a.GPS Original read count stats: ============================================== 2025-02-18 18:18:44_IP Bases: 429467 HitCounts: 2571724.0 Original read count stats: _IP Bases: 156866 HitCounts: 6278261.0 Original read count stats: Running with 1 threads ... _IP Bases: 449369 HitCounts: 3463305.0 Original read count stats: _IP Bases: 145009 HitCounts: 6444763.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 386 reads. Original read count stats: Original read count stats: _IP Bases: 1356886 HitCounts: 4840673.0 _IP Bases: 1390672 HitCounts: 4888022.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 620279 HitCounts: 6513850.0 Original read count stats: _IP Bases: 1313894 HitCounts: 5200693.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 99 reads. Original read count stats: _IP Bases: 2130689 HitCounts: 3077070.0 Original read count stats: _IP Bases: 1232969 HitCounts: 5596422.0 The genome is segmented into 8383 regions for analysis. Original read count stats: Original read count stats: _IP Bases: 852135 HitCounts: 6107258.0 _IP Bases: 860289 HitCounts: 6835099.0 The genome is segmented into 8228 regions for analysis. Original read count stats: _IP Bases: 685565 HitCounts: 3363701.0 Running with 1 threads ... Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 24 reads. _IP Bases: 1411476 HitCounts: 4931122.0 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 25 reads. _IP Bases: 1605878 HitCounts: 6106335.0 Running with 1 threads ... Original read count stats: _IP Bases: 1968046 HitCounts: 5481011.0 Original read count stats: _IP Bases: 2904512 HitCounts: 5833212.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 411 reads. Original read count stats: ============================================== 2025-02-18 18:18:45 Original read count stats: The genome is segmented into 8352 regions for analysis. ============================================== 2025-02-18 18:18:45 ============================================== 2025-02-18 18:18:45 The genome is segmented into 8575 regions for analysis. The genome is segmented into 8598 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 64 reads. _IP Bases: 2110906 HitCounts: 5656377.0 ============================================== 2025-02-18 18:18:45 ============================================== 2025-02-18 18:18:45 ============================================== 2025-02-18 18:18:45 The genome is segmented into 8330 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 173 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 70 reads. Original read count stats: ============================================== 2025-02-18 18:18:45 ============================================== 2025-02-18 18:18:45 ============================================== 2025-02-18 18:18:45 At Poisson p-value 1.0e-03, in a 301bp window, expect 99 reads. ============================================== 2025-02-18 18:18:46 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 264 reads. ============================================== 2025-02-18 18:18:45 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 62 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 126 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 425 reads. _IP Bases: 1946952 HitCounts: 3308046.0 ============================================== 2025-02-18 18:18:46 At Poisson p-value 1.0e-03, in a 301bp window, expect 450 reads. ============================================== 2025-02-18 18:18:45 At Poisson p-value 1.0e-03, in a 301bp window, expect 241 reads. The genome is segmented into 8183 regions for analysis. ============================================== 2025-02-18 18:18:46 ============================================== 2025-02-18 18:18:46 At Poisson p-value 1.0e-03, in a 301bp window, expect 106 reads. ============================================== 2025-02-18 18:18:46 At Poisson p-value 1.0e-03, in a 301bp window, expect 140 reads. ============================================== 2025-02-18 18:18:46 ============================================== 2025-02-18 18:18:46 ============================================== 2025-02-18 18:18:46 ============================================== 2025-02-18 18:18:46 Running with 1 threads ... ============================================== 2025-02-18 18:18:46_IP Bases: 3240889 HitCounts: 5686883.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 253 reads. ============================================== 2025-02-18 18:18:46 ============================================== 2025-02-18 18:18:46 At Poisson p-value 1.0e-03, in a 301bp window, expect 215 reads. _IP Bases: 3160771 HitCounts: 5742973.0 The genome is segmented into 8248 regions for analysis. Running with 1 threads ... _IP Bases: 3334713 HitCounts: 6489363.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_1.SE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4A3.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4A3.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2C4.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2C4.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 284 reads. ============================================== 2025-02-18 18:18:47 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_2.1x36mers.unique.GPS ============================================== 2025-02-18 18:18:47 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_1.SE.a.GPS Running with 1 threads ... The genome is segmented into 7374 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 323 reads. ============================================== 2025-02-18 18:18:47 The genome is segmented into 8628 regions for analysis. The genome is segmented into 8543 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 18:18:47 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_2.1x36mers.unique.GPS The genome is segmented into 8535 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_1.SE.a.GPS Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_1.SE.a.GPS Original read count stats: Running with 1 threads ... The genome is segmented into 8441 regions for analysis. The genome is segmented into 8575 regions for analysis. Original read count stats: _IP Bases: 197128 HitCounts: 2954162.0 _IP Bases: 114463 HitCounts: 3631357.0 Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8309 regions for analysis. Original read count stats: _IP Bases: 183313 HitCounts: 3260068.0 Original read count stats: Original read count stats: _IP Bases: 517323 HitCounts: 2837900.0 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 286 reads. _IP Bases: 452679 HitCounts: 4045064.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 314 reads. _IP Bases: 441401 HitCounts: 3764103.0 ============================================== 2025-02-18 18:18:47 Original read count stats: Running with 1 threads ... _IP Bases: 165808 HitCounts: 7350691.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 328 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_2.1x36mers.unique.GPS The genome is segmented into 8410 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 312 reads. Original read count stats: _IP Bases: 178293 HitCounts: 7104045.0 Original read count stats: _IP Bases: 362985 HitCounts: 3182015.0 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 36 reads. Original read count stats: Original read count stats: _IP Bases: 1450262 HitCounts: 6406893.0 Original read count stats: _IP Bases: 854781 HitCounts: 7655358.0 _IP Bases: 1522155 HitCounts: 5863153.0 _IP Bases: 804059 HitCounts: 7421408.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 443 reads. Running with 1 threads ... Original read count stats: _IP Bases: 913067 HitCounts: 7552335.0 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 327 reads. _IP Bases: 1182779 HitCounts: 5215102.0 Original read count stats: Original read count stats: _IP Bases: 376910 HitCounts: 3980197.0 _IP Bases: 797568 HitCounts: 6989487.0 Original read count stats: _IP Bases: 1450149 HitCounts: 5757885.0 Original read count stats: _IP Bases: 941493 HitCounts: 6950530.0 ============================================== 2025-02-18 18:18:47 Original read count stats: _IP Bases: 1488402 HitCounts: 6742863.0 Original read count stats: _IP Bases: 1344031 HitCounts: 6725849.0 The genome is segmented into 8494 regions for analysis. Original read count stats: The genome is segmented into 8267 regions for analysis. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 29 reads. _IP Bases: 1403477 HitCounts: 6442082.0 _IP Bases: 556501 HitCounts: 7975945.0 The genome is segmented into 7567 regions for analysis. Running with 1 threads ... Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_2.SE.a.GPS _IP Bases: 1436452 HitCounts: 6820786.0 Running with 1 threads ... Running with 1 threads ... Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 30 reads. _IP Bases: 257785 HitCounts: 4136652.0 Original read count stats: _IP Bases: 2750841 HitCounts: 7043756.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 385 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 350 reads. The genome is segmented into 8532 regions for analysis. Original read count stats: _IP Bases: 2462479 HitCounts: 7247385.0 The genome is segmented into 8302 regions for analysis. Original read count stats: Running with 1 threads ... _IP Bases: 3351352 HitCounts: 7288614.0 ============================================== 2025-02-18 18:18:48 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 74 reads. The genome is segmented into 8362 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4A1.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4A1.1x36mers.unique.GPS The genome is segmented into 8798 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 70 reads. The genome is segmented into 8482 regions for analysis. The genome is segmented into 8347 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 102 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 106 reads. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8753 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 65 reads. The genome is segmented into 8805 regions for analysis. The genome is segmented into 8534 regions for analysis. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 140 reads. The genome is segmented into 8246 regions for analysis. Original read count stats: ============================================== 2025-02-18 18:18:49 The genome is segmented into 8421 regions for analysis. ============================================== 2025-02-18 18:18:49 ============================================== 2025-02-18 18:18:49 ============================================== 2025-02-18 18:18:48 The genome is segmented into 8738 regions for analysis. The genome is segmented into 8294 regions for analysis. The genome is segmented into 8205 regions for analysis. ============================================== 2025-02-18 18:18:48 At Poisson p-value 1.0e-03, in a 301bp window, expect 296 reads. ============================================== 2025-02-18 18:18:49 At Poisson p-value 1.0e-03, in a 301bp window, expect 317 reads. ============================================== 2025-02-18 18:18:49 The genome is segmented into 8169 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 289 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 90 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 95 reads. The genome is segmented into 8069 regions for analysis. ============================================== 2025-02-18 18:18:50_IP Bases: 287692 HitCounts: 8129856.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 359 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 207 reads. Running with 1 threads ... The genome is segmented into 8434 regions for analysis. ============================================== 2025-02-18 18:18:49 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 491 reads. The genome is segmented into 8440 regions for analysis. The genome is segmented into 8204 regions for analysis. Running with 1 threads ... The genome is segmented into 8132 regions for analysis. ============================================== 2025-02-18 18:18:50 At Poisson p-value 1.0e-03, in a 301bp window, expect 319 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 288 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 410 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 277 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 314 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_2.SE.a.GPS Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-18 18:18:50_IP Bases: 920710 HitCounts: 8063244.0 Running with 1 threads ... ============================================== 2025-02-18 18:18:50 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2B6.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2B6.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_M4.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_M4.1x36mers.unique.GPS Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5G8.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5G8.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_1.SE.a.GPS Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-18 18:18:50 At Poisson p-value 1.0e-03, in a 301bp window, expect 366 reads. ============================================== 2025-02-18 18:18:50 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_1.SE.a.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 322 reads. The genome is segmented into 8531 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_1.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_1.1x36mers.unique.GPS The genome is segmented into 8376 regions for analysis. The genome is segmented into 8543 regions for analysis. The genome is segmented into 8612 regions for analysis. ============================================== 2025-02-18 18:18:51 At Poisson p-value 1.0e-03, in a 301bp window, expect 398 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 41 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 355 reads. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8407 regions for analysis. Running with 1 threads ... The genome is segmented into 8365 regions for analysis. ============================================== 2025-02-18 18:18:51 The genome is segmented into 8372 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5B6.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5B6.1x36mers.unique.GPS ============================================== 2025-02-18 18:18:51 The genome is segmented into 8434 regions for analysis. The genome is segmented into 8505 regions for analysis. ============================================== 2025-02-18 18:18:51 Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8475 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_2.1x36mers.unique.GPS Original read count stats: Running with 1 threads ... _IP Bases: 1222750 HitCounts: 6738796.0 Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4A1.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4A1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_1.1x36mers.unique.GPS The genome is segmented into 8398 regions for analysis. Original read count stats: Running with 1 threads ... _IP Bases: 220431 HitCounts: 7508069.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 394 reads. Original read count stats: _IP Bases: 1352522 HitCounts: 6715028.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 398 reads. The genome is segmented into 8435 regions for analysis. Original read count stats: The genome is segmented into 8638 regions for analysis. _IP Bases: 654785 HitCounts: 8279064.0 Original read count stats: ============================================== 2025-02-18 18:18:51_IP Bases: 720579 HitCounts: 8883232.0 Running with 1 threads ... Original read count stats: The genome is segmented into 8354 regions for analysis. Original read count stats: _IP Bases: 548133 HitCounts: 9086539.0 Original read count stats: Running with 1 threads ... _IP Bases: 1209369 HitCounts: 4179052.0 The genome is segmented into 8544 regions for analysis. _IP Bases: 1389334 HitCounts: 8331264.0 The genome is segmented into 8065 regions for analysis. Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_2.SE.a.GPS _IP Bases: 565857 HitCounts: 9369885.0 Original read count stats: Running with 1 threads ... _IP Bases: 636117 HitCounts: 9548724.0 Running with 1 threads ... Running with 1 threads ... Original read count stats: Original read count stats: _IP Bases: 466311 HitCounts: 8920212.0 _IP Bases: 1559847 HitCounts: 7592534.0 ============================================== 2025-02-18 18:18:51 The genome is segmented into 8339 regions for analysis. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 33 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2B6.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2B6.SE.a.GPS _IP Bases: 3950846 HitCounts: 8499004.0 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 490 reads. _IP Bases: 1753507 HitCounts: 8189330.0 Original read count stats: _IP Bases: 129134 HitCounts: 8252072.0 Original read count stats: Running with 1 threads ... _IP Bases: 742261 HitCounts: 4357971.0 The genome is segmented into 8646 regions for analysis. ============================================== 2025-02-18 18:18:51 The genome is segmented into 8683 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 329388 HitCounts: 9512563.0 The genome is segmented into 8443 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5G8.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5G8.SE.a.GPS The genome is segmented into 8410 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 22 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 499 reads. Running with 1 threads ... The genome is segmented into 8531 regions for analysis. Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 2778481 HitCounts: 4188234.0 The genome is segmented into 8624 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 18:18:52 Original read count stats: _IP Bases: 1630466 HitCounts: 8843712.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 560 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 100 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_1.SE.a.GPS The genome is segmented into 8204 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 53 reads. Original read count stats: _IP Bases: 1516471 HitCounts: 9518752.0 Original read count stats: _IP Bases: 251020 HitCounts: 8521110.0 ============================================== 2025-02-18 18:18:52 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2A1.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2A1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 555 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 142 reads. The genome is segmented into 8340 regions for analysis. Running with 1 threads ... The genome is segmented into 8611 regions for analysis. ============================================== 2025-02-18 18:18:52 At Poisson p-value 1.0e-03, in a 301bp window, expect 221 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 42 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 579 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4D6.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4D6.1x36mers.unique.GPS Original read count stats: _IP Bases: 554955 HitCounts: 9829692.0 The genome is segmented into 8313 regions for analysis. ============================================== 2025-02-18 18:18:53 Original read count stats: _IP Bases: 276835 HitCounts: 9756631.0 Running with 1 threads ... The genome is segmented into 8693 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5B6.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5B6.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 208002 HitCounts: 4654936.0 The genome is segmented into 8300 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 276 reads. ============================================== 2025-02-18 18:18:53 The genome is segmented into 8157 regions for analysis. Running with 1 threads ... The genome is segmented into 8426 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2A1.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2A1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 41 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 31 reads. ============================================== 2025-02-18 18:18:53 Original read count stats: _IP Bases: 146474 HitCounts: 9194710.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5B9.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5B9.1x36mers.unique.GPS The genome is segmented into 8242 regions for analysis. Running with 1 threads ... The genome is segmented into 8384 regions for analysis. The genome is segmented into 8144 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 304 reads. The genome is segmented into 8476 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 615 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 338 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 360 reads. Running with 1 threads ... The genome is segmented into 8459 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 26 reads. Running with 1 threads ... ============================================== 2025-02-18 18:18:54 ============================================== 2025-02-18 18:18:54 Original read count stats: _IP Bases: 311629 HitCounts: 1.0997578E7 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_M4.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_M4.SE.a.GPS The genome is segmented into 8197 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2D6.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2D6.1x36mers.unique.GPS The genome is segmented into 8829 regions for analysis. Original read count stats: Running with 1 threads ... _IP Bases: 399555 HitCounts: 9214127.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 342 reads. ============================================== 2025-02-18 18:18:54 The genome is segmented into 8474 regions for analysis. The genome is segmented into 8539 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 382 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 371 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 56 reads. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 421 reads. The genome is segmented into 8318 regions for analysis. ============================================== 2025-02-18 18:18:54 ============================================== 2025-02-18 18:18:55 ============================================== 2025-02-18 18:18:56 ============================================== 2025-02-18 18:18:55 At Poisson p-value 1.0e-03, in a 301bp window, expect 54 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 379 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 464 reads. _IP Bases: 4143008 HitCounts: 1.0028549E7 The genome is segmented into 8139 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 403 reads. ============================================== 2025-02-18 18:18:55 Original read count stats: The genome is segmented into 8547 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 458 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 374 reads. ============================================== 2025-02-18 18:18:55 ============================================== 2025-02-18 18:18:56 At Poisson p-value 1.0e-03, in a 301bp window, expect 444 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_1.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_1.SE.a.GPS ============================================== 2025-02-18 18:18:56_IP Bases: 417328 HitCounts: 1.039868E7 Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_8B2.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_8B2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_7B10.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_7B10.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_1.SE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2D6.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2D6.SE.a.GPS ============================================== 2025-02-18 18:18:56 ============================================== 2025-02-18 18:18:56 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5B9.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5B9.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4D6.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4D6.SE.a.GPS The genome is segmented into 8290 regions for analysis. Running with 1 threads ... The genome is segmented into 8566 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 551649 HitCounts: 4882493.0 The genome is segmented into 8612 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 61 reads. Original read count stats: ============================================== 2025-02-18 18:18:57_IP Bases: 438847 HitCounts: 1.1954406E7 The genome is segmented into 8595 regions for analysis. The genome is segmented into 8609 regions for analysis. Running with 1 threads ... Original read count stats: The genome is segmented into 8252 regions for analysis. The genome is segmented into 8204 regions for analysis. _IP Bases: 794971 HitCounts: 4973064.0 The genome is segmented into 8305 regions for analysis. Original read count stats: _IP Bases: 466036 HitCounts: 5064924.0 Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_8B2.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_8B2.1x36mers.unique.GPS _IP Bases: 237298 HitCounts: 5314314.0 Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Original read count stats: Running with 1 threads ... Original read count stats: _IP Bases: 599100 HitCounts: 1.0067819E7 Running with 1 threads ... _IP Bases: 2127271 HitCounts: 9963407.0 Original read count stats: Original read count stats: _IP Bases: 706868 HitCounts: 1.082474E7 _IP Bases: 466240 HitCounts: 1.1744E7 Original read count stats: _IP Bases: 448613 HitCounts: 1.0410012E7 --------------------------- Events discovered Significant: 23 Insignificant: 0 Filtered: 0 Finish binding event prediction: 16.1s Original read count stats: _IP Bases: 2274847 HitCounts: 1.0487437E7 The genome is segmented into 8594 regions for analysis. Refine read distribution from 9 binding events. At Poisson p-value 1.0e-03, in a 301bp window, expect 498 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 40 reads. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8708 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 716 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 106 reads. Original read count stats: The genome is segmented into 8584 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 85 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 79 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 97 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 75 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 235 reads. The genome is segmented into 8261 regions for analysis. ============================================== 2025-02-18 18:18:58 At Poisson p-value 1.0e-03, in a 301bp window, expect 109 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 145 reads. The genome is segmented into 8671 regions for analysis. The genome is segmented into 8089 regions for analysis. _IP Bases: 391474 HitCounts: 1.058095E7 Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_1.SE.a.GPS Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8473 regions for analysis. The genome is segmented into 8401 regions for analysis. Running with 1 threads ... The genome is segmented into 8328 regions for analysis. Running with 1 threads ... The genome is segmented into 8309 regions for analysis. The genome is segmented into 8434 regions for analysis. The genome is segmented into 8480 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8330 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 57 reads. The genome is segmented into 8451 regions for analysis. ============================================== 2025-02-18 18:19:00 ============================================== 2025-02-18 18:19:00 Running with 1 threads ... The genome is segmented into 8331 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5F9.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5F9.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_7B10.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_7B10.SE.a.GPS Running with 1 threads ... ============================================== 2025-02-18 18:19:00 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 546315 HitCounts: 1.2045912E7 The genome is segmented into 8295 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 18:19:00 Original read count stats: _IP Bases: 263858 HitCounts: 1.1960133E7 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_2.SE.a.GPS Original read count stats: Original read count stats: _IP Bases: 1327066 HitCounts: 1.2793148E7 _IP Bases: 676295 HitCounts: 1.1784235E7 ============================================== 2025-02-18 18:19:01 At Poisson p-value 1.0e-03, in a 301bp window, expect 39 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 349608 HitCounts: 1.3037946E7 The genome is segmented into 8413 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 383488 HitCounts: 1.3975146E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 179 reads. ============================================== 2025-02-18 18:19:02 The genome is segmented into 8454 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2.SE.a.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 679 reads. Original read count stats: _IP Bases: 1438729 HitCounts: 1.3776992E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 841 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 726 reads. The genome is segmented into 8344 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 18:19:04 ============================================== 2025-02-18 18:19:04 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5F9.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5F9.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_1.1x36mers.unique.GPS The genome is segmented into 8347 regions for analysis. The genome is segmented into 8498 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 298245 HitCounts: 1.3534434E7 Original read count stats: _IP Bases: 901866 HitCounts: 1.4750543E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 50 reads. The genome is segmented into 8621 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 616 reads. Running with 1 threads ... The genome is segmented into 8616 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 571 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 736 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 547 reads. The genome is segmented into 8670 regions for analysis. Running with 1 threads ... The genome is segmented into 8685 regions for analysis. The genome is segmented into 8252 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 299 reads. The genome is segmented into 8284 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 0 Finish binding event prediction: 22.1s Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 801 reads. The genome is segmented into 8425 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 0 --------------------------- Events discovered Significant: 10 Insignificant: 0 Filtered: 1 Finish binding event prediction: 27.8s Finish binding event prediction: 22.4s Running with 1 threads ... Refine read distribution from 4 binding events. Running with 1 threads ... ============================================== 2025-02-18 18:19:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_2.SE.a.GPS --------------------------- Events discovered Significant: 20 Insignificant: 2 Filtered: 0 Finish binding event prediction: 18.1s Refine read distribution from 15 binding events. Original read count stats: _IP Bases: 984688 HitCounts: 1.8378499E7 --------------------------- Events discovered Significant: 21 Insignificant: 2 Filtered: 0 Finish binding event prediction: 34.1s Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 1 Finish binding event prediction: 33.1s Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 873 reads. The genome is segmented into 8503 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 0 Finish binding event prediction: 13.0s --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 0 Finish binding event prediction: 21.4s No valid binding event was found. --------------------------- Events discovered Significant: 12 Insignificant: 5 Filtered: 0 Finish binding event prediction: 23.1s Refine read distribution from 10 binding events. --------------------------- Events discovered Significant: 39 Insignificant: 6 Filtered: 13 Finish binding event prediction: 44.1s Refine read distribution from 26 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 1 Finish binding event prediction: 14.1s --------------------------- Events discovered Significant: 38 Insignificant: 28 Filtered: 19 Finish binding event prediction: 54.1s Refine read distribution from 24 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 21 Insignificant: 10 Filtered: 0 Finish binding event prediction: 27.0s Refine read distribution from 21 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 0 Filtered: 0 --------------------------- Events discovered Significant: 29 Insignificant: 22 Filtered: 0 Finish binding event prediction: 54.2s Finish binding event prediction: 9.7s Running with 1 threads ... Refine read distribution from 27 binding events. --------------------------- Events discovered Significant: 24 Insignificant: 48 Filtered: 22 Finish binding event prediction: 54.3s Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 313 Insignificant: 1 Filtered: 29 Finish binding event prediction: 1.3m --------------------------- Events discovered Significant: 21 Insignificant: 8 Filtered: 6 Refine read distribution from 83 binding events. Finish binding event prediction: 1.1m Running with 1 threads ... Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 109 Insignificant: 83 Filtered: 20 Finish binding event prediction: 1.2m Refine read distribution from 25 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 79 Insignificant: 1 Filtered: 14 Finish binding event prediction: 1.2m Refine read distribution from 23 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 1.1m Running with 1 threads ... --------------------------- Events discovered Significant: 30 Insignificant: 21 Filtered: 0 Finish binding event prediction: 19.1s Refine read distribution from 22 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.2m Running with 1 threads ... --------------------------- Events discovered Significant: 78 Insignificant: 14 Filtered: 0 Finish binding event prediction: 13.1s Refine read distribution from 51 binding events. --------------------------- Events discovered Significant: 294 Insignificant: 4 Filtered: 18 Finish binding event prediction: 1.6m Refine read distribution from 73 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 0 Filtered: 0 Finish binding event prediction: 22.0s --------------------------- Events discovered Significant: 14 Insignificant: 0 Filtered: 3 Finish binding event prediction: 1.2m Refine read distribution from 7 binding events. Running with 1 threads ... ============================================== 2025-02-18 18:20:11 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_1.SE.a.GPS --------------------------- Events discovered Significant: 65 Insignificant: 0 Filtered: 21 Finish binding event prediction: 1.5m Refine read distribution from 16 binding events. Running with 1 threads ... Original read count stats: _IP Bases: 1028077 HitCounts: 3.9191654E7 --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 15.0s --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 14.0s --------------------------- Events discovered Significant: 34 Insignificant: 17 Filtered: 17 Finish binding event prediction: 1.4m Refine read distribution from 21 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.5m Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 1576 reads. --------------------------- Events discovered Significant: 108 Insignificant: 0 Filtered: 34 Finish binding event prediction: 1.8m Refine read distribution from 84 binding events. Running with 1 threads ... The genome is segmented into 8439 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 69 Insignificant: 6 Filtered: 16 --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.9m Finish binding event prediction: 1.5m Running with 1 threads ... Refine read distribution from 38 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 34 Insignificant: 49 Filtered: 10 Finish binding event prediction: 1.6m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 35 Insignificant: 15 Filtered: 0 --------------------------- Events discovered Significant: 23 Insignificant: 25 Filtered: 14 Finish binding event prediction: 38.6s Finish binding event prediction: 1.6m Refine read distribution from 26 binding events. Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 124 Insignificant: 0 Filtered: 35 Finish binding event prediction: 1.9m --------------------------- Events discovered Significant: 109 Insignificant: 0 Filtered: 35 Finish binding event prediction: 1.9m Refine read distribution from 88 binding events. Running with 1 threads ... Refine read distribution from 85 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 77 Insignificant: 61 Filtered: 14 Finish binding event prediction: 1.6m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 308 Insignificant: 40 Filtered: 2 Finish binding event prediction: 48.7s Refine read distribution from 160 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 0 Finish binding event prediction: 15.1s --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 0 Finish binding event prediction: 21.0s --------------------------- Events discovered Significant: 34 Insignificant: 57 Filtered: 10 Finish binding event prediction: 1.7m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 81 Insignificant: 72 Filtered: 8 Finish binding event prediction: 1.9m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 107 Insignificant: 53 Filtered: 43 Finish binding event prediction: 2.1m Refine read distribution from 32 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 86 Insignificant: 70 Filtered: 10 --------------------------- Events discovered Significant: 23 Insignificant: 30 Filtered: 5 Finish binding event prediction: 2.0m Finish binding event prediction: 2.1m Refine read distribution from 9 binding events. Running with 1 threads ... Refine read distribution from 28 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 76 Insignificant: 3 Filtered: 20 Finish binding event prediction: 2.4m Refine read distribution from 43 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 171 Insignificant: 2 Filtered: 35 Finish binding event prediction: 2.3m Refine read distribution from 85 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 16 Insignificant: 13 Filtered: 0 Finish binding event prediction: 50.1s Refine read distribution from 9 binding events. --------------------------- Events discovered Significant: 43 Insignificant: 63 Filtered: 17 --------------------------- Events discovered Significant: 82 Insignificant: 3 Filtered: 6 Finish binding event prediction: 1.9m Finish binding event prediction: 1.1m Refine read distribution from 33 binding events. Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 57 Insignificant: 49 Filtered: 12 Finish binding event prediction: 2.1m Refine read distribution from 21 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 30 Insignificant: 0 Filtered: 9 Finish binding event prediction: 2.4m Refine read distribution from 30 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.1m Running with 1 threads ... --------------------------- Events discovered Significant: 62 Insignificant: 2 Filtered: 3 Finish binding event prediction: 54.0s Refine read distribution from 39 binding events. --------------------------- Events discovered Significant: 46 Insignificant: 21 Filtered: 21 Finish binding event prediction: 2.1m Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 158 Insignificant: 82 Filtered: 67 --------------------------- Events discovered Significant: 32 Insignificant: 12 Filtered: 14 Finish binding event prediction: 2.4m --------------------------- Events discovered Significant: 37 Insignificant: 16 Filtered: 17 Finish binding event prediction: 2.2m Finish binding event prediction: 2.1m Refine read distribution from 20 binding events. Refine read distribution from 25 binding events. Running with 1 threads ... Refine read distribution from 29 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 43 Insignificant: 20 Filtered: 0 Finish binding event prediction: 46.1s Refine read distribution from 32 binding events. --------------------------- Events discovered Significant: 227 Insignificant: 31 Filtered: 2 Finish binding event prediction: 37.1s Refine read distribution from 205 binding events. --------------------------- Events discovered Significant: 95 Insignificant: 36 Filtered: 20 Finish binding event prediction: 2.4m Refine read distribution from 25 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 70 Insignificant: 7 Filtered: 24 --------------------------- Events discovered Significant: 265 Insignificant: 27 Filtered: 4 Finish binding event prediction: 2.2m Finish binding event prediction: 1.1m Refine read distribution from 142 binding events. Refine read distribution from 39 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 65 Insignificant: 8 Filtered: 22 Finish binding event prediction: 2.1m Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.3m Running with 1 threads ... --------------------------- Events discovered Significant: 66 Insignificant: 18 Filtered: 0 Finish binding event prediction: 40.1s Refine read distribution from 38 binding events. --------------------------- Events discovered Significant: 119 Insignificant: 73 Filtered: 27 Finish binding event prediction: 2.6m Refine read distribution from 28 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 98 Insignificant: 10 Filtered: 35 Finish binding event prediction: 2.1m Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 92 Insignificant: 41 Filtered: 22 Finish binding event prediction: 2.4m Refine read distribution from 28 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 57 Insignificant: 27 Filtered: 0 Finish binding event prediction: 11.4s Refine read distribution from 35 binding events. --------------------------- Events discovered Significant: 271 Insignificant: 4 Filtered: 33 --------------------------- Events discovered Significant: 128 Insignificant: 0 Filtered: 40 Finish binding event prediction: 2.5m Finish binding event prediction: 2.7m --------------------------- Events discovered Significant: 61 Insignificant: 1 Filtered: 16 Finish binding event prediction: 2.7m Refine read distribution from 44 binding events. Running with 1 threads ... Refine read distribution from 38 binding events. Refine read distribution from 99 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 31 Insignificant: 45 Filtered: 12 Finish binding event prediction: 2.3m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 306 Insignificant: 3 Filtered: 24 Finish binding event prediction: 2.5m Refine read distribution from 53 binding events. --------------------------- Events discovered Significant: 49 Insignificant: 13 Filtered: 0 Finish binding event prediction: 15.1s Running with 1 threads ... Refine read distribution from 34 binding events. --------------------------- Events discovered Significant: 119 Insignificant: 10 Filtered: 27 Finish binding event prediction: 2.4m Refine read distribution from 45 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 124 Insignificant: 6 Filtered: 36 Finish binding event prediction: 2.5m Refine read distribution from 57 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 17 Insignificant: 31 Filtered: 7 Finish binding event prediction: 2.5m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 164 Insignificant: 31 Filtered: 45 Finish binding event prediction: 2.6m Refine read distribution from 109 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 276 Insignificant: 3 Filtered: 35 Finish binding event prediction: 2.6m Refine read distribution from 51 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 48 Insignificant: 23 Filtered: 0 Finish binding event prediction: 19.1s Refine read distribution from 37 binding events. --------------------------- Events discovered Significant: 71 Insignificant: 24 Filtered: 0 Finish binding event prediction: 15.0s Refine read distribution from 44 binding events. --------------------------- Events discovered Significant: 145 Insignificant: 1 Filtered: 33 Finish binding event prediction: 2.7m Refine read distribution from 42 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 32 Insignificant: 0 Filtered: 10 Finish binding event prediction: 2.6m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 57 Insignificant: 22 Filtered: 0 Finish binding event prediction: 13.1s Refine read distribution from 43 binding events. --------------------------- Events discovered Significant: 656 Insignificant: 73 Filtered: 4 Finish binding event prediction: 1.1m Refine read distribution from 593 binding events. --------------------------- Events discovered Significant: 129 Insignificant: 1 Filtered: 20 Finish binding event prediction: 2.8m Refine read distribution from 57 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 25 Insignificant: 29 Filtered: 9 Finish binding event prediction: 2.6m Refine read distribution from 11 binding events. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 33 Insignificant: 48 Filtered: 12 --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 --------------------------- Events discovered Significant: 37 Insignificant: 0 Filtered: 12 Finish binding event prediction: 2.3m Finish binding event prediction: 3.0m Finish binding event prediction: 3.1m Running with 1 threads ... Refine read distribution from 37 binding events. Refine read distribution from 10 binding events. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-18 18:21:44 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_2.1x36mers.unique.GPS --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Original read count stats: Finish binding event prediction: 39.9s _IP Bases: 537466 HitCounts: 1237879.0 --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 32.1s --------------------------- Events discovered Significant: 57 Insignificant: 25 Filtered: 0 Finish binding event prediction: 49.1s Refine read distribution from 30 binding events. --------------------------- Events discovered Significant: 679 Insignificant: 40 Filtered: 3 Finish binding event prediction: 1.2m Refine read distribution from 614 binding events. --------------------------- Events discovered Significant: 133 Insignificant: 1 Filtered: 35 Finish binding event prediction: 3.0m Refine read distribution from 61 binding events. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 87 reads. --------------------------- Events discovered Significant: 85 Insignificant: 24 Filtered: 20 Finish binding event prediction: 2.8m Refine read distribution from 33 binding events. Running with 1 threads ... The genome is segmented into 8490 regions for analysis. --------------------------- Events discovered Significant: 101 Insignificant: 38 Filtered: 18 --------------------------- Events discovered Significant: 97 Insignificant: 19 Filtered: 6 --------------------------- Events discovered Significant: 36 Insignificant: 0 Filtered: 11 Finish binding event prediction: 3.0m Finish binding event prediction: 54.5s --------------------------- Events discovered Significant: 96 Insignificant: 11 Filtered: 35 Running with 1 threads ... Finish binding event prediction: 2.7m Finish binding event prediction: 3.1m Refine read distribution from 66 binding events. Refine read distribution from 43 binding events. Refine read distribution from 12 binding events. Running with 1 threads ... Running with 1 threads ... Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 29 Insignificant: 0 Filtered: 9 Finish binding event prediction: 3.1m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 17 Insignificant: 0 Filtered: 5 Finish binding event prediction: 3.0m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 670 Insignificant: 0 Filtered: 105 Finish binding event prediction: 3.0m Refine read distribution from 448 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 121 Insignificant: 54 Filtered: 9 Finish binding event prediction: 35.1s Refine read distribution from 66 binding events. --------------------------- Events discovered Significant: 107 Insignificant: 57 Filtered: 17 Finish binding event prediction: 1.9m Refine read distribution from 65 binding events. --------------------------- Events discovered Significant: 102 Insignificant: 35 Filtered: 0 Finish binding event prediction: 46.1s Refine read distribution from 63 binding events. ============================================== 2025-02-18 18:21:51 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_2.SE.a.GPS Original read count stats: _IP Bases: 524330 HitCounts: 2532401.0 --------------------------- Events discovered Significant: 20 Insignificant: 33 Filtered: 10 --------------------------- Events discovered Significant: 17 Insignificant: 0 Filtered: 5 At Poisson p-value 1.0e-03, in a 301bp window, expect 132 reads. --------------------------- Events discovered Significant: 19 Insignificant: 1 Filtered: 6 Finish binding event prediction: 3.0m Finish binding event prediction: 2.8m Finish binding event prediction: 3.0m --------------------------- Events discovered Significant: 165 Insignificant: 10 Filtered: 0 Finish binding event prediction: 48.1s Refine read distribution from 10 binding events. Running with 1 threads ... Refine read distribution from 10 binding events. Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 144 Insignificant: 48 Filtered: 2 Running with 1 threads ... Finish binding event prediction: 33.1s Refine read distribution from 164 binding events. Refine read distribution from 65 binding events. The genome is segmented into 8618 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 689 Insignificant: 64 Filtered: 1 Finish binding event prediction: 1.3m Refine read distribution from 629 binding events. --------------------------- Events discovered Significant: 166 Insignificant: 13 Filtered: 42 Finish binding event prediction: 3.1m Refine read distribution from 27 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 2 Finish binding event prediction: 3.1m Running with 1 threads ... --------------------------- Events discovered Significant: 371 Insignificant: 2 Filtered: 80 Finish binding event prediction: 3.1m Refine read distribution from 263 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 192 Insignificant: 3 Filtered: 37 Finish binding event prediction: 3.1m Refine read distribution from 74 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 132 Insignificant: 3 Filtered: 33 Finish binding event prediction: 3.2m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 129 Insignificant: 0 Filtered: 26 Finish binding event prediction: 3.3m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 96 Insignificant: 0 Filtered: 19 Finish binding event prediction: 3.2m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 83 Insignificant: 40 Filtered: 5 Finish binding event prediction: 1.4m Refine read distribution from 41 binding events. --------------------------- Events discovered Significant: 50 Insignificant: 29 Filtered: 20 Finish binding event prediction: 3.0m Refine read distribution from 5 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 131 Insignificant: 0 Filtered: 37 Finish binding event prediction: 3.3m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 29 Insignificant: 0 Filtered: 9 Finish binding event prediction: 3.1m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 325 Insignificant: 46 Filtered: 1 Finish binding event prediction: 42.2s Refine read distribution from 218 binding events. --------------------------- Events discovered Significant: 245 Insignificant: 72 Filtered: 3 Finish binding event prediction: 47.1s Refine read distribution from 177 binding events. --------------------------- Events discovered Significant: 201 Insignificant: 2 Filtered: 35 Finish binding event prediction: 2.9m Refine read distribution from 52 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 133 Insignificant: 28 Filtered: 0 Finish binding event prediction: 53.1s Refine read distribution from 94 binding events. --------------------------- Events discovered Significant: 157 Insignificant: 10 Filtered: 3 --------------------------- Events discovered Significant: 179 Insignificant: 37 Filtered: 2 --------------------------- Events discovered Significant: 13 Insignificant: 14 Filtered: 6 Finish binding event prediction: 32.8s Finish binding event prediction: 46.9s Finish binding event prediction: 3.2m Refine read distribution from 101 binding events. Refine read distribution from 79 binding events. Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 823 Insignificant: 0 Filtered: 124 --------------------------- Events discovered Significant: 405 Insignificant: 1 Filtered: 83 Finish binding event prediction: 3.4m Finish binding event prediction: 3.3m Refine read distribution from 287 binding events. Refine read distribution from 572 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 212 Insignificant: 74 Filtered: 3 Finish binding event prediction: 1.0m Refine read distribution from 136 binding events. --------------------------- Events discovered Significant: 132 Insignificant: 59 Filtered: 19 --------------------------- Events discovered Significant: 302 Insignificant: 31 Filtered: 6 Finish binding event prediction: 3.4m Finish binding event prediction: 50.3s Refine read distribution from 109 binding events. Refine read distribution from 55 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 780 Insignificant: 0 Filtered: 124 Finish binding event prediction: 3.4m Refine read distribution from 536 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 202 Insignificant: 18 Filtered: 1 Finish binding event prediction: 58.1s Refine read distribution from 178 binding events. --------------------------- Events discovered Significant: 16 Insignificant: 22 Filtered: 12 Finish binding event prediction: 3.4m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 308 Insignificant: 9 Filtered: 37 Finish binding event prediction: 3.5m Refine read distribution from 104 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 148 Insignificant: 66 Filtered: 1 Finish binding event prediction: 1.5m Refine read distribution from 97 binding events. --------------------------- Events discovered Significant: 60 Insignificant: 61 Filtered: 22 Finish binding event prediction: 3.2m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 302 Insignificant: 42 Filtered: 1 Finish binding event prediction: 44.2s Refine read distribution from 189 binding events. --------------------------- Events discovered Significant: 254 Insignificant: 8 Filtered: 4 --------------------------- Events discovered Significant: 175 Insignificant: 1 Filtered: 0 Finish binding event prediction: 1.5m Finish binding event prediction: 43.3s Refine read distribution from 230 binding events. Refine read distribution from 172 binding events. --------------------------- Events discovered Significant: 721 Insignificant: 55 Filtered: 1 Finish binding event prediction: 1.1m Refine read distribution from 640 binding events. --------------------------- Events discovered Significant: 18 Insignificant: 17 Filtered: 6 Finish binding event prediction: 3.5m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 53 Insignificant: 42 Filtered: 1 Finish binding event prediction: 1.7m Refine read distribution from 24 binding events. --------------------------- Events discovered Significant: 87 Insignificant: 22 Filtered: 0 Finish binding event prediction: 53.1s Refine read distribution from 58 binding events. --------------------------- Events discovered Significant: 115 Insignificant: 43 Filtered: 4 Finish binding event prediction: 1.9m Refine read distribution from 58 binding events. --------------------------- Events discovered Significant: 128 Insignificant: 14 Filtered: 36 --------------------------- Events discovered Significant: 195 Insignificant: 10 Filtered: 0 Finish binding event prediction: 3.8m Finish binding event prediction: 46.3s Refine read distribution from 19 binding events. Running with 1 threads ... Refine read distribution from 186 binding events. --------------------------- Events discovered Significant: 346 Insignificant: 60 Filtered: 0 Finish binding event prediction: 1.6m Refine read distribution from 239 binding events. --------------------------- Events discovered Significant: 46 Insignificant: 12 Filtered: 2 Finish binding event prediction: 43.1s Refine read distribution from 34 binding events. --------------------------- Events discovered Significant: 93 Insignificant: 41 Filtered: 1 Finish binding event prediction: 1.6m Refine read distribution from 62 binding events. --------------------------- Events discovered Significant: 102 Insignificant: 1 Filtered: 3 --------------------------- Events discovered Significant: 404 Insignificant: 0 Filtered: 92 Finish binding event prediction: 44.1s Finish binding event prediction: 3.8m Refine read distribution from 55 binding events. Refine read distribution from 299 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 222 Insignificant: 79 Filtered: 8 Finish binding event prediction: 1.2m Refine read distribution from 176 binding events. --------------------------- Events discovered Significant: 218 Insignificant: 78 Filtered: 2 Finish binding event prediction: 49.1s --------------------------- Events discovered Significant: 214 Insignificant: 5 Filtered: 0 Finish binding event prediction: 49.1s Refine read distribution from 141 binding events. Refine read distribution from 204 binding events. --------------------------- Events discovered Significant: 127 Insignificant: 80 Filtered: 7 Finish binding event prediction: 1.7m Refine read distribution from 60 binding events. --------------------------- Events discovered Significant: 199 Insignificant: 6 Filtered: 35 Finish binding event prediction: 3.9m Refine read distribution from 63 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 171 Insignificant: 17 Filtered: 7 Finish binding event prediction: 1.6m Refine read distribution from 30 binding events. --------------------------- Events discovered Significant: 221 Insignificant: 14 Filtered: 2 Finish binding event prediction: 1.2m Refine read distribution from 99 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 25 Filtered: 7 Finish binding event prediction: 3.8m Running with 1 threads ... --------------------------- Events discovered Significant: 74 Insignificant: 18 Filtered: 0 Finish binding event prediction: 51.5s Refine read distribution from 52 binding events. --------------------------- Events discovered Significant: 283 Insignificant: 10 Filtered: 39 Finish binding event prediction: 3.9m Refine read distribution from 101 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 104 Insignificant: 35 Filtered: 0 --------------------------- Events discovered Significant: 298 Insignificant: 4 Filtered: 5 Finish binding event prediction: 1.1m Finish binding event prediction: 44.0s Refine read distribution from 57 binding events. ============================================== 2025-02-18 18:22:48Refine read distribution from 205 binding events. ============================================== 2025-02-18 18:22:48 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_2.1x36mers.unique.GPS --------------------------- Events discovered Significant: 60 Insignificant: 30 Filtered: 0 Finish binding event prediction: 48.1s Refine read distribution from 29 binding events. Original read count stats: _IP Bases: 469116 HitCounts: 2416531.0 Original read count stats: _IP Bases: 625350 HitCounts: 2650724.0 --------------------------- Events discovered Significant: 109 Insignificant: 0 Filtered: 4 Finish binding event prediction: 59.1s Refine read distribution from 46 binding events. ============================================== 2025-02-18 18:22:49 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 112 reads. Original read count stats: _IP Bases: 503551 HitCounts: 2528048.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 137 reads. --------------------------- Events discovered Significant: 27 Insignificant: 1 Filtered: 8 Finish binding event prediction: 4.0m Refine read distribution from 21 binding events. Running with 1 threads ... The genome is segmented into 8396 regions for analysis. The genome is segmented into 8357 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 119 reads. --------------------------- Events discovered Significant: 310 Insignificant: 62 Filtered: 1 --------------------------- Events discovered Significant: 130 Insignificant: 0 Filtered: 34 ============================================== 2025-02-18 18:22:51Finish binding event prediction: 1.1m Running with 1 threads ... Running with 1 threads ... Finish binding event prediction: 4.2m ============================================== 2025-02-18 18:22:52Refine read distribution from 213 binding events. Refine read distribution from 19 binding events. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_1.SE.a.GPS The genome is segmented into 8615 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 542620 HitCounts: 3017843.0 Original read count stats: _IP Bases: 505484 HitCounts: 2878937.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 136 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 127 reads. The genome is segmented into 8532 regions for analysis. The genome is segmented into 8380 regions for analysis. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 158 Insignificant: 1 Filtered: 37 --------------------------- Events discovered Significant: 52 Insignificant: 17 Filtered: 0 Finish binding event prediction: 4.2m Finish binding event prediction: 49.3s Refine read distribution from 17 binding events. Running with 1 threads ... Refine read distribution from 34 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 302 Insignificant: 22 Filtered: 5 Finish binding event prediction: 1.7m Refine read distribution from 109 binding events. --------------------------- Events discovered Significant: 241 Insignificant: 0 Filtered: 45 Finish binding event prediction: 4.4m Refine read distribution from 154 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 202 Insignificant: 91 Filtered: 7 Finish binding event prediction: 1.3m Refine read distribution from 131 binding events. --------------------------- Events discovered Significant: 175 Insignificant: 9 Filtered: 21 Finish binding event prediction: 4.2m Refine read distribution from 87 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 433 Insignificant: 1 Filtered: 88 Finish binding event prediction: 4.2m Refine read distribution from 285 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 4.3m Running with 1 threads ... --------------------------- Events discovered Significant: 223 Insignificant: 38 Filtered: 35 Finish binding event prediction: 1.9m Refine read distribution from 122 binding events. --------------------------- Events discovered Significant: 80 Insignificant: 2 Filtered: 3 --------------------------- Events discovered Significant: 66 Insignificant: 18 Filtered: 0 --------------------------- Events discovered Significant: 346 Insignificant: 3 Filtered: 54 --------------------------- Events discovered Significant: 276 Insignificant: 20 Filtered: 2 Finish binding event prediction: 1.2m Finish binding event prediction: 43.7s Finish binding event prediction: 4.3m Finish binding event prediction: 51.3s Refine read distribution from 46 binding events. Refine read distribution from 44 binding events. Refine read distribution from 213 binding events. Refine read distribution from 212 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 32 Insignificant: 0 Filtered: 7 Finish binding event prediction: 4.4m Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 287 Insignificant: 18 Filtered: 6 Finish binding event prediction: 1.9m Refine read distribution from 98 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 11 Filtered: 4 Finish binding event prediction: 4.4m Running with 1 threads ... --------------------------- Events discovered Significant: 696 Insignificant: 1 Filtered: 131 Finish binding event prediction: 4.4m Refine read distribution from 480 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 333 Insignificant: 57 Filtered: 0 Finish binding event prediction: 1.4m Refine read distribution from 201 binding events. --------------------------- Events discovered Significant: 619 Insignificant: 3 Filtered: 109 Finish binding event prediction: 4.4m Refine read distribution from 394 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 260 Insignificant: 85 Filtered: 0 Finish binding event prediction: 1.1m Refine read distribution from 170 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.7m --------------------------- Events discovered Significant: 71 Insignificant: 2 Filtered: 19 Finish binding event prediction: 1.6m Refine read distribution from 46 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 177 Insignificant: 13 Filtered: 14 Finish binding event prediction: 4.5m Refine read distribution from 79 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 409 Insignificant: 53 Filtered: 3 Finish binding event prediction: 1.1m Refine read distribution from 214 binding events. --------------------------- Events discovered Significant: 125 Insignificant: 56 Filtered: 30 --------------------------- Events discovered Significant: 156 Insignificant: 9 Filtered: 39 Finish binding event prediction: 4.6m Finish binding event prediction: 4.7m Refine read distribution from 51 binding events. Refine read distribution from 36 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 77 Insignificant: 14 Filtered: 2 Finish binding event prediction: 1.6m Refine read distribution from 39 binding events. --------------------------- Events discovered Significant: 340 Insignificant: 37 Filtered: 2 Finish binding event prediction: 51.1s Refine read distribution from 196 binding events. --------------------------- Events discovered Significant: 94 Insignificant: 13 Filtered: 2 Finish binding event prediction: 1.7m Refine read distribution from 62 binding events. --------------------------- Events discovered Significant: 78 Insignificant: 10 Filtered: 1 Finish binding event prediction: 46.1s Refine read distribution from 55 binding events. --------------------------- Events discovered Significant: 128 Insignificant: 0 Filtered: 27 Finish binding event prediction: 4.9m Refine read distribution from 9 binding events. Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 38 Insignificant: 68 Filtered: 11 Finish binding event prediction: 3.2m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 81 Insignificant: 37 Filtered: 0 Finish binding event prediction: 1.3m Refine read distribution from 48 binding events. --------------------------- Events discovered Significant: 92 Insignificant: 26 Filtered: 1 Finish binding event prediction: 1.8m Refine read distribution from 58 binding events. --------------------------- Events discovered Significant: 283 Insignificant: 15 Filtered: 2 Finish binding event prediction: 1.7m Refine read distribution from 125 binding events. --------------------------- Events discovered Significant: 239 Insignificant: 2 Filtered: 48 Finish binding event prediction: 5.1m Refine read distribution from 156 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 2 Finish binding event prediction: 1.9m --------------------------- Events discovered Significant: 1100 Insignificant: 239 Filtered: 3 Finish binding event prediction: 2.0m Refine read distribution from 778 binding events. --------------------------- Events discovered Significant: 116 Insignificant: 1 Filtered: 28 Finish binding event prediction: 5.0m Refine read distribution from 23 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 178 Insignificant: 6 Filtered: 18 Finish binding event prediction: 5.0m Refine read distribution from 86 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 212 Insignificant: 87 Filtered: 2 Finish binding event prediction: 48.1s Refine read distribution from 188 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 5.1m Running with 1 threads ... --------------------------- Events discovered Significant: 849 Insignificant: 165 Filtered: 4 --------------------------- Events discovered Significant: 734 Insignificant: 1 Filtered: 123 Finish binding event prediction: 1.8m Finish binding event prediction: 5.1m Refine read distribution from 512 binding events. Refine read distribution from 656 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 241 Insignificant: 6 Filtered: 2 --------------------------- Events discovered Significant: 68 Insignificant: 11 Filtered: 4 --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 --------------------------- Events discovered Significant: 149 Insignificant: 4 Filtered: 29 --------------------------- Events discovered Significant: 2 Insignificant: 25 Filtered: 7 Finish binding event prediction: 43.9s Finish binding event prediction: 50.8s Finish binding event prediction: 5.2m Finish binding event prediction: 5.3m Finish binding event prediction: 1.4m Running with 1 threads ... Refine read distribution from 210 binding events. Refine read distribution from 42 binding events. Refine read distribution from 23 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 5.3m Running with 1 threads ... --------------------------- Events discovered Significant: 406 Insignificant: 57 Filtered: 6 --------------------------- Events discovered Significant: 131 Insignificant: 23 Filtered: 4 Finish binding event prediction: 1.4m Finish binding event prediction: 1.6m Refine read distribution from 87 binding events. Refine read distribution from 202 binding events. --------------------------- Events discovered Significant: 233 Insignificant: 75 Filtered: 1 Finish binding event prediction: 40.2s Refine read distribution from 163 binding events. --------------------------- Events discovered Significant: 650 Insignificant: 1 Filtered: 120 Finish binding event prediction: 5.2m Refine read distribution from 415 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 349 Insignificant: 2 Filtered: 67 Finish binding event prediction: 5.4m Refine read distribution from 224 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 70 Insignificant: 25 Filtered: 3 Finish binding event prediction: 1.3m Refine read distribution from 49 binding events. --------------------------- Events discovered Significant: 760 Insignificant: 103 Filtered: 3 Finish binding event prediction: 2.4m Refine read distribution from 615 binding events. --------------------------- Events discovered Significant: 14 Insignificant: 1 Filtered: 5 Finish binding event prediction: 5.6m Refine read distribution from 4 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 954 Insignificant: 143 Filtered: 3 --------------------------- Events discovered Significant: 1131 Insignificant: 267 Filtered: 4 Finish binding event prediction: 1.8m Finish binding event prediction: 2.2m Refine read distribution from 828 binding events. Refine read distribution from 753 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 5.5m Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 5.7m Running with 1 threads ... --------------------------- Events discovered Significant: 244 Insignificant: 34 Filtered: 24 Finish binding event prediction: 2.7m Refine read distribution from 129 binding events. --------------------------- Events discovered Significant: 68 Insignificant: 16 Filtered: 3 Finish binding event prediction: 1.6m Refine read distribution from 34 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 5.7m Running with 1 threads ... --------------------------- Events discovered Significant: 292 Insignificant: 46 Filtered: 10 Finish binding event prediction: 1.4m Refine read distribution from 238 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 5.4m Running with 1 threads ... --------------------------- Events discovered Significant: 207 Insignificant: 77 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 177 binding events. --------------------------- Events discovered Significant: 12 Insignificant: 1 Filtered: 4 Finish binding event prediction: 5.6m Refine read distribution from 4 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 337 Insignificant: 3 Filtered: 78 Finish binding event prediction: 5.8m Refine read distribution from 249 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 120 Insignificant: 26 Filtered: 3 Finish binding event prediction: 1.1m Refine read distribution from 82 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 No valid binding event was found. Finish binding event prediction: 1.5m Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 5.9m Running with 1 threads ... --------------------------- Events discovered Significant: 1141 Insignificant: 260 Filtered: 5 Finish binding event prediction: 2.5m Refine read distribution from 808 binding events. --------------------------- Events discovered Significant: 106 Insignificant: 21 Filtered: 3 Finish binding event prediction: 43.1s Refine read distribution from 56 binding events. --------------------------- Events discovered Significant: 217 Insignificant: 65 Filtered: 2 Finish binding event prediction: 57.1s Refine read distribution from 201 binding events. --------------------------- Events discovered Significant: 429 Insignificant: 0 Filtered: 94 Finish binding event prediction: 6.0m Refine read distribution from 315 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 102 Insignificant: 46 Filtered: 0 Finish binding event prediction: 1.3m Refine read distribution from 59 binding events. --------------------------- Events discovered Significant: 175 Insignificant: 30 Filtered: 44 Finish binding event prediction: 3.1m Refine read distribution from 123 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 637 Insignificant: 100 Filtered: 4 Finish binding event prediction: 1.8m Refine read distribution from 492 binding events. --------------------------- Events discovered Significant: 79 Insignificant: 12 Filtered: 13 Finish binding event prediction: 3.0m --------------------------- Events discovered Significant: 7 Insignificant: 6 Filtered: 3 Finish binding event prediction: 30.1s Refine read distribution from 53 binding events. --------------------------- Events discovered Significant: 320 Insignificant: 67 Filtered: 8 Finish binding event prediction: 1.3m Refine read distribution from 279 binding events. --------------------------- Events discovered Significant: 22 Insignificant: 4 Filtered: 7 Finish binding event prediction: 49.2s Refine read distribution from 11 binding events. --------------------------- Events discovered Significant: 423 Insignificant: 6 Filtered: 83 Finish binding event prediction: 2.3m Refine read distribution from 297 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 873 Insignificant: 173 Filtered: 3 Finish binding event prediction: 2.1m Refine read distribution from 671 binding events. --------------------------- Events discovered Significant: 479 Insignificant: 12 Filtered: 84 Finish binding event prediction: 2.3m Refine read distribution from 327 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 697 Insignificant: 0 Filtered: 124 Finish binding event prediction: 6.5m Refine read distribution from 465 binding events. Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 105 Insignificant: 5 Filtered: 2 Finish binding event prediction: 2.1m Refine read distribution from 84 binding events. --------------------------- Events discovered Significant: 980 Insignificant: 256 Filtered: 5 Finish binding event prediction: 2.4m Refine read distribution from 694 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 11 Filtered: 4 Finish binding event prediction: 2.5m --------------------------- Events discovered Significant: 997 Insignificant: 249 Filtered: 1 Finish binding event prediction: 2.6m Refine read distribution from 714 binding events. --------------------------- Events discovered Significant: 121 Insignificant: 14 Filtered: 3 Finish binding event prediction: 2.0m Refine read distribution from 81 binding events. --------------------------- Events discovered Significant: 166 Insignificant: 7 Filtered: 17 Finish binding event prediction: 7.2m Refine read distribution from 80 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 540 Insignificant: 164 Filtered: 15 Finish binding event prediction: 51.5s Refine read distribution from 455 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.7m --------------------------- Events discovered Significant: 995 Insignificant: 251 Filtered: 4 Finish binding event prediction: 2.3m Refine read distribution from 715 binding events. --------------------------- Events discovered Significant: 387 Insignificant: 0 Filtered: 68 Finish binding event prediction: 3.4m --------------------------- Events discovered Significant: 257 Insignificant: 80 Filtered: 5 Finish binding event prediction: 1.4m Refine read distribution from 260 binding events. Running with 1 threads ... Refine read distribution from 204 binding events. --------------------------- Events discovered Significant: 716 Insignificant: 83 Filtered: 4 Finish binding event prediction: 1.8m Refine read distribution from 600 binding events. --------------------------- Events discovered Significant: 979 Insignificant: 139 Filtered: 1 Finish binding event prediction: 1.6m Refine read distribution from 753 binding events. --------------------------- Events discovered Significant: 680 Insignificant: 114 Filtered: 1 Finish binding event prediction: 2.3m Refine read distribution from 528 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.5m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.2m --------------------------- Events discovered Significant: 531 Insignificant: 180 Filtered: 15 Finish binding event prediction: 1.8m Refine read distribution from 455 binding events. --------------------------- Events discovered Significant: 224 Insignificant: 64 Filtered: 3 Finish binding event prediction: 1.3m Refine read distribution from 204 binding events. --------------------------- Events discovered Significant: 984 Insignificant: 251 Filtered: 7 Finish binding event prediction: 3.2m Refine read distribution from 697 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.4m --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.1m --------------------------- Events discovered Significant: 1111 Insignificant: 227 Filtered: 9 Finish binding event prediction: 2.2m Refine read distribution from 787 binding events. --------------------------- Events discovered Significant: 557 Insignificant: 0 Filtered: 71 Finish binding event prediction: 4.7m Refine read distribution from 339 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 602 Insignificant: 106 Filtered: 16 Finish binding event prediction: 1.4m Refine read distribution from 530 binding events. --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 3.0m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.4m No valid binding event was found. No valid binding event was found. --------------------------- Events discovered Significant: 482 Insignificant: 0 Filtered: 85 Finish binding event prediction: 5.5m Refine read distribution from 322 binding events. Running with 1 threads ... No valid binding event was found. ============================================== 2025-02-18 18:29:03 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_1.SE.a.GPS Original read count stats: _IP Bases: 659345 HitCounts: 2784058.0 --------------------------- Events discovered Significant: 595 Insignificant: 141 Filtered: 9 Finish binding event prediction: 1.4m Refine read distribution from 496 binding events. At Poisson p-value 1.0e-03, in a 301bp window, expect 145 reads. The genome is segmented into 8536 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 5.3m ============================================== 2025-02-18 18:29:26 ============================================== 2025-02-18 18:29:27 ============================================== 2025-02-18 18:29:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 407209 HitCounts: 2534539.0 Original read count stats: _IP Bases: 602200 HitCounts: 2488977.0 Original read count stats: _IP Bases: 568146 HitCounts: 2362376.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 106 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 132 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 124 reads. The genome is segmented into 8409 regions for analysis. Running with 1 threads ... The genome is segmented into 8522 regions for analysis. Running with 1 threads ... The genome is segmented into 8376 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 18:29:33 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_1.SE.a.GPS Original read count stats: _IP Bases: 442568 HitCounts: 2668839.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 116 reads. The genome is segmented into 8614 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 18:29:36 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 467639 HitCounts: 2871187.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 118 reads. The genome is segmented into 8377 regions for analysis. Running with 1 threads ... ============================================== 2025-02-18 18:29:39 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_2.SE.a.GPS Original read count stats: _IP Bases: 508043 HitCounts: 3053198.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 131 reads. The genome is segmented into 8512 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 593 Insignificant: 126 Filtered: 13 Finish binding event prediction: 1.6m Refine read distribution from 492 binding events. --------------------------- Events discovered Significant: 340 Insignificant: 3 Filtered: 63 Finish binding event prediction: 2.0m Refine read distribution from 232 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 337 Insignificant: 2 Filtered: 70 Finish binding event prediction: 2.0m Refine read distribution from 254 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 13.0m Running with 1 threads ... --------------------------- Events discovered Significant: 425 Insignificant: 12 Filtered: 58 Finish binding event prediction: 2.3m Refine read distribution from 246 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 438 Insignificant: 6 Filtered: 57 Finish binding event prediction: 2.5m Refine read distribution from 243 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 504 Insignificant: 1 Filtered: 46 Finish binding event prediction: 3.0m Refine read distribution from 265 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 548 Insignificant: 141 Filtered: 9 Finish binding event prediction: 1.7m Refine read distribution from 481 binding events. --------------------------- Events discovered Significant: 556 Insignificant: 125 Filtered: 9 Finish binding event prediction: 1.3m Refine read distribution from 476 binding events. --------------------------- Events discovered Significant: 407 Insignificant: 110 Filtered: 12 Finish binding event prediction: 1.2m Refine read distribution from 330 binding events. --------------------------- Events discovered Significant: 371 Insignificant: 111 Filtered: 16 Finish binding event prediction: 1.6m Refine read distribution from 297 binding events. --------------------------- Events discovered Significant: 387 Insignificant: 116 Filtered: 8 Finish binding event prediction: 1.8m Refine read distribution from 298 binding events. --------------------------- Events discovered Significant: 402 Insignificant: 0 Filtered: 73 Finish binding event prediction: 4.5m Refine read distribution from 262 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 431 Insignificant: 0 Filtered: 54 Finish binding event prediction: 5.7m Refine read distribution from 257 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 585 Insignificant: 104 Filtered: 7 Finish binding event prediction: 1.4m Refine read distribution from 508 binding events. --------------------------- Events discovered Significant: 405 Insignificant: 104 Filtered: 11 Finish binding event prediction: 56.1s Refine read distribution from 334 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 15.1m ============================================== 2025-02-21 19:25:58 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_HS_i5006_DY330_rep2_17274.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_HS_i5006_DY330_rep2_17274.PE.a.GPS ============================================== 2025-02-21 19:25:59 Original read count stats: _IP Bases: 53848 HitCounts: 136870.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_MHS_i5006_DY330_rep2_17267.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_MHS_i5006_DY330_rep2_17267.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 14 reads. Original read count stats: _IP Bases: 89554 HitCounts: 198246.0 The genome is segmented into 3173 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 18 reads. The genome is segmented into 6845 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:26:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep1_20231.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep1_20231.PE.a.GPS Original read count stats: _IP Bases: 165138 HitCounts: 446192.0 ============================================== 2025-02-21 19:26:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep1_20227.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep1_20227.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 53 reads. The genome is segmented into 2598 regions for analysis. Original read count stats: _IP Bases: 450144 HitCounts: 716172.0 Running with 1 threads ... ============================================== 2025-02-21 19:26:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep2_20228.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep2_20228.PE.a.GPS ============================================== 2025-02-21 19:26:01 Original read count stats: _IP Bases: 486233 HitCounts: 782198.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_HS_i5006_DY330_rep1_19786.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_HS_i5006_DY330_rep1_19786.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 73 reads. Original read count stats: _IP Bases: 680597 HitCounts: 1187656.0 The genome is segmented into 7810 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 79 reads. Running with 1 threads ... ============================================== 2025-02-21 19:26:02 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep2_20232.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep2_20232.PE.a.GPS ============================================== 2025-02-21 19:26:02 Original read count stats: _IP Bases: 187281 HitCounts: 492290.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 110 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep2_20240.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep2_20240.PE.a.GPS The genome is segmented into 7949 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 287469 HitCounts: 970416.0 The genome is segmented into 8002 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 58 reads. The genome is segmented into 2987 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 97 reads. The genome is segmented into 6968 regions for analysis. ============================================== 2025-02-21 19:26:04 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep1_19790.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep1_19790.PE.a.GPS ============================================== 2025-02-21 19:26:04 Original read count stats: _IP Bases: 414702 HitCounts: 1247126.0 ============================================== 2025-02-21 19:26:04 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_HS_i5006_DY330_rep1_17259.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_HS_i5006_DY330_rep1_17259.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_HS_i5006_DY330_rep2_20238.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_HS_i5006_DY330_rep2_20238.PE.a.GPS Original read count stats: _IP Bases: 301403 HitCounts: 1442792.0 Original read count stats: _IP Bases: 1482498 HitCounts: 3175842.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 123 reads. The genome is segmented into 8207 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 134 reads. Running with 1 threads ... The genome is segmented into 6477 regions for analysis. ============================================== 2025-02-21 19:26:06 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_MHS_i5006_DY330_rep1_19780.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_MHS_i5006_DY330_rep1_19780.PE.a.GPS ============================================== 2025-02-21 19:26:06 ============================================== 2025-02-21 19:26:06 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep1_19784.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep1_19784.PE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep3_21307.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep3_21307.PE.a.GPS Original read count stats: _IP Bases: 388073 HitCounts: 1854138.0 Original read count stats: _IP Bases: 1021168 HitCounts: 1945622.0 Original read count stats: _IP Bases: 623692 HitCounts: 1704348.0 ============================================== 2025-02-21 19:26:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep3_21327.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep3_21327.PE.a.GPS ============================================== 2025-02-21 19:26:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep3_21322.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep3_21322.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 263 reads. Original read count stats: _IP Bases: 1021653 HitCounts: 1824548.0 Original read count stats: _IP Bases: 917436 HitCounts: 3371698.0 ============================================== 2025-02-21 19:26:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep2_20220.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep2_20220.PE.a.GPS ============================================== 2025-02-21 19:26:08 At Poisson p-value 1.0e-03, in a 301bp window, expect 169 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep1_20223.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep1_20223.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 168 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 163 reads. Original read count stats: _IP Bases: 1391608 HitCounts: 3633854.0 The genome is segmented into 7900 regions for analysis. Original read count stats: The genome is segmented into 7932 regions for analysis. _IP Bases: 519606 HitCounts: 3452990.0 Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 166 reads. The genome is segmented into 7953 regions for analysis. ============================================== 2025-02-21 19:26:09 The genome is segmented into 8245 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep3_21320.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep3_21320.PE.a.GPS Running with 1 threads ... ============================================== 2025-02-21 19:26:09 The genome is segmented into 8028 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep2_20236.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep2_20236.PE.a.GPS ============================================== 2025-02-21 19:26:09 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep1_20219.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep1_20219.PE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 1097330 HitCounts: 2214232.0 Original read count stats: _IP Bases: 703762 HitCounts: 4072330.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 285 reads. Original read count stats: _IP Bases: 1571309 HitCounts: 4200526.0 ============================================== 2025-02-21 19:26:10 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep4_21324.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep4_21324.PE.a.GPS ============================================== 2025-02-21 19:26:10 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep3_21323.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep3_21323.PE.a.GPS ============================================== 2025-02-21 19:26:10 The genome is segmented into 8216 regions for analysis. Original read count stats: _IP Bases: 1066920 HitCounts: 3988016.0 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep3_21315.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep3_21315.PE.a.GPS Original read count stats: _IP Bases: 1167065 HitCounts: 3961472.0 Original read count stats: _IP Bases: 695937 HitCounts: 5080032.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 295 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 294 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 195 reads. The genome is segmented into 6866 regions for analysis. Running with 1 threads ... The genome is segmented into 8019 regions for analysis. The genome is segmented into 7947 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-21 19:26:12 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep2_20224.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep2_20224.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 344 reads. Original read count stats: _IP Bases: 682268 HitCounts: 5004434.0 ============================================== 2025-02-21 19:26:13 The genome is segmented into 8096 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep1_17260.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep1_17260.PE.a.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 339 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 341 reads. Original read count stats: _IP Bases: 777235 HitCounts: 5673978.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 338 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 415 reads. The genome is segmented into 8137 regions for analysis. Running with 1 threads ... The genome is segmented into 8098 regions for analysis. Running with 1 threads ... The genome is segmented into 8237 regions for analysis. Running with 1 threads ... The genome is segmented into 7939 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:26:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep3_21299.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep3_21299.PE.a.GPS ============================================== 2025-02-21 19:26:16 Original read count stats: _IP Bases: 1339830 HitCounts: 7080250.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 415 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_MHS_i5006_DY330_rep1_20234.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_MHS_i5006_DY330_rep1_20234.PE.a.GPS The genome is segmented into 7611 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2515859 HitCounts: 7378876.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 450 reads. The genome is segmented into 8176 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:26:20 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep2_17275.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep2_17275.PE.a.GPS Original read count stats: _IP Bases: 904153 HitCounts: 8851466.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 582 reads. The genome is segmented into 7980 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 551 reads. The genome is segmented into 7815 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 660 reads. The genome is segmented into 8196 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 18 Filtered: 7 Finish binding event prediction: 42.0s Running with 1 threads ... ============================================== 2025-02-21 19:26:42 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep1_17252.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep1_17252.PE.a.GPS Original read count stats: _IP Bases: 1811030 HitCounts: 1.7383904E7 --------------------------- Events discovered Significant: 2 Insignificant: 3 Filtered: 1 Finish binding event prediction: 45.1s Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 1327 reads. The genome is segmented into 8076 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:27:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_MHS_i5006_DY330_rep1_17251.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_MHS_i5006_DY330_rep1_17251.PE.a.GPS Original read count stats: _IP Bases: 3557248 HitCounts: 2.4581446E7 --------------------------- Events discovered Significant: 340 Insignificant: 0 Filtered: 106 Finish binding event prediction: 1.2m Refine read distribution from 247 binding events. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 1900 reads. The genome is segmented into 7989 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 18 Filtered: 7 Finish binding event prediction: 49.0s --------------------------- Events discovered Significant: 2 Insignificant: 3 Filtered: 1 Finish binding event prediction: 47.0s --------------------------- Events discovered Significant: 52 Insignificant: 79 Filtered: 16 Finish binding event prediction: 1.8m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1520 Insignificant: 394 Filtered: 3 Finish binding event prediction: 54.2s Refine read distribution from 1181 binding events. --------------------------- Events discovered Significant: 61 Insignificant: 66 Filtered: 22 Finish binding event prediction: 2.1m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 54 Insignificant: 55 Filtered: 14 Finish binding event prediction: 2.0m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 60 Insignificant: 69 Filtered: 22 Finish binding event prediction: 2.2m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 47 Insignificant: 68 Filtered: 14 Finish binding event prediction: 2.2m Refine read distribution from 5 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 88 Insignificant: 1 Filtered: 29 Finish binding event prediction: 2.3m Refine read distribution from 64 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 28 Insignificant: 58 Filtered: 18 Finish binding event prediction: 2.4m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 372 Insignificant: 0 Filtered: 120 Finish binding event prediction: 2.3m Refine read distribution from 228 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 78 Insignificant: 39 Filtered: 18 Finish binding event prediction: 2.4m Refine read distribution from 5 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 51 Insignificant: 83 Filtered: 17 Finish binding event prediction: 2.4m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 64 Insignificant: 52 Filtered: 12 Finish binding event prediction: 2.4m Refine read distribution from 3 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 207 Insignificant: 0 Filtered: 69 Finish binding event prediction: 2.4m Refine read distribution from 55 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 22 Insignificant: 55 Filtered: 11 Finish binding event prediction: 1.9m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 212 Insignificant: 0 Filtered: 70 Finish binding event prediction: 2.7m Refine read distribution from 64 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 284 Insignificant: 0 Filtered: 93 Finish binding event prediction: 2.7m Refine read distribution from 179 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 10 Insignificant: 51 Filtered: 16 Finish binding event prediction: 2.7m Refine read distribution from 4 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 270 Insignificant: 0 Filtered: 82 Finish binding event prediction: 3.0m Refine read distribution from 81 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 57 Insignificant: 67 Filtered: 19 Finish binding event prediction: 3.1m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 237 Insignificant: 0 Filtered: 76 Finish binding event prediction: 3.1m Refine read distribution from 77 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 78 Insignificant: 69 Filtered: 17 Finish binding event prediction: 3.2m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 144 Insignificant: 61 Filtered: 6 Finish binding event prediction: 1.4m Refine read distribution from 87 binding events. --------------------------- Events discovered Significant: 34 Insignificant: 62 Filtered: 14 Finish binding event prediction: 3.3m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 81 Insignificant: 83 Filtered: 20 Finish binding event prediction: 3.1m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 134 Insignificant: 51 Filtered: 3 Finish binding event prediction: 1.3m Refine read distribution from 95 binding events. --------------------------- Events discovered Significant: 1415 Insignificant: 387 Filtered: 6 Finish binding event prediction: 1.5m Refine read distribution from 1133 binding events. --------------------------- Events discovered Significant: 105 Insignificant: 100 Filtered: 14 Finish binding event prediction: 3.7m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 311 Insignificant: 0 Filtered: 95 Finish binding event prediction: 3.9m Refine read distribution from 257 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 57 Insignificant: 41 Filtered: 16 Finish binding event prediction: 3.8m Refine read distribution from 18 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 147 Insignificant: 48 Filtered: 2 Finish binding event prediction: 1.8m Refine read distribution from 123 binding events. --------------------------- Events discovered Significant: 63 Insignificant: 44 Filtered: 1 Finish binding event prediction: 1.2m Refine read distribution from 29 binding events. --------------------------- Events discovered Significant: 126 Insignificant: 40 Filtered: 0 Finish binding event prediction: 1.2m Refine read distribution from 107 binding events. --------------------------- Events discovered Significant: 124 Insignificant: 62 Filtered: 4 Finish binding event prediction: 53.1s Refine read distribution from 68 binding events. --------------------------- Events discovered Significant: 169 Insignificant: 69 Filtered: 3 Finish binding event prediction: 1.7m --------------------------- Events discovered Significant: 139 Insignificant: 48 Filtered: 4 Finish binding event prediction: 2.0m Refine read distribution from 92 binding events. Refine read distribution from 128 binding events. --------------------------- Events discovered Significant: 116 Insignificant: 40 Filtered: 3 Finish binding event prediction: 1.2m Refine read distribution from 61 binding events. --------------------------- Events discovered Significant: 201 Insignificant: 71 Filtered: 3 Finish binding event prediction: 1.9m Refine read distribution from 157 binding events. --------------------------- Events discovered Significant: 1566 Insignificant: 523 Filtered: 1 Finish binding event prediction: 1.5m Refine read distribution from 1203 binding events. --------------------------- Events discovered Significant: 1374 Insignificant: 408 Filtered: 1 Finish binding event prediction: 1.3m Refine read distribution from 1066 binding events. --------------------------- Events discovered Significant: 157 Insignificant: 41 Filtered: 1 Finish binding event prediction: 1.6m Refine read distribution from 132 binding events. --------------------------- Events discovered Significant: 142 Insignificant: 51 Filtered: 2 Finish binding event prediction: 2.2m Refine read distribution from 113 binding events. --------------------------- Events discovered Significant: 1488 Insignificant: 471 Filtered: 1 Finish binding event prediction: 1.2m Refine read distribution from 1159 binding events. --------------------------- Events discovered Significant: 1573 Insignificant: 439 Filtered: 2 Finish binding event prediction: 1.6m Refine read distribution from 1210 binding events. --------------------------- Events discovered Significant: 42 Insignificant: 75 Filtered: 13 Finish binding event prediction: 3.2m Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 106 Insignificant: 101 Filtered: 17 Finish binding event prediction: 4.6m Refine read distribution from 18 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 143 Insignificant: 61 Filtered: 6 Finish binding event prediction: 2.2m Refine read distribution from 87 binding events. --------------------------- Events discovered Significant: 1489 Insignificant: 372 Filtered: 1 Finish binding event prediction: 55.2s Refine read distribution from 1150 binding events. --------------------------- Events discovered Significant: 130 Insignificant: 41 Filtered: 2 Finish binding event prediction: 1.5m Refine read distribution from 91 binding events. --------------------------- Events discovered Significant: 1709 Insignificant: 451 Filtered: 2 Finish binding event prediction: 2.6m Refine read distribution from 1280 binding events. --------------------------- Events discovered Significant: 242 Insignificant: 66 Filtered: 2 Finish binding event prediction: 1.2m Refine read distribution from 202 binding events. --------------------------- Events discovered Significant: 1564 Insignificant: 488 Filtered: 0 Finish binding event prediction: 2.8m Refine read distribution from 1195 binding events. --------------------------- Events discovered Significant: 174 Insignificant: 62 Filtered: 2 Finish binding event prediction: 2.1m Refine read distribution from 149 binding events. --------------------------- Events discovered Significant: 394 Insignificant: 0 Filtered: 130 Finish binding event prediction: 5.5m Refine read distribution from 232 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 106 Insignificant: 47 Filtered: 0 Finish binding event prediction: 1.3m Refine read distribution from 65 binding events. --------------------------- Events discovered Significant: 146 Insignificant: 69 Filtered: 4 Finish binding event prediction: 2.2m Refine read distribution from 120 binding events. --------------------------- Events discovered Significant: 154 Insignificant: 62 Filtered: 2 Finish binding event prediction: 2.2m Refine read distribution from 114 binding events. --------------------------- Events discovered Significant: 1749 Insignificant: 495 Filtered: 2 Finish binding event prediction: 3.6m Refine read distribution from 1297 binding events. ============================================== 2025-02-21 19:38:26 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_HS_i5006_DY330_rep2_20230.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_HS_i5006_DY330_rep2_20230.PE.a.GPS ============================================== 2025-02-21 19:38:27 Original read count stats: _IP Bases: 73661 HitCounts: 105598.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_HS_i5006_DY330_rep1_20229.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_HS_i5006_DY330_rep1_20229.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 17 reads. Original read count stats: _IP Bases: 72614 HitCounts: 103874.0 The genome is segmented into 4828 regions for analysis. ============================================== 2025-02-21 19:38:27 At Poisson p-value 1.0e-03, in a 301bp window, expect 16 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep4_21314.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep4_21314.PE.a.GPS The genome is segmented into 4929 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 124241 HitCounts: 186962.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 24 reads. The genome is segmented into 7546 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:38:29 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep2_17280.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep2_17280.PE.a.GPS Original read count stats: _IP Bases: 183440 HitCounts: 512120.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 44 reads. ============================================== 2025-02-21 19:38:29 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_MHS_i5006_DY330_rep2_20222.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_MHS_i5006_DY330_rep2_20222.PE.a.GPS The genome is segmented into 7670 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 258949 HitCounts: 448002.0 ============================================== 2025-02-21 19:38:30 At Poisson p-value 1.0e-03, in a 301bp window, expect 48 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep3_21313.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep3_21313.PE.a.GPS The genome is segmented into 8358 regions for analysis. Original read count stats: _IP Bases: 418150 HitCounts: 822736.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 78 reads. ============================================== 2025-02-21 19:38:31 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_MHS_i5006_DY330_rep1_20221.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_MHS_i5006_DY330_rep1_20221.PE.a.GPS Original read count stats: _IP Bases: 523824 HitCounts: 1061760.0 The genome is segmented into 8323 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:38:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep1_17265.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep1_17265.PE.a.GPS ============================================== 2025-02-21 19:38:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep2_17273.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep2_17273.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 97 reads. Original read count stats: _IP Bases: 533796 HitCounts: 1234136.0 Original read count stats: _IP Bases: 441474 HitCounts: 1310132.0 The genome is segmented into 8202 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:38:33 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_HS_i5006_DY330_rep1_17261.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_HS_i5006_DY330_rep1_17261.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 102 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 85 reads. Original read count stats: _IP Bases: 475505 HitCounts: 1459048.0 The genome is segmented into 8234 regions for analysis. Running with 1 threads ... The genome is segmented into 8246 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 127 reads. The genome is segmented into 8156 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:38:35 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep4_21306.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep4_21306.PE.a.GPS Original read count stats: _IP Bases: 968615 HitCounts: 1962960.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 179 reads. ============================================== 2025-02-21 19:38:37 The genome is segmented into 8140 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep1_17257.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep1_17257.PE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 1473988 HitCounts: 3836664.0 ============================================== 2025-02-21 19:38:39 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep3_21305.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep3_21305.PE.a.GPS Original read count stats: _IP Bases: 1162993 HitCounts: 2525756.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 304 reads. The genome is segmented into 8079 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 234 reads. ============================================== 2025-02-21 19:38:42 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_MHS_i5006_DY330_rep1_17253.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_MHS_i5006_DY330_rep1_17253.PE.a.GPS ============================================== 2025-02-21 19:38:42 The genome is segmented into 8101 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_MHS_i5006_DY330_rep2_17269.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_MHS_i5006_DY330_rep2_17269.PE.a.GPS Running with 1 threads ... ============================================== 2025-02-21 19:38:42 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoB_2.1x36mers.unique.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoB_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1501990 HitCounts: 5804828.0 ============================================== 2025-02-21 19:38:43 Original read count stats: _IP Bases: 1137507 HitCounts: 6443714.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoB_2.SE.a.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoB_2.SE.a.GPS Original read count stats: _IP Bases: 1618403 HitCounts: 4739985.0 Original read count stats: _IP Bases: 1622652 HitCounts: 5166553.0 ============================================== 2025-02-21 19:38:44 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoB_1.1x36mers.unique.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoB_1.1x36mers.unique.GPS ============================================== 2025-02-21 19:38:44 ============================================== 2025-02-21 19:38:44 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoB_1.SE.a.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoB_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep3_21316.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep3_21316.PE.a.GPS Original read count stats: _IP Bases: 1673120 HitCounts: 5250822.0 Original read count stats: _IP Bases: 1675720 HitCounts: 5701076.0 Original read count stats: _IP Bases: 800568 HitCounts: 7178086.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 445 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 351 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 452 reads. ============================================== 2025-02-21 19:38:46 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep4_21317.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep4_21317.PE.a.GPS The genome is segmented into 7992 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 365 reads. Original read count stats: _IP Bases: 736179 HitCounts: 8122668.0 Running with 1 threads ... The genome is segmented into 8510 regions for analysis. Running with 1 threads ... The genome is segmented into 8097 regions for analysis. The genome is segmented into 8688 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 382 reads. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 395 reads. The genome is segmented into 8652 regions for analysis. Running with 1 threads ... The genome is segmented into 8480 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 566 reads. The genome is segmented into 8212 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 620 reads. The genome is segmented into 8146 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:39:08 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoD_1.1x36mers.unique.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoD_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 941384 HitCounts: 1.5762234E7 --------------------------- Events discovered Significant: 134 Insignificant: 0 Filtered: 7 Finish binding event prediction: 46.1s Refine read distribution from 27 binding events. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 632 reads. The genome is segmented into 8589 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:39:18 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoD_1.SE.a.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoD_1.SE.a.GPS Original read count stats: _IP Bases: 1034491 HitCounts: 1.9330964E7 ============================================== 2025-02-21 19:39:23 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep2_17268.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep2_17268.PE.a.GPS Original read count stats: _IP Bases: 1762347 HitCounts: 2.4228782E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 848 reads. The genome is segmented into 8774 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 82 Insignificant: 2 Filtered: 16 Finish binding event prediction: 1.1m Refine read distribution from 19 binding events. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 1746 reads. The genome is segmented into 8176 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 141 Insignificant: 3 Filtered: 7 Finish binding event prediction: 1.2m Refine read distribution from 24 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 104 Insignificant: 22 Filtered: 5 Finish binding event prediction: 16.4s Refine read distribution from 85 binding events. --------------------------- Events discovered Significant: 138 Insignificant: 28 Filtered: 4 Finish binding event prediction: 59.0s Refine read distribution from 127 binding events. --------------------------- Events discovered Significant: 130 Insignificant: 55 Filtered: 31 Finish binding event prediction: 1.9m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 142 Insignificant: 37 Filtered: 3 Finish binding event prediction: 54.1s Refine read distribution from 131 binding events. --------------------------- Events discovered Significant: 82 Insignificant: 24 Filtered: 21 Finish binding event prediction: 2.0m Refine read distribution from 18 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 532 Insignificant: 22 Filtered: 85 Finish binding event prediction: 2.0m Refine read distribution from 174 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 27 Insignificant: 41 Filtered: 8 Finish binding event prediction: 2.3m Refine read distribution from 17 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 190 Insignificant: 1 Filtered: 37 Finish binding event prediction: 2.5m Refine read distribution from 38 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 152 Insignificant: 25 Filtered: 34 Finish binding event prediction: 2.5m Refine read distribution from 24 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 70 Insignificant: 65 Filtered: 15 Finish binding event prediction: 2.3m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 22 Insignificant: 29 Filtered: 6 Finish binding event prediction: 2.6m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 115 Insignificant: 40 Filtered: 23 Finish binding event prediction: 2.8m Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 76 Insignificant: 21 Filtered: 30 Finish binding event prediction: 2.2m Refine read distribution from 27 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 102 Insignificant: 100 Filtered: 25 Finish binding event prediction: 2.0m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 137 Insignificant: 29 Filtered: 3 Finish binding event prediction: 36.1s Refine read distribution from 102 binding events. --------------------------- Events discovered Significant: 163 Insignificant: 47 Filtered: 3 Finish binding event prediction: 1.1m Refine read distribution from 121 binding events. --------------------------- Events discovered Significant: 90 Insignificant: 81 Filtered: 19 Finish binding event prediction: 2.9m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 81 Insignificant: 25 Filtered: 25 Finish binding event prediction: 3.1m Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 168 Insignificant: 27 Filtered: 3 Finish binding event prediction: 1.4m Refine read distribution from 108 binding events. --------------------------- Events discovered Significant: 176 Insignificant: 0 Filtered: 58 Finish binding event prediction: 3.0m Refine read distribution from 143 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 113 Insignificant: 32 Filtered: 1 Finish binding event prediction: 43.1s Refine read distribution from 88 binding events. --------------------------- Events discovered Significant: 264 Insignificant: 58 Filtered: 1 Finish binding event prediction: 47.1s Refine read distribution from 210 binding events. --------------------------- Events discovered Significant: 117 Insignificant: 47 Filtered: 3 Finish binding event prediction: 1.0m Refine read distribution from 66 binding events. --------------------------- Events discovered Significant: 230 Insignificant: 43 Filtered: 18 Finish binding event prediction: 1.3m Refine read distribution from 218 binding events. --------------------------- Events discovered Significant: 691 Insignificant: 176 Filtered: 11 Finish binding event prediction: 1.7m Refine read distribution from 551 binding events. --------------------------- Events discovered Significant: 166 Insignificant: 0 Filtered: 52 Finish binding event prediction: 3.6m Refine read distribution from 145 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 186 Insignificant: 27 Filtered: 4 Finish binding event prediction: 1.6m Refine read distribution from 140 binding events. --------------------------- Events discovered Significant: 144 Insignificant: 71 Filtered: 2 Finish binding event prediction: 1.0m Refine read distribution from 112 binding events. --------------------------- Events discovered Significant: 172 Insignificant: 0 Filtered: 57 Finish binding event prediction: 4.0m --------------------------- Events discovered Significant: 151 Insignificant: 26 Filtered: 0 Finish binding event prediction: 1.0m Refine read distribution from 147 binding events. Refine read distribution from 124 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 234 Insignificant: 11 Filtered: 44 Finish binding event prediction: 4.3m Refine read distribution from 49 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 130 Insignificant: 110 Filtered: 8 Finish binding event prediction: 1.6m Refine read distribution from 99 binding events. --------------------------- Events discovered Significant: 208 Insignificant: 69 Filtered: 2 Finish binding event prediction: 1.8m Refine read distribution from 166 binding events. --------------------------- Events discovered Significant: 612 Insignificant: 2 Filtered: 120 Finish binding event prediction: 4.7m Refine read distribution from 165 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 746 Insignificant: 1 Filtered: 169 Finish binding event prediction: 4.7m Refine read distribution from 188 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 102 Insignificant: 11 Filtered: 36 Finish binding event prediction: 4.2m Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 163 Insignificant: 1 Filtered: 53 Finish binding event prediction: 5.2m Refine read distribution from 134 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1373 Insignificant: 212 Filtered: 5 Finish binding event prediction: 2.3m Refine read distribution from 967 binding events. --------------------------- Events discovered Significant: 285 Insignificant: 99 Filtered: 6 Finish binding event prediction: 1.5m Refine read distribution from 242 binding events. --------------------------- Events discovered Significant: 824 Insignificant: 211 Filtered: 6 Finish binding event prediction: 1.7m Refine read distribution from 655 binding events. --------------------------- Events discovered Significant: 959 Insignificant: 256 Filtered: 4 Finish binding event prediction: 1.8m Refine read distribution from 744 binding events. --------------------------- Events discovered Significant: 1299 Insignificant: 217 Filtered: 8 Finish binding event prediction: 3.9m Refine read distribution from 954 binding events. ============================================== 2025-02-21 19:46:29 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_2.SE.a.GPS Original read count stats: _IP Bases: 598377 HitCounts: 707006.0 ============================================== 2025-02-21 19:46:30 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 75 reads. Original read count stats: _IP Bases: 571035 HitCounts: 657365.0 The genome is segmented into 8454 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 70 reads. The genome is segmented into 8246 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:46:35 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 2165662 HitCounts: 3119754.0 ============================================== 2025-02-21 19:46:36 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_1.SE.a.GPS Original read count stats: _IP Bases: 2185373 HitCounts: 3383306.0 ============================================== 2025-02-21 19:46:37 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_2.1x36mers.unique.GPS ============================================== 2025-02-21 19:46:37 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_HS_i5006_DY330_rep2_17276.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_HS_i5006_DY330_rep2_17276.PE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 279 reads. ============================================== 2025-02-21 19:46:38 ============================================== 2025-02-21 19:46:38 Original read count stats: _IP Bases: 570062 HitCounts: 2725132.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1755383 HitCounts: 4080521.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_1.1x36mers.unique.GPS The genome is segmented into 8011 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:46:38 ============================================== 2025-02-21 19:46:38 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1483852 HitCounts: 4703384.0 Original read count stats: _IP Bases: 1953345 HitCounts: 4389034.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 296 reads. Original read count stats: _IP Bases: 1900893 HitCounts: 4263208.0 ============================================== 2025-02-21 19:46:39 ============================================== 2025-02-21 19:46:39 Original read count stats: _IP Bases: 1767394 HitCounts: 4123733.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 202 reads. ============================================== 2025-02-21 19:46:39 The genome is segmented into 8172 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_1.1x36mers.unique.GPS Running with 1 threads ... ============================================== 2025-02-21 19:46:40 The genome is segmented into 8211 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1810502 HitCounts: 2466644.0 Original read count stats: _IP Bases: 1585789 HitCounts: 5415469.0 Running with 1 threads ... Original read count stats: _IP Bases: 1821232 HitCounts: 2505475.0 Original read count stats: _IP Bases: 1607573 HitCounts: 5320582.0 ============================================== 2025-02-21 19:46:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 339 reads. ============================================== 2025-02-21 19:46:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_1.SE.a.GPS Original read count stats: _IP Bases: 1850186 HitCounts: 2695555.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 226 reads. The genome is segmented into 8296 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:46:42 ============================================== 2025-02-21 19:46:42 At Poisson p-value 1.0e-03, in a 301bp window, expect 225 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 362 reads. Original read count stats: _IP Bases: 1907600 HitCounts: 6308264.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 372 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 361 reads. ============================================== 2025-02-21 19:46:42 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 342 reads. ============================================== 2025-02-21 19:46:42 The genome is segmented into 8048 regions for analysis. ============================================== 2025-02-21 19:46:42 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_2.1x36mers.unique.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_2.SE.a.GPS Original read count stats: _IP Bases: 1715285 HitCounts: 6130646.0 Original read count stats: _IP Bases: 1895202 HitCounts: 6225039.0 The genome is segmented into 8346 regions for analysis. Running with 1 threads ... The genome is segmented into 8014 regions for analysis. The genome is segmented into 8168 regions for analysis. Original read count stats: Running with 1 threads ... _IP Bases: 1763292 HitCounts: 5674213.0 Running with 1 threads ... Original read count stats: _IP Bases: 1709225 HitCounts: 5435299.0 Original read count stats: _IP Bases: 1835925 HitCounts: 2673012.0 ============================================== 2025-02-21 19:46:43 At Poisson p-value 1.0e-03, in a 301bp window, expect 238 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_1.SE.a.GPS The genome is segmented into 8376 regions for analysis. The genome is segmented into 8288 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 405 reads. The genome is segmented into 8226 regions for analysis. Original read count stats: _IP Bases: 1771946 HitCounts: 6222577.0 ============================================== 2025-02-21 19:46:44 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 403 reads. Original read count stats: _IP Bases: 1717195 HitCounts: 5955316.0 The genome is segmented into 8176 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 239 reads. Running with 1 threads ... The genome is segmented into 8352 regions for analysis. Running with 1 threads ... The genome is segmented into 8183 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 435 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 490 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 418 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 485 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 452 reads. The genome is segmented into 8458 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 456 reads. The genome is segmented into 8357 regions for analysis. Running with 1 threads ... The genome is segmented into 8307 regions for analysis. Running with 1 threads ... The genome is segmented into 8292 regions for analysis. The genome is segmented into 8483 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8473 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 438 reads. The genome is segmented into 8480 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:46:51 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_2.SE.a.GPS ============================================== 2025-02-21 19:46:51 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_1.SE.a.GPS Original read count stats: _IP Bases: 1936530 HitCounts: 1.0173744E7 Original read count stats: _IP Bases: 1986820 HitCounts: 1.0355888E7 --------------------------- Events discovered Significant: 689 Insignificant: 72 Filtered: 25 Finish binding event prediction: 3.3m Refine read distribution from 232 binding events. At Poisson p-value 1.0e-03, in a 301bp window, expect 713 reads. The genome is segmented into 8488 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 724 reads. Running with 1 threads ... The genome is segmented into 8549 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:47:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoD_2.1x36mers.unique.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoD_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 919518 HitCounts: 1.511547E7 --------------------------- Events discovered Significant: 1341 Insignificant: 200 Filtered: 10 Finish binding event prediction: 4.3m Refine read distribution from 959 binding events. At Poisson p-value 1.0e-03, in a 301bp window, expect 609 reads. The genome is segmented into 8592 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 1332 Insignificant: 224 Filtered: 8 Finish binding event prediction: 3.2m Refine read distribution from 962 binding events. ============================================== 2025-02-21 19:47:11 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoD_2.SE.a.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoD_2.SE.a.GPS Original read count stats: _IP Bases: 1007508 HitCounts: 1.810954E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 800 reads. The genome is segmented into 8789 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 18 Insignificant: 0 Filtered: 5 Finish binding event prediction: 1.7m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 18 Insignificant: 0 Filtered: 5 Finish binding event prediction: 1.9m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 34 Insignificant: 0 Filtered: 0 Finish binding event prediction: 18.1s Refine read distribution from 30 binding events. --------------------------- Events discovered Significant: 37 Insignificant: 0 Filtered: 0 Finish binding event prediction: 19.1s Refine read distribution from 33 binding events. --------------------------- Events discovered Significant: 322 Insignificant: 0 Filtered: 100 Finish binding event prediction: 2.7m Refine read distribution from 249 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 329 Insignificant: 0 Filtered: 107 Finish binding event prediction: 2.8m Refine read distribution from 265 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 79 Insignificant: 17 Filtered: 31 Finish binding event prediction: 2.9m Refine read distribution from 34 binding events. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 13 Insignificant: 0 Filtered: 4 Finish binding event prediction: 3.5m Refine read distribution from 6 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 102 Insignificant: 63 Filtered: 23 Finish binding event prediction: 3.4m Refine read distribution from 24 binding events. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 103 Insignificant: 53 Filtered: 15 Finish binding event prediction: 3.5m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 527 Insignificant: 0 Filtered: 164 Finish binding event prediction: 3.8m Refine read distribution from 400 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 12 Insignificant: 0 Filtered: 3 Finish binding event prediction: 3.9m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 115 Insignificant: 27 Filtered: 31 Finish binding event prediction: 3.8m Refine read distribution from 45 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 123 Insignificant: 3 Filtered: 31 Finish binding event prediction: 3.9m Refine read distribution from 54 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 585 Insignificant: 16 Filtered: 102 Finish binding event prediction: 4.0m Refine read distribution from 147 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 33 Insignificant: 0 Filtered: 0 Finish binding event prediction: 30.1s Refine read distribution from 29 binding events. --------------------------- Events discovered Significant: 493 Insignificant: 0 Filtered: 149 Finish binding event prediction: 4.0m Refine read distribution from 383 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 118 Insignificant: 22 Filtered: 33 Finish binding event prediction: 4.2m Refine read distribution from 48 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 379 Insignificant: 0 Filtered: 116 Finish binding event prediction: 4.3m Refine read distribution from 285 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 182 Insignificant: 1 Filtered: 38 Finish binding event prediction: 4.4m Refine read distribution from 61 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 37 Insignificant: 0 Filtered: 0 Finish binding event prediction: 38.1s Refine read distribution from 33 binding events. --------------------------- Events discovered Significant: 131 Insignificant: 1 Filtered: 31 Finish binding event prediction: 4.5m Refine read distribution from 60 binding events. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 389 Insignificant: 0 Filtered: 126 Finish binding event prediction: 4.9m Refine read distribution from 310 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 257 Insignificant: 77 Filtered: 4 Finish binding event prediction: 1.5m Refine read distribution from 205 binding events. --------------------------- Events discovered Significant: 271 Insignificant: 66 Filtered: 5 Finish binding event prediction: 1.4m Refine read distribution from 215 binding events. --------------------------- Events discovered Significant: 101 Insignificant: 18 Filtered: 38 Finish binding event prediction: 4.7m Refine read distribution from 41 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1476 Insignificant: 296 Filtered: 10 Finish binding event prediction: 2.6m Refine read distribution from 1039 binding events. --------------------------- Events discovered Significant: 197 Insignificant: 87 Filtered: 9 Finish binding event prediction: 2.1m Refine read distribution from 124 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 189 Insignificant: 3 Filtered: 41 Finish binding event prediction: 5.6m Refine read distribution from 65 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1533 Insignificant: 276 Filtered: 13 Finish binding event prediction: 2.7m Refine read distribution from 1049 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 517 Insignificant: 84 Filtered: 0 Finish binding event prediction: 1.9m Refine read distribution from 357 binding events. --------------------------- Events discovered Significant: 517 Insignificant: 0 Filtered: 163 Finish binding event prediction: 5.8m Refine read distribution from 391 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 514 Insignificant: 0 Filtered: 157 Finish binding event prediction: 5.8m Refine read distribution from 382 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 432 Insignificant: 108 Filtered: 4 Finish binding event prediction: 2.1m Refine read distribution from 299 binding events. --------------------------- Events discovered Significant: 441 Insignificant: 64 Filtered: 3 Finish binding event prediction: 1.8m Refine read distribution from 283 binding events. --------------------------- Events discovered Significant: 733 Insignificant: 192 Filtered: 13 Finish binding event prediction: 2.4m Refine read distribution from 583 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 1489 Insignificant: 299 Filtered: 7 Finish binding event prediction: 2.3m Refine read distribution from 1048 binding events. --------------------------- Events discovered Significant: 500 Insignificant: 81 Filtered: 4 Finish binding event prediction: 2.2m Refine read distribution from 354 binding events. --------------------------- Events discovered Significant: 448 Insignificant: 100 Filtered: 5 Finish binding event prediction: 2.8m --------------------------- Events discovered Significant: 1582 Insignificant: 307 Filtered: 5 Finish binding event prediction: 3.2m Refine read distribution from 315 binding events. Refine read distribution from 1067 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 458 Insignificant: 61 Filtered: 4 Finish binding event prediction: 2.0m Refine read distribution from 278 binding events. --------------------------- Events discovered Significant: 1532 Insignificant: 319 Filtered: 4 Finish binding event prediction: 3.6m Refine read distribution from 1087 binding events. --------------------------- Events discovered Significant: 752 Insignificant: 106 Filtered: 25 Finish binding event prediction: 2.8m Refine read distribution from 301 binding events. --------------------------- Events discovered Significant: 1521 Insignificant: 310 Filtered: 13 Finish binding event prediction: 3.7m Refine read distribution from 1049 binding events. ============================================== 2025-02-21 19:55:39 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_1.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_1.SE.a.GPS ============================================== 2025-02-21 19:55:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_1.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1790554 HitCounts: 3634616.0 Original read count stats: _IP Bases: 879852 HitCounts: 2870506.0 ============================================== 2025-02-21 19:55:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_2.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 149 reads. ============================================== 2025-02-21 19:55:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_2.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1687970 HitCounts: 3324397.0 Original read count stats: _IP Bases: 1540452 HitCounts: 2276189.0 The genome is segmented into 8162 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:55:42 ============================================== 2025-02-21 19:55:42 At Poisson p-value 1.0e-03, in a 301bp window, expect 307 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_1.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_1.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_1.SE.a.GPS The genome is segmented into 8273 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1038960 HitCounts: 3517299.0 Original read count stats: _IP Bases: 1642500 HitCounts: 2492751.0 ============================================== 2025-02-21 19:55:43 ============================================== 2025-02-21 19:55:43 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 04-E.coli-ArgR-GSE60546/ArgR_arg_rep1.1x36mers.unique.bam --out 04-E.coli-ArgR-GSE60546/ArgR_arg_rep1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 04-E.coli-ArgR-GSE60546/ArgR_arg_rep2.1x36mers.unique.bam --out 04-E.coli-ArgR-GSE60546/ArgR_arg_rep2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 202 reads. Original read count stats: _IP Bases: 241009 HitCounts: 5702723.0 Original read count stats: _IP Bases: 554728 HitCounts: 6069441.0 ============================================== 2025-02-21 19:55:43 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 286 reads. ============================================== 2025-02-21 19:55:44 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_2.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_2.SE.a.GPS ============================================== 2025-02-21 19:55:44 Original read count stats: _IP Bases: 403577 HitCounts: 1956914.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 04-E.coli-ArgR-GSE60546/ArgR_arg_rep2.SE.a.bam --out 04-E.coli-ArgR-GSE60546/ArgR_arg_rep2.SE.a.GPS The genome is segmented into 8257 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 219 reads. Original read count stats: _IP Bases: 267279 HitCounts: 6134545.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 62 reads. Original read count stats: _IP Bases: 769277 HitCounts: 3912487.0 ============================================== 2025-02-21 19:55:44 The genome is segmented into 8098 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_1.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 245 reads. The genome is segmented into 8424 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 150 reads. Original read count stats: _IP Bases: 915950 HitCounts: 2287249.0 The genome is segmented into 8298 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 229 reads. Running with 1 threads ... The genome is segmented into 8364 regions for analysis. ============================================== 2025-02-21 19:55:45 ============================================== 2025-02-21 19:55:45 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_2.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_2.SE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 04-E.coli-ArgR-GSE60546/ArgR_arg_rep1.SE.a.bam --out 04-E.coli-ArgR-GSE60546/ArgR_arg_rep1.SE.a.GPS The genome is segmented into 8192 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 163 reads. The genome is segmented into 8104 regions for analysis. Original read count stats: Running with 1 threads ... _IP Bases: 607199 HitCounts: 6606419.0 The genome is segmented into 8481 regions for analysis. Original read count stats: _IP Bases: 1256873 HitCounts: 4854615.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 220 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 153 reads. The genome is segmented into 8408 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:55:47 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_1.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_1.SE.a.GPS ============================================== 2025-02-21 19:55:47 The genome is segmented into 8223 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_2.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_2.1x36mers.unique.GPS Running with 1 threads ... ============================================== 2025-02-21 19:55:47 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_1.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1003959 HitCounts: 5736651.0 Original read count stats: _IP Bases: 1328803 HitCounts: 5194382.0 Original read count stats: _IP Bases: 1276938 HitCounts: 5447865.0 ============================================== 2025-02-21 19:55:48 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_2.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_2.SE.a.GPS ============================================== 2025-02-21 19:55:48 At Poisson p-value 1.0e-03, in a 301bp window, expect 256 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_2.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 347 reads. Original read count stats: _IP Bases: 1351825 HitCounts: 5573370.0 The genome is segmented into 8375 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1122611 HitCounts: 2513055.0 The genome is segmented into 8302 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 19:55:49 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_1.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_1.SE.a.GPS Original read count stats: _IP Bases: 1318880 HitCounts: 6071004.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 309 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 174 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 348 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 342 reads. ============================================== 2025-02-21 19:55:51 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_2.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_2.1x36mers.unique.GPS The genome is segmented into 8313 regions for analysis. Running with 1 threads ... The genome is segmented into 8338 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 658719 HitCounts: 2511341.0 The genome is segmented into 8143 regions for analysis. The genome is segmented into 8379 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 364 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 120 reads. The genome is segmented into 8580 regions for analysis. The genome is segmented into 8248 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 343 reads. The genome is segmented into 8506 regions for analysis. Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 1584 Insignificant: 292 Filtered: 6 Finish binding event prediction: 3.5m Refine read distribution from 1085 binding events. --------------------------- Events discovered Significant: 1521 Insignificant: 335 Filtered: 5 Finish binding event prediction: 3.7m Refine read distribution from 1068 binding events. --------------------------- Events discovered Significant: 33 Insignificant: 44 Filtered: 7 Finish binding event prediction: 1.7m Refine read distribution from 9 binding events. Running with 1 threads ... ============================================== 2025-02-21 19:57:43 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 06-E.coli-UvrY-GSE74810/UvrY-ChIP-exo.1x36mers.unique.bam --out 06-E.coli-UvrY-GSE74810/UvrY-ChIP-exo.1x36mers.unique.GPS Original read count stats: _IP Bases: 7535219 HitCounts: 4.4173122E7 --------------------------- Events discovered Significant: 51 Insignificant: 33 Filtered: 17 Finish binding event prediction: 2.0m Refine read distribution from 17 binding events. Running with 1 threads ... ============================================== 2025-02-21 19:57:58 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 06-E.coli-UvrY-GSE74810/UvrY-ChIP-exo.SE.a.bam --out 06-E.coli-UvrY-GSE74810/UvrY-ChIP-exo.SE.a.GPS --------------------------- Events discovered Significant: 49 Insignificant: 1 Filtered: 16 Finish binding event prediction: 2.3m Refine read distribution from 33 binding events. Running with 1 threads ... Original read count stats: _IP Bases: 7730863 HitCounts: 5.0298113E7 --------------------------- Events discovered Significant: 65 Insignificant: 2 Filtered: 20 Finish binding event prediction: 2.3m Refine read distribution from 41 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 70 Insignificant: 43 Filtered: 18 Finish binding event prediction: 2.4m Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 8 Insignificant: 20 Filtered: 5 Finish binding event prediction: 2.5m Running with 1 threads ... --------------------------- Events discovered Significant: 748 Insignificant: 3 Filtered: 67 Finish binding event prediction: 2.4m Refine read distribution from 428 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 99 Insignificant: 34 Filtered: 1 Finish binding event prediction: 41.1s Refine read distribution from 64 binding events. --------------------------- Events discovered Significant: 28 Insignificant: 44 Filtered: 5 Finish binding event prediction: 2.5m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 987 Insignificant: 9 Filtered: 152 Finish binding event prediction: 2.6m Refine read distribution from 722 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 217 Insignificant: 5 Filtered: 61 Finish binding event prediction: 2.5m Refine read distribution from 186 binding events. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 3397 reads. The genome is segmented into 8018 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 33 Insignificant: 0 Filtered: 10 Finish binding event prediction: 2.6m Refine read distribution from 24 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.7m Running with 1 threads ... --------------------------- Events discovered Significant: 132 Insignificant: 29 Filtered: 0 Finish binding event prediction: 44.1s Refine read distribution from 104 binding events. --------------------------- Events discovered Significant: 60 Insignificant: 0 Filtered: 19 Finish binding event prediction: 2.7m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 810 Insignificant: 4 Filtered: 80 Finish binding event prediction: 2.8m Refine read distribution from 450 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 140 Insignificant: 13 Filtered: 4 Finish binding event prediction: 31.1s Refine read distribution from 93 binding events. --------------------------- Events discovered Significant: 87 Insignificant: 4 Filtered: 14 Finish binding event prediction: 2.8m Refine read distribution from 31 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 14 Insignificant: 21 Filtered: 3 Finish binding event prediction: 2.9m Refine read distribution from 6 binding events. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 3789 reads. The genome is segmented into 8177 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 158 Insignificant: 47 Filtered: 0 Finish binding event prediction: 42.1s Refine read distribution from 114 binding events. --------------------------- Events discovered Significant: 150 Insignificant: 15 Filtered: 0 Finish binding event prediction: 53.1s Refine read distribution from 83 binding events. --------------------------- Events discovered Significant: 86 Insignificant: 35 Filtered: 1 Finish binding event prediction: 39.1s Refine read distribution from 48 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.4m Running with 1 threads ... --------------------------- Events discovered Significant: 120 Insignificant: 5 Filtered: 18 Finish binding event prediction: 3.3m Refine read distribution from 41 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 69 Insignificant: 9 Filtered: 9 Finish binding event prediction: 44.1s Refine read distribution from 27 binding events. --------------------------- Events discovered Significant: 154 Insignificant: 23 Filtered: 0 Finish binding event prediction: 44.1s Refine read distribution from 120 binding events. --------------------------- Events discovered Significant: 516 Insignificant: 179 Filtered: 37 Finish binding event prediction: 52.2s Refine read distribution from 370 binding events. --------------------------- Events discovered Significant: 44 Insignificant: 17 Filtered: 0 Finish binding event prediction: 46.2s Refine read distribution from 26 binding events. --------------------------- Events discovered Significant: 54 Insignificant: 0 Filtered: 17 Finish binding event prediction: 3.8m Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 496 Insignificant: 168 Filtered: 16 Finish binding event prediction: 1.6m Refine read distribution from 371 binding events. --------------------------- Events discovered Significant: 746 Insignificant: 417 Filtered: 28 Finish binding event prediction: 1.5m Refine read distribution from 584 binding events. --------------------------- Events discovered Significant: 749 Insignificant: 137 Filtered: 2 Finish binding event prediction: 1.5m Refine read distribution from 591 binding events. --------------------------- Events discovered Significant: 8 Insignificant: 20 Filtered: 5 Finish binding event prediction: 1.7m --------------------------- Events discovered Significant: 202 Insignificant: 35 Filtered: 2 Finish binding event prediction: 43.1s Refine read distribution from 145 binding events. --------------------------- Events discovered Significant: 598 Insignificant: 60 Filtered: 11 Finish binding event prediction: 1.6m Refine read distribution from 344 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.9m --------------------------- Events discovered Significant: 895 Insignificant: 21 Filtered: 188 Finish binding event prediction: 4.9m Refine read distribution from 671 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 265 Insignificant: 0 Filtered: 70 Finish binding event prediction: 5.1m Refine read distribution from 221 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 1.9m --------------------------- Events discovered Significant: 565 Insignificant: 81 Filtered: 6 Finish binding event prediction: 1.5m Refine read distribution from 324 binding events. --------------------------- Events discovered Significant: 743 Insignificant: 384 Filtered: 54 Finish binding event prediction: 59.1s Refine read distribution from 547 binding events. --------------------------- Events discovered Significant: 849 Insignificant: 96 Filtered: 2 Finish binding event prediction: 1.4m Refine read distribution from 655 binding events. No valid binding event was found. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... ============================================== 2025-02-21 20:05:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS ============================================== 2025-02-21 20:05:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS Original read count stats: _IP Bases: 1450451 HitCounts: 3253124.0 Original read count stats: _IP Bases: 1093392 HitCounts: 1955404.0 ============================================== 2025-02-21 20:05:14 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS ============================================== 2025-02-21 20:05:15 Original read count stats: _IP Bases: 170791 HitCounts: 1654337.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 150 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 28 reads. The genome is segmented into 8493 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 370472 HitCounts: 3715975.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 239 reads. ============================================== 2025-02-21 20:05:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS ============================================== 2025-02-21 20:05:15 ============================================== 2025-02-21 20:05:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS ============================================== 2025-02-21 20:05:16 ============================================== 2025-02-21 20:05:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 59 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS Original read count stats: _IP Bases: 298289 HitCounts: 2198544.0 ============================================== 2025-02-21 20:05:16 The genome is segmented into 8043 regions for analysis. Original read count stats: _IP Bases: 43126 HitCounts: 4641200.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS Running with 1 threads ... The genome is segmented into 8165 regions for analysis. The genome is segmented into 8295 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2043716 HitCounts: 2922358.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 16 reads. ============================================== 2025-02-21 20:05:16 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 48 reads. ============================================== 2025-02-21 20:05:16 The genome is segmented into 2372 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS Original read count stats: Running with 1 threads ... _IP Bases: 1209448 HitCounts: 2337412.0 Original read count stats: _IP Bases: 1815087 HitCounts: 2871295.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS The genome is segmented into 8326 regions for analysis. Original read count stats: _IP Bases: 903223 HitCounts: 2090759.0 Running with 1 threads ... Original read count stats: _IP Bases: 422303 HitCounts: 4330588.0 ============================================== 2025-02-21 20:05:17 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS Original read count stats: _IP Bases: 1973635 HitCounts: 3023774.0 ============================================== 2025-02-21 20:05:17 Original read count stats: _IP Bases: 337150 HitCounts: 2529783.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 77 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 128 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 180 reads. ============================================== 2025-02-21 20:05:18 At Poisson p-value 1.0e-03, in a 301bp window, expect 58 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc.SE.a.GPS The genome is segmented into 8463 regions for analysis. Original read count stats: _IP Bases: 2118413 HitCounts: 3492695.0 Running with 1 threads ... ============================================== 2025-02-21 20:05:18 The genome is segmented into 8494 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc.1x36mers.unique.GPS Original read count stats: _IP Bases: 492080 HitCounts: 3161780.0 The genome is segmented into 8205 regions for analysis. ============================================== 2025-02-21 20:05:18 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS Running with 1 threads ... ============================================== 2025-02-21 20:05:18 At Poisson p-value 1.0e-03, in a 301bp window, expect 252 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 268 reads. Original read count stats: _IP Bases: 49864 HitCounts: 3196328.0 The genome is segmented into 8102 regions for analysis. ============================================== 2025-02-21 20:05:18 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 15 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS The genome is segmented into 4937 regions for analysis. Original read count stats: _IP Bases: 1006893 HitCounts: 2500403.0 Running with 1 threads ... Original read count stats: _IP Bases: 201974 HitCounts: 2111315.0 Original read count stats: _IP Bases: 251784 HitCounts: 2038834.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 265 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 146 reads. ============================================== 2025-02-21 20:05:19 The genome is segmented into 8134 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 44 reads. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS ============================================== 2025-02-21 20:05:19 At Poisson p-value 1.0e-03, in a 301bp window, expect 44 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS The genome is segmented into 8103 regions for analysis. The genome is segmented into 8692 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 96119 HitCounts: 4944494.0 The genome is segmented into 8619 regions for analysis. Running with 1 threads ... The genome is segmented into 8456 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 18 reads. Original read count stats: _IP Bases: 108011 HitCounts: 4093880.0 The genome is segmented into 7978 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 20 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 159 reads. Running with 1 threads ... The genome is segmented into 8116 regions for analysis. Running with 1 threads ... The genome is segmented into 8270 regions for analysis. Running with 1 threads ... The genome is segmented into 8262 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 302 reads. Running with 1 threads ... The genome is segmented into 8137 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:05:21 ============================================== 2025-02-21 20:05:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS Original read count stats: _IP Bases: 59012 HitCounts: 3767043.0 ============================================== 2025-02-21 20:05:21 Original read count stats: _IP Bases: 414734 HitCounts: 2588211.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 17 reads. The genome is segmented into 4607 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 64 reads. Original read count stats: _IP Bases: 131208 HitCounts: 5110059.0 ============================================== 2025-02-21 20:05:22 The genome is segmented into 8282 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS ============================================== 2025-02-21 20:05:22 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 31 reads. The genome is segmented into 8298 regions for analysis. Original read count stats: _IP Bases: 35696 HitCounts: 3927513.0 Running with 1 threads ... Original read count stats: _IP Bases: 119260 HitCounts: 6376516.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 15 reads. The genome is segmented into 2420 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 31 reads. ============================================== 2025-02-21 20:05:23 The genome is segmented into 7967 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS ============================================== 2025-02-21 20:05:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS Original read count stats: _IP Bases: 1678388 HitCounts: 2459239.0 Original read count stats: _IP Bases: 464480 HitCounts: 2957006.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 78 reads. ============================================== 2025-02-21 20:05:25 ============================================== 2025-02-21 20:05:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS The genome is segmented into 8447 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 219 reads. Original read count stats: _IP Bases: 1321313 HitCounts: 2708218.0 Original read count stats: _IP Bases: 1900000 HitCounts: 2508739.0 The genome is segmented into 7988 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 197 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 234 reads. The genome is segmented into 8012 regions for analysis. Running with 1 threads ... The genome is segmented into 7944 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 118 Insignificant: 0 Filtered: 11 Finish binding event prediction: 20.1s Refine read distribution from 65 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 107 Insignificant: 1 Filtered: 19 Finish binding event prediction: 22.1s Refine read distribution from 77 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 98 Insignificant: 0 Filtered: 18 Finish binding event prediction: 23.1s Refine read distribution from 60 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 159 Insignificant: 0 Filtered: 7 Finish binding event prediction: 24.1s Refine read distribution from 65 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 118 Insignificant: 13 Filtered: 0 Finish binding event prediction: 10.1s Refine read distribution from 94 binding events. --------------------------- Events discovered Significant: 208 Insignificant: 11 Filtered: 31 Finish binding event prediction: 41.1s Refine read distribution from 85 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 137 Insignificant: 5 Filtered: 2 Finish binding event prediction: 12.1s Refine read distribution from 90 binding events. --------------------------- Events discovered Significant: 142 Insignificant: 18 Filtered: 1 Finish binding event prediction: 22.0s Refine read distribution from 106 binding events. --------------------------- Events discovered Significant: 56 Insignificant: 0 Filtered: 15 Finish binding event prediction: 50.1s Refine read distribution from 38 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 139 Insignificant: 55 Filtered: 45 Finish binding event prediction: 52.1s Refine read distribution from 78 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 147 Insignificant: 24 Filtered: 0 Finish binding event prediction: 34.1s Refine read distribution from 105 binding events. --------------------------- Events discovered Significant: 98 Insignificant: 61 Filtered: 42 Finish binding event prediction: 57.1s Refine read distribution from 61 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 207 Insignificant: 27 Filtered: 3 Finish binding event prediction: 24.0s Refine read distribution from 137 binding events. --------------------------- Events discovered Significant: 171 Insignificant: 14 Filtered: 35 Finish binding event prediction: 1.0m Refine read distribution from 76 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 157 Insignificant: 0 Filtered: 24 Finish binding event prediction: 1.4m Refine read distribution from 61 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 131 Insignificant: 15 Filtered: 0 Finish binding event prediction: 37.1s Refine read distribution from 99 binding events. --------------------------- Events discovered Significant: 161 Insignificant: 21 Filtered: 35 Finish binding event prediction: 1.4m Refine read distribution from 78 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 190 Insignificant: 0 Filtered: 23 Finish binding event prediction: 1.5m Refine read distribution from 71 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 50 Insignificant: 50 Filtered: 11 Finish binding event prediction: 1.5m Refine read distribution from 21 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 166 Insignificant: 0 Filtered: 30 Finish binding event prediction: 1.5m Refine read distribution from 61 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 198 Insignificant: 12 Filtered: 31 Finish binding event prediction: 1.6m Refine read distribution from 81 binding events. Running with 1 threads ... No valid binding event was found. No valid binding event was found. --------------------------- Events discovered Significant: 175 Insignificant: 58 Filtered: 1 Finish binding event prediction: 40.1s Refine read distribution from 120 binding events. --------------------------- Events discovered Significant: 162 Insignificant: 60 Filtered: 3 Finish binding event prediction: 46.1s Refine read distribution from 128 binding events. --------------------------- Events discovered Significant: 242 Insignificant: 17 Filtered: 1 Finish binding event prediction: 30.1s Refine read distribution from 181 binding events. --------------------------- Events discovered Significant: 131 Insignificant: 37 Filtered: 52 Finish binding event prediction: 1.8m Refine read distribution from 66 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 226 Insignificant: 11 Filtered: 2 Finish binding event prediction: 22.1s Refine read distribution from 169 binding events. --------------------------- Events discovered Significant: 258 Insignificant: 69 Filtered: 4 Finish binding event prediction: 29.1s Refine read distribution from 191 binding events. --------------------------- Events discovered Significant: 253 Insignificant: 21 Filtered: 1 Finish binding event prediction: 24.0s Refine read distribution from 196 binding events. --------------------------- Events discovered Significant: 152 Insignificant: 33 Filtered: 9 Finish binding event prediction: 55.1s Refine read distribution from 117 binding events. --------------------------- Events discovered Significant: 276 Insignificant: 0 Filtered: 31 Finish binding event prediction: 2.0m Refine read distribution from 104 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 246 Insignificant: 61 Filtered: 3 Finish binding event prediction: 28.1s Refine read distribution from 175 binding events. --------------------------- Events discovered Significant: 89 Insignificant: 60 Filtered: 14 Finish binding event prediction: 43.1s Refine read distribution from 52 binding events. --------------------------- Events discovered Significant: 264 Insignificant: 26 Filtered: 1 Finish binding event prediction: 14.1s Refine read distribution from 178 binding events. --------------------------- Events discovered Significant: 36 Insignificant: 1 Filtered: 11 Finish binding event prediction: 2.3m Refine read distribution from 25 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 23 Insignificant: 0 Filtered: 6 Finish binding event prediction: 2.4m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 26 Insignificant: 0 Filtered: 7 Finish binding event prediction: 2.4m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 145 Insignificant: 50 Filtered: 0 Finish binding event prediction: 43.1s Refine read distribution from 123 binding events. --------------------------- Events discovered Significant: 31 Insignificant: 1 Filtered: 8 Finish binding event prediction: 3.0m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 103 Insignificant: 17 Filtered: 0 Finish binding event prediction: 36.1s Refine read distribution from 88 binding events. --------------------------- Events discovered Significant: 133 Insignificant: 37 Filtered: 0 Finish binding event prediction: 44.1s Refine read distribution from 109 binding events. --------------------------- Events discovered Significant: 18 Insignificant: 0 Filtered: 6 Finish binding event prediction: 2.9m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 91 Insignificant: 7 Filtered: 0 Finish binding event prediction: 47.1s Refine read distribution from 77 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.3m Running with 1 threads ... --------------------------- Events discovered Significant: 23 Insignificant: 1 Filtered: 8 Finish binding event prediction: 3.4m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.5m Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.5m Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.6m Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.6m Running with 1 threads ... --------------------------- Events discovered Significant: 122 Insignificant: 22 Filtered: 0 Finish binding event prediction: 39.2s Refine read distribution from 103 binding events. --------------------------- Events discovered Significant: 68 Insignificant: 6 Filtered: 0 Finish binding event prediction: 37.1s Refine read distribution from 62 binding events. --------------------------- Events discovered Significant: 174 Insignificant: 3 Filtered: 37 Finish binding event prediction: 3.7m Refine read distribution from 77 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.8m Running with 1 threads ... --------------------------- Events discovered Significant: 112 Insignificant: 19 Filtered: 0 Finish binding event prediction: 41.1s Refine read distribution from 94 binding events. --------------------------- Events discovered Significant: 285 Insignificant: 68 Filtered: 0 Finish binding event prediction: 35.1s Refine read distribution from 209 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 2.0m --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.1m --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.1m --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.1m --------------------------- Events discovered Significant: 2 Insignificant: 1 Filtered: 1 Finish binding event prediction: 2.8m --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.4m ============================================== 2025-02-21 20:16:58 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp.1x36mers.unique.GPS Original read count stats: _IP Bases: 249264 HitCounts: 292606.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 36 reads. ============================================== 2025-02-21 20:16:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp.SE.a.GPS The genome is segmented into 8413 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 298261 HitCounts: 365756.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 44 reads. The genome is segmented into 8573 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:17:02 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS Original read count stats: _IP Bases: 381825 HitCounts: 473216.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 52 reads. ============================================== 2025-02-21 20:17:03 The genome is segmented into 8333 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 443679 HitCounts: 575080.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 61 reads. The genome is segmented into 8493 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:17:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS ============================================== 2025-02-21 20:17:06 Original read count stats: ============================================== 2025-02-21 20:17:06_IP Bases: 1749494 HitCounts: 2918843.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp.SE.a.GPS ============================================== 2025-02-21 20:17:06 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS Original read count stats: _IP Bases: 585366 HitCounts: 3124186.0 Original read count stats: _IP Bases: 1187307 HitCounts: 3006417.0 ============================================== 2025-02-21 20:17:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS ============================================== 2025-02-21 20:17:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp.SE.a.GPS Original read count stats: _IP Bases: 1352171 HitCounts: 1862734.0 ============================================== 2025-02-21 20:17:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp.SE.a.GPS Original read count stats: _IP Bases: 687742 HitCounts: 3202622.0 ============================================== 2025-02-21 20:17:07 At Poisson p-value 1.0e-03, in a 301bp window, expect 106 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp.1x36mers.unique.GPS ============================================== 2025-02-21 20:17:07 Original read count stats: _IP Bases: 294160 HitCounts: 2531484.0 Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp.SE.a.GPS _IP Bases: 1794159 HitCounts: 2976561.0 ============================================== 2025-02-21 20:17:08 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif.1x36mers.unique.GPS Original read count stats: _IP Bases: 1119996 HitCounts: 2105800.0 The genome is segmented into 8429 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 248 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 72 reads. Original read count stats: _IP Bases: 1899921 HitCounts: 3590135.0 ============================================== 2025-02-21 20:17:08 Original read count stats: _IP Bases: 1148670 HitCounts: 2637507.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 134 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 169 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 233 reads. ============================================== 2025-02-21 20:17:08 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp.SE.a.GPS The genome is segmented into 8635 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif.1x36mers.unique.GPS The genome is segmented into 8416 regions for analysis. Running with 1 threads ... The genome is segmented into 8356 regions for analysis. ============================================== 2025-02-21 20:17:09 At Poisson p-value 1.0e-03, in a 301bp window, expect 162 reads. Running with 1 threads ... ============================================== 2025-02-21 20:17:09 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif.SE.a.GPS ============================================== 2025-02-21 20:17:09 Original read count stats: _IP Bases: 1402243 HitCounts: 2155081.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif.1x36mers.unique.GPS Original read count stats: _IP Bases: 1009392 HitCounts: 1740862.0 The genome is segmented into 8137 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 175 reads. The genome is segmented into 8055 regions for analysis. The genome is segmented into 8174 regions for analysis. Original read count stats: Running with 1 threads ... _IP Bases: 1039546 HitCounts: 1878542.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 260 reads. Original read count stats: _IP Bases: 1170659 HitCounts: 2046616.0 Original read count stats: _IP Bases: 1179824 HitCounts: 2834809.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 134 reads. The genome is segmented into 8248 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 301 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 144 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 192 reads. The genome is segmented into 8084 regions for analysis. The genome is segmented into 8091 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 160 reads. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8291 regions for analysis. Running with 1 threads ... The genome is segmented into 8256 regions for analysis. The genome is segmented into 8244 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 187 reads. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-21 20:17:11 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif.SE.a.GPS ============================================== 2025-02-21 20:17:11 The genome is segmented into 8220 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS Running with 1 threads ... ============================================== 2025-02-21 20:17:12 The genome is segmented into 8068 regions for analysis. Original read count stats: _IP Bases: 1200936 HitCounts: 2203541.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp.1x36mers.unique.GPS Running with 1 threads ... Original read count stats: _IP Bases: 1750069 HitCounts: 2575882.0 Original read count stats: _IP Bases: 1924300 HitCounts: 3825109.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 171 reads. The genome is segmented into 8241 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 230 reads. ============================================== 2025-02-21 20:17:14 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp.SE.a.GPS Original read count stats: _IP Bases: 2081926 HitCounts: 4844593.0 ============================================== 2025-02-21 20:17:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 303 reads. The genome is segmented into 8087 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 642093 HitCounts: 2835927.0 The genome is segmented into 8086 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 109 reads. ============================================== 2025-02-21 20:17:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS Original read count stats: _IP Bases: 549043 HitCounts: 2852730.0 The genome is segmented into 8238 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 88 reads. Running with 1 threads ... The genome is segmented into 8237 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 381 reads. The genome is segmented into 8242 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:17:23 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS Original read count stats: _IP Bases: 3125560 HitCounts: 9701821.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 688 reads. ============================================== 2025-02-21 20:17:30 The genome is segmented into 8069 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 3310667 HitCounts: 1.194029E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 842 reads. The genome is segmented into 8223 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 66 Insignificant: 0 Filtered: 13 Finish binding event prediction: 1.1m Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 67 Insignificant: 1 Filtered: 17 Finish binding event prediction: 1.4m Refine read distribution from 40 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 206 Insignificant: 40 Filtered: 46 Finish binding event prediction: 1.4m Refine read distribution from 113 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 208 Insignificant: 12 Filtered: 43 Finish binding event prediction: 1.5m Refine read distribution from 106 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 110 Insignificant: 0 Filtered: 15 Finish binding event prediction: 1.6m Refine read distribution from 59 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 126 Insignificant: 5 Filtered: 0 Finish binding event prediction: 34.1s Refine read distribution from 111 binding events. --------------------------- Events discovered Significant: 142 Insignificant: 39 Filtered: 0 Finish binding event prediction: 15.2s Refine read distribution from 115 binding events. --------------------------- Events discovered Significant: 228 Insignificant: 90 Filtered: 6 Finish binding event prediction: 26.1s Refine read distribution from 172 binding events. --------------------------- Events discovered Significant: 173 Insignificant: 7 Filtered: 0 Finish binding event prediction: 20.1s Refine read distribution from 151 binding events. --------------------------- Events discovered Significant: 320 Insignificant: 70 Filtered: 1 Finish binding event prediction: 31.4s Refine read distribution from 237 binding events. --------------------------- Events discovered Significant: 62 Insignificant: 0 Filtered: 14 Finish binding event prediction: 2.0m Refine read distribution from 44 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 90 Insignificant: 7 Filtered: 19 Finish binding event prediction: 2.2m Refine read distribution from 62 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 72 Insignificant: 34 Filtered: 16 Finish binding event prediction: 2.3m Refine read distribution from 42 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 24 Insignificant: 0 Filtered: 3 Finish binding event prediction: 2.3m Refine read distribution from 21 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 27 Insignificant: 0 Filtered: 9 Finish binding event prediction: 2.4m Refine read distribution from 20 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 187 Insignificant: 2 Filtered: 41 Finish binding event prediction: 2.5m Refine read distribution from 96 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 53 Insignificant: 0 Filtered: 15 Finish binding event prediction: 2.4m Refine read distribution from 42 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 83 Insignificant: 2 Filtered: 17 Finish binding event prediction: 2.5m Refine read distribution from 55 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 182 Insignificant: 27 Filtered: 0 Finish binding event prediction: 27.1s Refine read distribution from 155 binding events. --------------------------- Events discovered Significant: 18 Insignificant: 0 Filtered: 6 Finish binding event prediction: 2.7m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 187 Insignificant: 8 Filtered: 0 Finish binding event prediction: 47.1s Refine read distribution from 163 binding events. --------------------------- Events discovered Significant: 116 Insignificant: 18 Filtered: 0 Finish binding event prediction: 34.1s Refine read distribution from 113 binding events. --------------------------- Events discovered Significant: 222 Insignificant: 0 Filtered: 35 Finish binding event prediction: 2.8m Refine read distribution from 88 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 317 Insignificant: 53 Filtered: 3 Finish binding event prediction: 29.1s Refine read distribution from 234 binding events. --------------------------- Events discovered Significant: 108 Insignificant: 24 Filtered: 0 Finish binding event prediction: 31.1s Refine read distribution from 105 binding events. --------------------------- Events discovered Significant: 178 Insignificant: 43 Filtered: 0 Finish binding event prediction: 52.1s Refine read distribution from 132 binding events. --------------------------- Events discovered Significant: 193 Insignificant: 26 Filtered: 0 Finish binding event prediction: 42.1s Refine read distribution from 175 binding events. --------------------------- Events discovered Significant: 208 Insignificant: 6 Filtered: 1 Finish binding event prediction: 43.1s Refine read distribution from 154 binding events. --------------------------- Events discovered Significant: 90 Insignificant: 6 Filtered: 1 Finish binding event prediction: 27.1s Refine read distribution from 90 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.3m Running with 1 threads ... --------------------------- Events discovered Significant: 276 Insignificant: 26 Filtered: 0 Finish binding event prediction: 25.1s Refine read distribution from 221 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.4m Running with 1 threads ... --------------------------- Events discovered Significant: 10 Insignificant: 1 Filtered: 3 Finish binding event prediction: 3.4m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 52 Insignificant: 0 Filtered: 14 Finish binding event prediction: 3.5m Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 25 Insignificant: 0 Filtered: 6 Finish binding event prediction: 3.5m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 48 Insignificant: 1 Filtered: 16 Finish binding event prediction: 3.6m Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 94 Insignificant: 6 Filtered: 0 Finish binding event prediction: 32.1s Refine read distribution from 90 binding events. --------------------------- Events discovered Significant: 120 Insignificant: 2 Filtered: 0 Finish binding event prediction: 33.1s Refine read distribution from 105 binding events. --------------------------- Events discovered Significant: 51 Insignificant: 14 Filtered: 0 Finish binding event prediction: 40.1s Refine read distribution from 41 binding events. --------------------------- Events discovered Significant: 228 Insignificant: 0 Filtered: 36 Finish binding event prediction: 4.0m Refine read distribution from 87 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 130 Insignificant: 14 Filtered: 0 Finish binding event prediction: 41.1s Refine read distribution from 107 binding events. --------------------------- Events discovered Significant: 81 Insignificant: 6 Filtered: 16 Finish binding event prediction: 4.2m Refine read distribution from 53 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.6m Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 43 Insignificant: 2 Filtered: 11 Finish binding event prediction: 4.3m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 97 Insignificant: 0 Filtered: 18 Finish binding event prediction: 4.7m Refine read distribution from 53 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 310 Insignificant: 16 Filtered: 2 Finish binding event prediction: 46.1s Refine read distribution from 221 binding events. --------------------------- Events discovered Significant: 48 Insignificant: 0 Filtered: 12 Finish binding event prediction: 5.1m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 1 Finish binding event prediction: 2.0m --------------------------- Events discovered Significant: 197 Insignificant: 34 Filtered: 1 Finish binding event prediction: 1.1m Refine read distribution from 156 binding events. --------------------------- Events discovered Significant: 143 Insignificant: 7 Filtered: 0 Finish binding event prediction: 1.0m Refine read distribution from 120 binding events. --------------------------- Events discovered Significant: 201 Insignificant: 3 Filtered: 0 Finish binding event prediction: 1.4m Refine read distribution from 157 binding events. --------------------------- Events discovered Significant: 142 Insignificant: 5 Filtered: 0 Finish binding event prediction: 54.2s Refine read distribution from 127 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.5m ============================================== 2025-02-21 20:30:31 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc.1x36mers.unique.GPS Original read count stats: _IP Bases: 163457 HitCounts: 1721380.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 30 reads. The genome is segmented into 8504 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:30:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp.1x36mers.unique.GPS ============================================== 2025-02-21 20:30:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp.SE.a.GPS ============================================== 2025-02-21 20:30:32 ============================================== 2025-02-21 20:30:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc.SE.a.GPS Original read count stats: _IP Bases: 1160578 HitCounts: 1729799.0 Original read count stats: _IP Bases: 1319551 HitCounts: 2858938.0 Original read count stats: _IP Bases: 188802 HitCounts: 2032736.0 Original read count stats: _IP Bases: 1477153 HitCounts: 3092701.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 42 reads. The genome is segmented into 8722 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 152 reads. ============================================== 2025-02-21 20:30:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp.1x36mers.unique.GPS ============================================== 2025-02-21 20:30:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp.SE.a.GPS ============================================== 2025-02-21 20:30:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 223 reads. Original read count stats: _IP Bases: 1186793 HitCounts: 2178001.0 ============================================== 2025-02-21 20:30:34 Original read count stats: _IP Bases: 1216223 HitCounts: 2066333.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod.1x36mers.unique.GPS Original read count stats: _IP Bases: 1348584 HitCounts: 2256281.0 The genome is segmented into 8352 regions for analysis. The genome is segmented into 8237 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 255 reads. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 748183 HitCounts: 1823069.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 169 reads. ============================================== 2025-02-21 20:30:35 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod.SE.a.GPS The genome is segmented into 8334 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 180 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 187 reads. ============================================== 2025-02-21 20:30:36 Original read count stats: _IP Bases: 1178616 HitCounts: 3241046.0 ============================================== 2025-02-21 20:30:36 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod.1x36mers.unique.GPS ============================================== 2025-02-21 20:30:36 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 156 reads. The genome is segmented into 8174 regions for analysis. The genome is segmented into 8421 regions for analysis. The genome is segmented into 8163 regions for analysis. Original read count stats: _IP Bases: 806937 HitCounts: 1974463.0 Running with 1 threads ... Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 834608 HitCounts: 2056572.0 Original read count stats: _IP Bases: 913929 HitCounts: 2052805.0 The genome is segmented into 8338 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:30:37 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc.1x36mers.unique.GPS ============================================== 2025-02-21 20:30:37 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 166 reads. Original read count stats: _IP Bases: 75295 HitCounts: 2787467.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 17 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 172 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 173 reads. The genome is segmented into 7607 regions for analysis. Running with 1 threads ... The genome is segmented into 8276 regions for analysis. Original read count stats: _IP Bases: 1334139 HitCounts: 3793306.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 249 reads. The genome is segmented into 8278 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:30:39 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod.SE.a.GPS The genome is segmented into 8518 regions for analysis. Running with 1 threads ... The genome is segmented into 8280 regions for analysis. Original read count stats: Running with 1 threads ... _IP Bases: 834020 HitCounts: 2373223.0 ============================================== 2025-02-21 20:30:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod.1x36mers.unique.GPS ============================================== 2025-02-21 20:30:41 At Poisson p-value 1.0e-03, in a 301bp window, expect 276 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 191 reads. Original read count stats: _IP Bases: 1008992 HitCounts: 2623163.0 Original read count stats: _IP Bases: 1008583 HitCounts: 2646749.0 ============================================== 2025-02-21 20:30:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod.1x36mers.unique.GPS The genome is segmented into 8414 regions for analysis. The genome is segmented into 8511 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 1073587 HitCounts: 2454437.0 ============================================== 2025-02-21 20:30:43 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod.SE.a.GPS ============================================== 2025-02-21 20:30:43 At Poisson p-value 1.0e-03, in a 301bp window, expect 209 reads. Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod.SE.a.GPS _IP Bases: 919414 HitCounts: 2624573.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 209 reads. ============================================== 2025-02-21 20:30:43 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 204 reads. Original read count stats: _IP Bases: 894720 HitCounts: 2545263.0 Original read count stats: _IP Bases: 1451878 HitCounts: 6223388.0 The genome is segmented into 8443 regions for analysis. The genome is segmented into 8332 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8352 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 205 reads. Running with 1 threads ... ============================================== 2025-02-21 20:30:45 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 200 reads. The genome is segmented into 8437 regions for analysis. Original read count stats: _IP Bases: 88830 HitCounts: 3267184.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 22 reads. The genome is segmented into 8455 regions for analysis. The genome is segmented into 7438 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 406 reads. The genome is segmented into 8609 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 135 Insignificant: 0 Filtered: 2 Finish binding event prediction: 20.1s Refine read distribution from 46 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 107 Insignificant: 16 Filtered: 0 Finish binding event prediction: 14.0s Refine read distribution from 82 binding events. --------------------------- Events discovered Significant: 152 Insignificant: 0 Filtered: 9 Finish binding event prediction: 53.1s Refine read distribution from 47 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 155 Insignificant: 41 Filtered: 31 Finish binding event prediction: 1.1m Refine read distribution from 63 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 168 Insignificant: 26 Filtered: 45 Finish binding event prediction: 56.1s Refine read distribution from 56 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 137 Insignificant: 10 Filtered: 0 Finish binding event prediction: 33.0s Refine read distribution from 108 binding events. --------------------------- Events discovered Significant: 174 Insignificant: 65 Filtered: 5 Finish binding event prediction: 35.0s Refine read distribution from 130 binding events. --------------------------- Events discovered Significant: 68 Insignificant: 0 Filtered: 14 Finish binding event prediction: 1.7m Refine read distribution from 44 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 170 Insignificant: 37 Filtered: 1 Finish binding event prediction: 40.1s Refine read distribution from 113 binding events. --------------------------- Events discovered Significant: 72 Insignificant: 6 Filtered: 17 Finish binding event prediction: 2.0m Refine read distribution from 57 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 63 Insignificant: 17 Filtered: 18 Finish binding event prediction: 2.3m Refine read distribution from 42 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 171 Insignificant: 1 Filtered: 0 Finish binding event prediction: 39.1s Refine read distribution from 125 binding events. --------------------------- Events discovered Significant: 994 Insignificant: 0 Filtered: 106 Finish binding event prediction: 2.5m Refine read distribution from 626 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 173 Insignificant: 25 Filtered: 0 Finish binding event prediction: 31.1s Refine read distribution from 148 binding events. --------------------------- Events discovered Significant: 93 Insignificant: 0 Filtered: 15 Finish binding event prediction: 2.6m Refine read distribution from 70 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 23 Insignificant: 18 Filtered: 6 Finish binding event prediction: 2.9m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 968 Insignificant: 1 Filtered: 120 Finish binding event prediction: 2.8m Refine read distribution from 608 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 185 Insignificant: 31 Filtered: 0 Finish binding event prediction: 42.1s Refine read distribution from 140 binding events. --------------------------- Events discovered Significant: 158 Insignificant: 1 Filtered: 1 Finish binding event prediction: 35.1s Refine read distribution from 135 binding events. --------------------------- Events discovered Significant: 19 Insignificant: 0 Filtered: 5 Finish binding event prediction: 3.2m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 77 Insignificant: 16 Filtered: 0 Finish binding event prediction: 43.2s Refine read distribution from 58 binding events. --------------------------- Events discovered Significant: 989 Insignificant: 1 Filtered: 119 Finish binding event prediction: 3.7m Refine read distribution from 651 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 992 Insignificant: 3 Filtered: 118 Finish binding event prediction: 3.8m Refine read distribution from 619 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 56 Insignificant: 0 Filtered: 0 Finish binding event prediction: 56.1s Refine read distribution from 54 binding events. --------------------------- Events discovered Significant: 991 Insignificant: 0 Filtered: 83 Finish binding event prediction: 4.0m Refine read distribution from 654 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 631 Insignificant: 2 Filtered: 98 Finish binding event prediction: 4.1m Refine read distribution from 432 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 831 Insignificant: 0 Filtered: 103 Finish binding event prediction: 4.3m Refine read distribution from 546 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1008 Insignificant: 0 Filtered: 124 Finish binding event prediction: 4.3m Refine read distribution from 645 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1127 Insignificant: 289 Filtered: 4 Finish binding event prediction: 1.9m Refine read distribution from 814 binding events. --------------------------- Events discovered Significant: 946 Insignificant: 2 Filtered: 103 Finish binding event prediction: 4.4m Refine read distribution from 599 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 803 Insignificant: 2 Filtered: 112 Finish binding event prediction: 4.6m Refine read distribution from 507 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 361 Insignificant: 0 Filtered: 75 Finish binding event prediction: 4.8m Refine read distribution from 223 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1069 Insignificant: 285 Filtered: 2 Finish binding event prediction: 2.2m Refine read distribution from 776 binding events. --------------------------- Events discovered Significant: 1109 Insignificant: 302 Filtered: 2 Finish binding event prediction: 1.5m Refine read distribution from 797 binding events. --------------------------- Events discovered Significant: 1154 Insignificant: 287 Filtered: 2 Finish binding event prediction: 2.2m Refine read distribution from 844 binding events. --------------------------- Events discovered Significant: 639 Insignificant: 1 Filtered: 89 Finish binding event prediction: 6.0m Refine read distribution from 413 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 336 Insignificant: 5 Filtered: 38 Finish binding event prediction: 5.9m Refine read distribution from 178 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1179 Insignificant: 297 Filtered: 3 Finish binding event prediction: 1.8m Refine read distribution from 852 binding events. --------------------------- Events discovered Significant: 990 Insignificant: 182 Filtered: 2 Finish binding event prediction: 2.1m Refine read distribution from 728 binding events. --------------------------- Events discovered Significant: 1015 Insignificant: 271 Filtered: 1 Finish binding event prediction: 2.0m Refine read distribution from 750 binding events. --------------------------- Events discovered Significant: 967 Insignificant: 246 Filtered: 3 Finish binding event prediction: 2.1m Refine read distribution from 690 binding events. --------------------------- Events discovered Significant: 1076 Insignificant: 208 Filtered: 1 Finish binding event prediction: 2.6m Refine read distribution from 778 binding events. --------------------------- Events discovered Significant: 1168 Insignificant: 295 Filtered: 6 Finish binding event prediction: 2.7m Refine read distribution from 819 binding events. ============================================== 2025-02-21 20:37:38 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod.1x36mers.unique.GPS ============================================== 2025-02-21 20:37:39 Original read count stats: _IP Bases: 428463 HitCounts: 805679.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1-2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1-2.1x36mers.unique.GPS Original read count stats: _IP Bases: 79741 HitCounts: 942573.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 28 reads. ============================================== 2025-02-21 20:37:39 The genome is segmented into 2050 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 80 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod.SE.a.GPS Original read count stats: _IP Bases: 488308 HitCounts: 1020135.0 The genome is segmented into 8378 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:37:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1-2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1-2.SE.a.GPS Original read count stats: _IP Bases: 99628 HitCounts: 1197830.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 95 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 37 reads. The genome is segmented into 1972 regions for analysis. The genome is segmented into 8563 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-21 20:37:42 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod.1x36mers.unique.GPS --------------------------- Events discovered Significant: 731 Insignificant: 85 Filtered: 2 Finish binding event prediction: 2.2m Refine read distribution from 560 binding events. Original read count stats: _IP Bases: 744572 HitCounts: 1598433.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 140 reads. ============================================== 2025-02-21 20:37:44 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod.SE.a.GPS The genome is segmented into 8419 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1112024 HitCounts: 3337018.0 ============================================== 2025-02-21 20:37:45 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod.SE.a.GPS Original read count stats: _IP Bases: 837256 HitCounts: 2062163.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 251 reads. The genome is segmented into 8491 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 172 reads. The genome is segmented into 8595 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:38:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 228210 HitCounts: 1.5836484E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 271 reads. The genome is segmented into 4255 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 854 Insignificant: 1 Filtered: 77 Finish binding event prediction: 1.6m Refine read distribution from 344 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 917 Insignificant: 209 Filtered: 4 Finish binding event prediction: 2.8m Refine read distribution from 666 binding events. --------------------------- Events discovered Significant: 674 Insignificant: 82 Filtered: 8 Finish binding event prediction: 35.1s Refine read distribution from 469 binding events. --------------------------- Events discovered Significant: 601 Insignificant: 95 Filtered: 0 Finish binding event prediction: 3.2m Refine read distribution from 452 binding events. --------------------------- Events discovered Significant: 817 Insignificant: 6 Filtered: 96 Finish binding event prediction: 2.8m Refine read distribution from 319 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1324 Insignificant: 0 Filtered: 81 Finish binding event prediction: 2.4m Refine read distribution from 509 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 789 Insignificant: 174 Filtered: 26 Finish binding event prediction: 24.1s Refine read distribution from 529 binding events. --------------------------- Events discovered Significant: 826 Insignificant: 0 Filtered: 84 Finish binding event prediction: 3.5m Refine read distribution from 584 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 841 Insignificant: 2 Filtered: 91 Finish binding event prediction: 3.6m Refine read distribution from 555 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 943 Insignificant: 2 Filtered: 90 Finish binding event prediction: 3.5m Refine read distribution from 618 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 803 Insignificant: 2 Filtered: 87 Finish binding event prediction: 3.5m Refine read distribution from 549 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 644 Insignificant: 115 Filtered: 11 Finish binding event prediction: 1.1m Refine read distribution from 397 binding events. --------------------------- Events discovered Significant: 878 Insignificant: 0 Filtered: 84 Finish binding event prediction: 4.0m Refine read distribution from 604 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1079 Insignificant: 244 Filtered: 2 Finish binding event prediction: 1.5m Refine read distribution from 782 binding events. --------------------------- Events discovered Significant: 974 Insignificant: 237 Filtered: 3 Finish binding event prediction: 1.5m Refine read distribution from 673 binding events. --------------------------- Events discovered Significant: 1042 Insignificant: 238 Filtered: 1 Finish binding event prediction: 1.2m Refine read distribution from 747 binding events. --------------------------- Events discovered Significant: 1087 Insignificant: 300 Filtered: 2 Finish binding event prediction: 1.7m Refine read distribution from 751 binding events. --------------------------- Events discovered Significant: 996 Insignificant: 217 Filtered: 2 Finish binding event prediction: 2.7m Refine read distribution from 696 binding events. ============================================== 2025-02-21 20:49:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 09-E.coli-OmpR-GSE88979/OmpR_NaCl_1.1x36mers.unique.bam --out 09-E.coli-OmpR-GSE88979/OmpR_NaCl_1.1x36mers.unique.GPS ============================================== 2025-02-21 20:49:59 Original read count stats: _IP Bases: 619219 HitCounts: 1262962.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 231019 HitCounts: 1963578.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 84 reads. ============================================== 2025-02-21 20:50:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 91635 HitCounts: 2183353.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 78 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 40 reads. The genome is segmented into 4737 regions for analysis. Running with 1 threads ... The genome is segmented into 2102 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:50:01 The genome is segmented into 8224 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 09-E.coli-OmpR-GSE88979/OmpR_NaCl_1.SE.a.bam --out 09-E.coli-OmpR-GSE88979/OmpR_NaCl_1.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 675501 HitCounts: 1566952.0 ============================================== 2025-02-21 20:50:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 108 reads. Original read count stats: _IP Bases: 260615 HitCounts: 2369911.0 The genome is segmented into 8410 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 95 reads. The genome is segmented into 4789 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:50:03 ============================================== 2025-02-21 20:50:03 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2.SE.a.GPS Original read count stats: _IP Bases: 119255 HitCounts: 2908697.0 Original read count stats: _IP Bases: 149901 HitCounts: 2135890.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 43 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 58 reads. The genome is segmented into 2003 regions for analysis. Running with 1 threads ... The genome is segmented into 8554 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:50:05 ============================================== 2025-02-21 20:50:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 09-E.coli-OmpR-GSE88979/OmpR_NaCl_2.1x36mers.unique.bam --out 09-E.coli-OmpR-GSE88979/OmpR_NaCl_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 200808 HitCounts: 4623573.0 Original read count stats: _IP Bases: 979321 HitCounts: 2037491.0 ============================================== 2025-02-21 20:50:06 ============================================== 2025-02-21 20:50:06 At Poisson p-value 1.0e-03, in a 301bp window, expect 124 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 09-E.coli-OmpR-GSE88979/OmpR_NaCl_2.SE.a.bam --out 09-E.coli-OmpR-GSE88979/OmpR_NaCl_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 141 reads. The genome is segmented into 8310 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 528315 HitCounts: 4692658.0 Original read count stats: _IP Bases: 1037999 HitCounts: 2515025.0 ============================================== 2025-02-21 20:50:07 The genome is segmented into 8126 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_1.1x36mers.unique.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 175 reads. Original read count stats: ============================================== 2025-02-21 20:50:08_IP Bases: 457073 HitCounts: 2595928.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_1.1x36mers.unique.GPS The genome is segmented into 8324 regions for analysis. Original read count stats: _IP Bases: 149880 HitCounts: 3031819.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 218 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 84 reads. The genome is segmented into 8373 regions for analysis. The genome is segmented into 8521 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 55 reads. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8394 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:50:11 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_2.SE.a.GPS Original read count stats: _IP Bases: 197077 HitCounts: 3162472.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 90 reads. The genome is segmented into 8574 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:50:19 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 362514 HitCounts: 1.2193127E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 232 reads. The genome is segmented into 6077 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:50:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2.SE.a.GPS Original read count stats: _IP Bases: 408312 HitCounts: 1.520003E7 ============================================== 2025-02-21 20:50:28 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2-2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2-2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 303 reads. Original read count stats: _IP Bases: 177241 HitCounts: 1.6325999E7 The genome is segmented into 6084 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:50:30 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 202055 HitCounts: 1.5130991E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 206 reads. The genome is segmented into 2998 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 205 reads. The genome is segmented into 4754 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:50:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_1.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_1.1x36mers.unique.GPS ============================================== 2025-02-21 20:50:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1.SE.a.GPS Original read count stats: _IP Bases: 328674 HitCounts: 1.7509608E7 Original read count stats: _IP Bases: 255148 HitCounts: 1.8840967E7 ============================================== 2025-02-21 20:50:36 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2-2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2-2.SE.a.GPS Original read count stats: _IP Bases: 196735 HitCounts: 1.8967515E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 320 reads. The genome is segmented into 7740 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 338 reads. Running with 1 threads ... The genome is segmented into 4252 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:50:39 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_2.SE.a.GPS Original read count stats: _IP Bases: 221557 HitCounts: 1.8350328E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 250 reads. The genome is segmented into 3086 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 270 reads. The genome is segmented into 4785 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:50:45 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_1.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_1.SE.a.GPS Original read count stats: _IP Bases: 358181 HitCounts: 2.1232522E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 410 reads. The genome is segmented into 7998 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 260 Insignificant: 2 Filtered: 19 Finish binding event prediction: 1.2m Refine read distribution from 61 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 40 Insignificant: 0 Filtered: 6 Finish binding event prediction: 1.5m Refine read distribution from 24 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 221 Insignificant: 1 Filtered: 20 Finish binding event prediction: 1.7m Refine read distribution from 71 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1086 Insignificant: 0 Filtered: 107 Finish binding event prediction: 1.4m Refine read distribution from 470 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 111 Insignificant: 15 Filtered: 2 Finish binding event prediction: 40.1s Refine read distribution from 103 binding events. --------------------------- Events discovered Significant: 74 Insignificant: 17 Filtered: 18 Finish binding event prediction: 2.1m Refine read distribution from 52 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1260 Insignificant: 0 Filtered: 214 Finish binding event prediction: 2.3m Refine read distribution from 625 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 677 Insignificant: 148 Filtered: 51 Finish binding event prediction: 19.1s Refine read distribution from 475 binding events. --------------------------- Events discovered Significant: 36 Insignificant: 14 Filtered: 9 Finish binding event prediction: 2.2m Refine read distribution from 26 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 197 Insignificant: 29 Filtered: 3 Finish binding event prediction: 43.1s Refine read distribution from 109 binding events. --------------------------- Events discovered Significant: 190 Insignificant: 32 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 116 binding events. --------------------------- Events discovered Significant: 1378 Insignificant: 0 Filtered: 72 Finish binding event prediction: 1.9m Refine read distribution from 554 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 178 Insignificant: 84 Filtered: 52 Finish binding event prediction: 2.4m Refine read distribution from 42 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 223 Insignificant: 1 Filtered: 35 Finish binding event prediction: 2.4m Refine read distribution from 62 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 92 Insignificant: 69 Filtered: 15 Finish binding event prediction: 2.6m Refine read distribution from 20 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 166 Insignificant: 62 Filtered: 1 Finish binding event prediction: 36.1s Refine read distribution from 123 binding events. --------------------------- Events discovered Significant: 1137 Insignificant: 237 Filtered: 19 Finish binding event prediction: 37.2s Refine read distribution from 739 binding events. --------------------------- Events discovered Significant: 822 Insignificant: 189 Filtered: 22 --------------------------- Events discovered Significant: 1293 Insignificant: 2 Filtered: 92 Finish binding event prediction: 27.2s Finish binding event prediction: 2.3m Refine read distribution from 572 binding events. Refine read distribution from 476 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 118 Insignificant: 44 Filtered: 0 Finish binding event prediction: 36.1s Refine read distribution from 96 binding events. --------------------------- Events discovered Significant: 867 Insignificant: 13 Filtered: 120 Finish binding event prediction: 3.0m Refine read distribution from 343 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1169 Insignificant: 0 Filtered: 126 Finish binding event prediction: 2.5m Refine read distribution from 457 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 172 Insignificant: 68 Filtered: 48 Finish binding event prediction: 2.8m Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 156 Insignificant: 44 Filtered: 35 Finish binding event prediction: 34.1s Refine read distribution from 79 binding events. --------------------------- Events discovered Significant: 693 Insignificant: 154 Filtered: 49 Finish binding event prediction: 9.1s Refine read distribution from 473 binding events. --------------------------- Events discovered Significant: 308 Insignificant: 32 Filtered: 1 Finish binding event prediction: 41.1s Refine read distribution from 151 binding events. --------------------------- Events discovered Significant: 1309 Insignificant: 6 Filtered: 262 Finish binding event prediction: 2.9m Refine read distribution from 600 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 614 Insignificant: 109 Filtered: 25 Finish binding event prediction: 29.1s Refine read distribution from 386 binding events. --------------------------- Events discovered Significant: 801 Insignificant: 142 Filtered: 33 Finish binding event prediction: 32.1s Refine read distribution from 530 binding events. --------------------------- Events discovered Significant: 149 Insignificant: 61 Filtered: 6 Finish binding event prediction: 35.1s Refine read distribution from 98 binding events. --------------------------- Events discovered Significant: 937 Insignificant: 0 Filtered: 77 Finish binding event prediction: 3.6m Refine read distribution from 369 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1025 Insignificant: 0 Filtered: 106 Finish binding event prediction: 3.0m Refine read distribution from 466 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 147 Insignificant: 48 Filtered: 0 Finish binding event prediction: 1.0m Refine read distribution from 88 binding events. --------------------------- Events discovered Significant: 1390 Insignificant: 0 Filtered: 286 Finish binding event prediction: 3.5m Refine read distribution from 668 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 661 Insignificant: 113 Filtered: 13 Finish binding event prediction: 16.1s Refine read distribution from 415 binding events. --------------------------- Events discovered Significant: 1010 Insignificant: 218 Filtered: 68 Finish binding event prediction: 41.2s Refine read distribution from 649 binding events. --------------------------- Events discovered Significant: 28 Insignificant: 0 Filtered: 3 Finish binding event prediction: 4.0m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1155 Insignificant: 0 Filtered: 139 Finish binding event prediction: 3.8m Refine read distribution from 462 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 659 Insignificant: 147 Filtered: 49 Finish binding event prediction: 46.1s Refine read distribution from 456 binding events. --------------------------- Events discovered Significant: 1269 Insignificant: 5 Filtered: 195 Finish binding event prediction: 4.6m Refine read distribution from 605 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 82 Insignificant: 4 Filtered: 0 Finish binding event prediction: 39.1s Refine read distribution from 61 binding events. --------------------------- Events discovered Significant: 1267 Insignificant: 0 Filtered: 71 Finish binding event prediction: 3.9m Refine read distribution from 532 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1077 Insignificant: 243 Filtered: 65 Finish binding event prediction: 58.2s Refine read distribution from 690 binding events. --------------------------- Events discovered Significant: 698 Insignificant: 143 Filtered: 51 Finish binding event prediction: 39.1s Refine read distribution from 490 binding events. --------------------------- Events discovered Significant: 1105 Insignificant: 218 Filtered: 19 Finish binding event prediction: 38.1s Refine read distribution from 680 binding events. --------------------------- Events discovered Significant: 795 Insignificant: 183 Filtered: 22 Finish binding event prediction: 34.2s Refine read distribution from 549 binding events. ============================================== 2025-02-21 20:59:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 446872 HitCounts: 1845860.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 74 reads. ============================================== 2025-02-21 20:59:22 The genome is segmented into 8392 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_2.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 516410 HitCounts: 3209017.0 ============================================== 2025-02-21 20:59:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 167 reads. Original read count stats: _IP Bases: 735590 HitCounts: 3882562.0 The genome is segmented into 8579 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 20:59:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_2.SE.a.GPS ============================================== 2025-02-21 20:59:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 653794 HitCounts: 4092634.0 Original read count stats: _IP Bases: 667227 HitCounts: 2443037.0 ============================================== 2025-02-21 20:59:26 At Poisson p-value 1.0e-03, in a 301bp window, expect 214 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_1.1x36mers.unique.GPS ============================================== 2025-02-21 20:59:26 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_2.1x36mers.unique.GPS The genome is segmented into 8431 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 116 reads. Original read count stats: _IP Bases: 585107 HitCounts: 2539290.0 Original read count stats: _IP Bases: 2134910 HitCounts: 4406669.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 208 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 106 reads. The genome is segmented into 8285 regions for analysis. Running with 1 threads ... The genome is segmented into 8519 regions for analysis. Running with 1 threads ... The genome is segmented into 8358 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 382 reads. ============================================== 2025-02-21 20:59:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_1.SE.a.GPS The genome is segmented into 8579 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2298417 HitCounts: 6888464.0 ============================================== 2025-02-21 20:59:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1872599 HitCounts: 3878171.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 338 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 560 reads. The genome is segmented into 8755 regions for analysis. Running with 1 threads ... The genome is segmented into 8530 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 90 Insignificant: 58 Filtered: 17 Finish binding event prediction: 1.7m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 188 Insignificant: 0 Filtered: 36 Finish binding event prediction: 2.3m Refine read distribution from 74 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 132 Insignificant: 52 Filtered: 20 Finish binding event prediction: 2.2m Refine read distribution from 39 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 85 Insignificant: 58 Filtered: 23 Finish binding event prediction: 2.7m Refine read distribution from 34 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 174 Insignificant: 0 Filtered: 29 Finish binding event prediction: 2.7m Refine read distribution from 67 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 259 Insignificant: 33 Filtered: 3 Finish binding event prediction: 34.1s Refine read distribution from 142 binding events. --------------------------- Events discovered Significant: 146 Insignificant: 66 Filtered: 3 Finish binding event prediction: 1.2m Refine read distribution from 96 binding events. --------------------------- Events discovered Significant: 185 Insignificant: 56 Filtered: 1 Finish binding event prediction: 1.1m Refine read distribution from 136 binding events. --------------------------- Events discovered Significant: 233 Insignificant: 30 Filtered: 5 Finish binding event prediction: 41.1s Refine read distribution from 138 binding events. --------------------------- Events discovered Significant: 158 Insignificant: 48 Filtered: 4 Finish binding event prediction: 1.1m Refine read distribution from 110 binding events. --------------------------- Events discovered Significant: 198 Insignificant: 2 Filtered: 29 Finish binding event prediction: 4.2m Refine read distribution from 68 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 52 Insignificant: 0 Filtered: 15 Finish binding event prediction: 4.3m Refine read distribution from 31 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 255 Insignificant: 31 Filtered: 4 Finish binding event prediction: 53.1s Refine read distribution from 140 binding events. --------------------------- Events discovered Significant: 21 Insignificant: 0 Filtered: 7 Finish binding event prediction: 5.8m Refine read distribution from 17 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 32 Insignificant: 21 Filtered: 17 Finish binding event prediction: 5.9m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 255 Insignificant: 16 Filtered: 0 Finish binding event prediction: 1.9m Refine read distribution from 194 binding events. --------------------------- Events discovered Significant: 112 Insignificant: 4 Filtered: 0 Finish binding event prediction: 1.6m Refine read distribution from 85 binding events. --------------------------- Events discovered Significant: 124 Insignificant: 21 Filtered: 1 Finish binding event prediction: 1.7m Refine read distribution from 82 binding events. ============================================== 2025-02-21 21:08:58 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_1.1x36mers.unique.GPS ============================================== 2025-02-21 21:08:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 2075470 HitCounts: 3947063.0 ============================================== 2025-02-21 21:08:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 2075470 HitCounts: 3947063.0 Original read count stats: _IP Bases: 2059637 HitCounts: 4263014.0 ============================================== 2025-02-21 21:09:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc1_ChIPexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 1187546 HitCounts: 2271039.0 ============================================== 2025-02-21 21:09:02 At Poisson p-value 1.0e-03, in a 301bp window, expect 175 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc2_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-21 21:09:02 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc2_ChIPexo.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 343 reads. The genome is segmented into 8148 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1618403 HitCounts: 4739985.0 Original read count stats: _IP Bases: 1622652 HitCounts: 5166553.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 343 reads. ============================================== 2025-02-21 21:09:03 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_2.SE.a.GPS ============================================== 2025-02-21 21:09:03 At Poisson p-value 1.0e-03, in a 301bp window, expect 364 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc1_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-21 21:09:03 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc1_ChIPexo.SE.a.GPS ============================================== 2025-02-21 21:09:03 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_2.SE.a.GPS The genome is segmented into 8448 regions for analysis. ============================================== 2025-02-21 21:09:03 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_1.SE.a.GPS Original read count stats: ============================================== 2025-02-21 21:09:04_IP Bases: 2217025 HitCounts: 5965128.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_1.SE.a.GPS Original read count stats: _IP Bases: 1673120 HitCounts: 5250822.0 The genome is segmented into 8448 regions for analysis. Original read count stats: _IP Bases: 1675720 HitCounts: 5701076.0 Running with 1 threads ... Original read count stats: _IP Bases: 2237823 HitCounts: 5848235.0 ============================================== 2025-02-21 21:09:04 Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_2.SE.a.GPS _IP Bases: 2237823 HitCounts: 5848235.0 Original read count stats: _IP Bases: 2118691 HitCounts: 5559372.0 The genome is segmented into 8542 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2029489 HitCounts: 6375548.0 ============================================== 2025-02-21 21:09:05 ============================================== 2025-02-21 21:09:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc1_ChIPexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc1_ChIPexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 351 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 365 reads. Original read count stats: _IP Bases: 369555 HitCounts: 6482466.0 Original read count stats: _IP Bases: 1327092 HitCounts: 5721611.0 The genome is segmented into 8510 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 76 reads. The genome is segmented into 8402 regions for analysis. The genome is segmented into 8688 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:09:07 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 382 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 395 reads. Original read count stats: _IP Bases: 1962927 HitCounts: 3916062.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 483 reads. The genome is segmented into 8480 regions for analysis. The genome is segmented into 8652 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 455 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 484 reads. The genome is segmented into 8714 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 484 reads. The genome is segmented into 8684 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 518 reads. The genome is segmented into 8607 regions for analysis. Running with 1 threads ... The genome is segmented into 8607 regions for analysis. Running with 1 threads ... The genome is segmented into 8714 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 428 reads. Running with 1 threads ... The genome is segmented into 8310 regions for analysis. ============================================== 2025-02-21 21:09:10 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc2_ChIPexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 338 reads. Original read count stats: _IP Bases: 457192 HitCounts: 9211598.0 The genome is segmented into 8525 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 104 reads. ============================================== 2025-02-21 21:09:12 The genome is segmented into 8327 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc1_ChIPexo.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 458281 HitCounts: 1.0303767E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 265 reads. The genome is segmented into 8573 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:09:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc2_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 554652 HitCounts: 1.4257693E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 356 reads. The genome is segmented into 8485 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 285 Insignificant: 2 Filtered: 36 Finish binding event prediction: 1.5m Refine read distribution from 86 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 328 Insignificant: 37 Filtered: 3 Finish binding event prediction: 41.1s Refine read distribution from 172 binding events. --------------------------- Events discovered Significant: 108 Insignificant: 87 Filtered: 27 Finish binding event prediction: 2.2m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 176 Insignificant: 0 Filtered: 58 Finish binding event prediction: 2.8m Refine read distribution from 143 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 31 Insignificant: 1 Filtered: 10 Finish binding event prediction: 2.9m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 139 Insignificant: 66 Filtered: 23 Finish binding event prediction: 2.8m Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 18 Insignificant: 33 Filtered: 6 Finish binding event prediction: 3.1m Refine read distribution from 6 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 321 Insignificant: 2 Filtered: 28 Finish binding event prediction: 3.1m Refine read distribution from 89 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 59 Insignificant: 14 Filtered: 20 Finish binding event prediction: 3.3m Refine read distribution from 34 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 166 Insignificant: 0 Filtered: 52 Finish binding event prediction: 3.4m Refine read distribution from 145 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 47 Insignificant: 36 Filtered: 19 Finish binding event prediction: 3.4m Refine read distribution from 18 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 163 Insignificant: 1 Filtered: 53 Finish binding event prediction: 3.4m Refine read distribution from 134 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 32 Insignificant: 1 Filtered: 11 Finish binding event prediction: 3.5m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 42 Insignificant: 19 Filtered: 11 Finish binding event prediction: 44.1s Refine read distribution from 13 binding events. --------------------------- Events discovered Significant: 48 Insignificant: 13 Filtered: 20 Finish binding event prediction: 3.8m Refine read distribution from 30 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 44 Insignificant: 34 Filtered: 2 Finish binding event prediction: 48.2s Refine read distribution from 13 binding events. --------------------------- Events discovered Significant: 46 Insignificant: 1 Filtered: 15 Finish binding event prediction: 4.0m Refine read distribution from 31 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 175 Insignificant: 70 Filtered: 9 Finish binding event prediction: 1.0m Refine read distribution from 99 binding events. --------------------------- Events discovered Significant: 17 Insignificant: 9 Filtered: 8 Finish binding event prediction: 4.2m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 146 Insignificant: 73 Filtered: 4 Finish binding event prediction: 2.0m Refine read distribution from 62 binding events. --------------------------- Events discovered Significant: 383 Insignificant: 59 Filtered: 5 Finish binding event prediction: 1.2m Refine read distribution from 222 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 2 Filtered: 2 Finish binding event prediction: 4.5m Running with 1 threads ... --------------------------- Events discovered Significant: 17 Insignificant: 9 Filtered: 8 Finish binding event prediction: 4.5m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 172 Insignificant: 0 Filtered: 57 Finish binding event prediction: 4.5m Refine read distribution from 147 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 242 Insignificant: 39 Filtered: 0 Finish binding event prediction: 1.3m Refine read distribution from 175 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 2 Filtered: 2 Finish binding event prediction: 4.9m Running with 1 threads ... --------------------------- Events discovered Significant: 272 Insignificant: 10 Filtered: 2 Finish binding event prediction: 1.6m Refine read distribution from 209 binding events. --------------------------- Events discovered Significant: 320 Insignificant: 36 Filtered: 1 Finish binding event prediction: 1.7m Refine read distribution from 237 binding events. --------------------------- Events discovered Significant: 59 Insignificant: 15 Filtered: 1 Finish binding event prediction: 1.0m Refine read distribution from 46 binding events. --------------------------- Events discovered Significant: 1373 Insignificant: 212 Filtered: 5 Finish binding event prediction: 2.6m Refine read distribution from 967 binding events. --------------------------- Events discovered Significant: 292 Insignificant: 40 Filtered: 1 Finish binding event prediction: 1.6m Refine read distribution from 229 binding events. --------------------------- Events discovered Significant: 59 Insignificant: 15 Filtered: 1 Finish binding event prediction: 57.2s Refine read distribution from 46 binding events. --------------------------- Events discovered Significant: 323 Insignificant: 15 Filtered: 0 Finish binding event prediction: 1.5m Refine read distribution from 262 binding events. --------------------------- Events discovered Significant: 1299 Insignificant: 217 Filtered: 8 Finish binding event prediction: 2.3m Refine read distribution from 954 binding events. --------------------------- Events discovered Significant: 1332 Insignificant: 224 Filtered: 8 Finish binding event prediction: 2.4m Refine read distribution from 962 binding events. --------------------------- Events discovered Significant: 1341 Insignificant: 200 Filtered: 10 Finish binding event prediction: 2.7m Refine read distribution from 959 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 2 Filtered: 2 Finish binding event prediction: 3.0m --------------------------- Events discovered Significant: 5 Insignificant: 2 Filtered: 2 Finish binding event prediction: 3.4m ============================================== 2025-02-21 21:18:10 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/Ybih_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/Ybih_glc2_ChIPexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 543195 HitCounts: 1392083.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 82 reads. ============================================== 2025-02-21 21:18:11 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc1_ChIPexo.1x36mers.unique.GPS The genome is segmented into 8336 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1831636 HitCounts: 2670029.0 ============================================== 2025-02-21 21:18:12 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc1_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 1875154 HitCounts: 3158304.0 ============================================== 2025-02-21 21:18:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/Ybih_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/Ybih_glc2_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 639738 HitCounts: 2052870.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 237 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 132 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 274 reads. The genome is segmented into 8500 regions for analysis. Running with 1 threads ... The genome is segmented into 8027 regions for analysis. Running with 1 threads ... The genome is segmented into 8188 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:18:17 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc2_ChIPexo.SE.a.GPS ============================================== 2025-02-21 21:18:17 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc2_ChIPexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 2266622 HitCounts: 4559295.0 Original read count stats: _IP Bases: 1205994 HitCounts: 2678812.0 ============================================== 2025-02-21 21:18:19 ============================================== 2025-02-21 21:18:19 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace1_ChIPexp.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace1_ChIPexp.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc2_ChIPexo.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 192 reads. Original read count stats: _IP Bases: 597430 HitCounts: 5335290.0 Original read count stats: _IP Bases: 1346539 HitCounts: 7092185.0 ============================================== 2025-02-21 21:18:20 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbiH_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbiH_glc1_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-21 21:18:21 Original read count stats: _IP Bases: 843900 HitCounts: 5931041.0 The genome is segmented into 8190 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace2_ChIPexo.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 369 reads. Running with 1 threads ... Original read count stats: _IP Bases: 546927 HitCounts: 5781067.0 The genome is segmented into 8298 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:18:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc2_ChIPexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 216 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 180 reads. The genome is segmented into 8460 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2106195 HitCounts: 3620796.0 The genome is segmented into 8235 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:18:23 At Poisson p-value 1.0e-03, in a 301bp window, expect 214 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace1_ChIPexp.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace1_ChIPexp.1x36mers.unique.GPS Original read count stats: _IP Bases: 494928 HitCounts: 3533937.0 The genome is segmented into 8518 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 505 reads. ============================================== 2025-02-21 21:18:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace2_ChIPexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 98 reads. The genome is segmented into 8365 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 300 reads. Original read count stats: _IP Bases: 448563 HitCounts: 3762205.0 The genome is segmented into 8310 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 90 reads. The genome is segmented into 8119 regions for analysis. Running with 1 threads ... The genome is segmented into 8352 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:18:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbiH_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbiH_glc1_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 963221 HitCounts: 8703987.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 348 reads. The genome is segmented into 8389 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 56 Insignificant: 28 Filtered: 21 Finish binding event prediction: 1.6m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 127 Insignificant: 54 Filtered: 25 Finish binding event prediction: 2.3m Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 94 Insignificant: 46 Filtered: 23 Finish binding event prediction: 2.2m Refine read distribution from 27 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 75 Insignificant: 0 Filtered: 17 Finish binding event prediction: 2.6m Refine read distribution from 37 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 117 Insignificant: 49 Filtered: 28 Finish binding event prediction: 2.5m Refine read distribution from 37 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 188 Insignificant: 65 Filtered: 2 Finish binding event prediction: 1.3m Refine read distribution from 133 binding events. --------------------------- Events discovered Significant: 251 Insignificant: 25 Filtered: 3 Finish binding event prediction: 34.1s Refine read distribution from 193 binding events. --------------------------- Events discovered Significant: 32 Insignificant: 2 Filtered: 10 Finish binding event prediction: 3.1m Refine read distribution from 18 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 231 Insignificant: 0 Filtered: 31 Finish binding event prediction: 3.0m Refine read distribution from 92 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 170 Insignificant: 60 Filtered: 2 Finish binding event prediction: 50.1s Refine read distribution from 117 binding events. --------------------------- Events discovered Significant: 261 Insignificant: 78 Filtered: 2 Finish binding event prediction: 52.1s Refine read distribution from 184 binding events. --------------------------- Events discovered Significant: 253 Insignificant: 1 Filtered: 28 Finish binding event prediction: 3.5m Refine read distribution from 91 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 4 Filtered: 4 Finish binding event prediction: 3.7m Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 4 Filtered: 3 Finish binding event prediction: 3.6m Running with 1 threads ... --------------------------- Events discovered Significant: 20 Insignificant: 33 Filtered: 6 Finish binding event prediction: 3.7m Refine read distribution from 6 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 151 Insignificant: 0 Filtered: 35 Finish binding event prediction: 3.9m Refine read distribution from 69 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 46 Insignificant: 22 Filtered: 14 Finish binding event prediction: 1.0m Refine read distribution from 14 binding events. --------------------------- Events discovered Significant: 13 Insignificant: 0 Filtered: 4 Finish binding event prediction: 4.2m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 279 Insignificant: 65 Filtered: 2 Finish binding event prediction: 1.0m Refine read distribution from 164 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 4.1m Running with 1 threads ... --------------------------- Events discovered Significant: 185 Insignificant: 72 Filtered: 1 Finish binding event prediction: 1.8m Refine read distribution from 117 binding events. --------------------------- Events discovered Significant: 366 Insignificant: 51 Filtered: 3 Finish binding event prediction: 51.1s Refine read distribution from 259 binding events. --------------------------- Events discovered Significant: 41 Insignificant: 3 Filtered: 1 Finish binding event prediction: 46.1s Refine read distribution from 37 binding events. --------------------------- Events discovered Significant: 50 Insignificant: 51 Filtered: 4 Finish binding event prediction: 1.2m Refine read distribution from 17 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 4 Filtered: 3 Finish binding event prediction: 1.7m --------------------------- Events discovered Significant: 9 Insignificant: 4 Filtered: 4 Finish binding event prediction: 2.0m --------------------------- Events discovered Significant: 278 Insignificant: 40 Filtered: 1 Finish binding event prediction: 2.3m Refine read distribution from 168 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 2.8m ============================================== 2025-02-21 21:26:49 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc1_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-21 21:26:49 ============================================== 2025-02-21 21:26:49 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc2_ChIPexo.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc1_ChIPexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 1282628 HitCounts: 3060253.0 Original read count stats: _IP Bases: 1047968 HitCounts: 2265185.0 Original read count stats: _IP Bases: 1656846 HitCounts: 3399376.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 164 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 211 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 261 reads. ============================================== 2025-02-21 21:26:52 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_2_ChIPexo.1x36mers.unique.GPS The genome is segmented into 8063 regions for analysis. Running with 1 threads ... The genome is segmented into 8067 regions for analysis. Running with 1 threads ... Original read count stats: ============================================== 2025-02-21 21:26:53_IP Bases: 990904 HitCounts: 4627757.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc2_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-21 21:26:53 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc1_ChIPexo.SE.a.GPS ============================================== 2025-02-21 21:26:53 The genome is segmented into 8115 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc1_ChIPexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 1075222 HitCounts: 2515621.0 Running with 1 threads ... Original read count stats: _IP Bases: 1481417 HitCounts: 3297764.0 Original read count stats: _IP Bases: 1709302 HitCounts: 4724037.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 210 reads. ============================================== 2025-02-21 21:26:54 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_2_ChIPexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 168 reads. The genome is segmented into 8261 regions for analysis. Original read count stats: _IP Bases: 1074920 HitCounts: 3305175.0 Running with 1 threads ... ============================================== 2025-02-21 21:26:55 At Poisson p-value 1.0e-03, in a 301bp window, expect 244 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc2_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-21 21:26:55 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_1_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-21 21:26:55 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc1_ChIPexo.1x36mers.unique.GPS The genome is segmented into 8093 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1356204 HitCounts: 3389580.0 Original read count stats: _IP Bases: 2205925 HitCounts: 6047454.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 195 reads. Original read count stats: _IP Bases: 1978188 HitCounts: 5553881.0 The genome is segmented into 8173 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 352 reads. Running with 1 threads ... The genome is segmented into 8244 regions for analysis. Running with 1 threads ... The genome is segmented into 8177 regions for analysis. ============================================== 2025-02-21 21:26:57 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc1_ChIPexo.SE.a.GPS ============================================== 2025-02-21 21:26:57 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc1_ChIPexo.SE.a.GPS ============================================== 2025-02-21 21:26:57 At Poisson p-value 1.0e-03, in a 301bp window, expect 235 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc1_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 2122957 HitCounts: 6414530.0 Original read count stats: _IP Bases: 1628172 HitCounts: 7375457.0 The genome is segmented into 8190 regions for analysis. ============================================== 2025-02-21 21:26:58 Running with 1 threads ... Original read count stats: _IP Bases: 1347668 HitCounts: 5571014.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc2_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-21 21:26:58 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc2_ChIPexo.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 354 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 397 reads. Original read count stats: _IP Bases: 1241813 HitCounts: 3868336.0 ============================================== 2025-02-21 21:26:59 ============================================== 2025-02-21 21:26:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc2_ChIPexo.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc2_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 1380503 HitCounts: 7734162.0 The genome is segmented into 8056 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1175323 HitCounts: 3446599.0 Original read count stats: _IP Bases: 2361437 HitCounts: 6990153.0 ============================================== 2025-02-21 21:27:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_1_ChIPexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 223 reads. The genome is segmented into 7998 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 917095 HitCounts: 4325586.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 412 reads. The genome is segmented into 8200 regions for analysis. Running with 1 threads ... The genome is segmented into 8235 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 383 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 250 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 516 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 195 reads. ============================================== 2025-02-21 21:27:02 The genome is segmented into 8189 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_1_ChIPexo.SE.a.GPS Running with 1 threads ... The genome is segmented into 8325 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 479 reads. The genome is segmented into 8265 regions for analysis. Original read count stats: _IP Bases: 1044243 HitCounts: 9439826.0 Running with 1 threads ... The genome is segmented into 8303 regions for analysis. Running with 1 threads ... The genome is segmented into 8357 regions for analysis. ============================================== 2025-02-21 21:27:03 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_2_ChIPexo.SE.a.GPS ============================================== 2025-02-21 21:27:04 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_1_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 1209739 HitCounts: 1.0516335E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 462 reads. ============================================== 2025-02-21 21:27:04 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_2_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 1501320 HitCounts: 1.0192229E7 The genome is segmented into 8170 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1122985 HitCounts: 1.0082213E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 507 reads. The genome is segmented into 8450 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 645 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 568 reads. The genome is segmented into 8350 regions for analysis. Running with 1 threads ... The genome is segmented into 8421 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 668 reads. The genome is segmented into 8352 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 52 Insignificant: 45 Filtered: 10 Finish binding event prediction: 2.1m Refine read distribution from 17 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 25 Insignificant: 12 Filtered: 8 Finish binding event prediction: 2.3m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 117 Insignificant: 3 Filtered: 29 Finish binding event prediction: 2.4m Refine read distribution from 28 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 33 Insignificant: 54 Filtered: 12 Finish binding event prediction: 2.3m Refine read distribution from 17 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 13 Insignificant: 0 Filtered: 4 Finish binding event prediction: 2.6m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 133 Insignificant: 2 Filtered: 32 Finish binding event prediction: 2.8m Refine read distribution from 47 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 90 Insignificant: 0 Filtered: 25 Finish binding event prediction: 2.7m Refine read distribution from 35 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 36 Insignificant: 58 Filtered: 14 Finish binding event prediction: 2.7m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 57 Insignificant: 51 Filtered: 13 Finish binding event prediction: 2.7m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 154 Insignificant: 3 Filtered: 38 Finish binding event prediction: 2.8m --------------------------- Events discovered Significant: 8 Insignificant: 20 Filtered: 9 Finish binding event prediction: 2.8m Refine read distribution from 57 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 12 Insignificant: 26 Filtered: 4 Finish binding event prediction: 2.8m Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 17 Insignificant: 17 Filtered: 6 Finish binding event prediction: 2.9m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 30 Insignificant: 44 Filtered: 10 Finish binding event prediction: 2.8m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 46 Insignificant: 2 Filtered: 11 Finish binding event prediction: 3.2m Refine read distribution from 28 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 16 Insignificant: 28 Filtered: 4 Finish binding event prediction: 3.1m Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 193 Insignificant: 7 Filtered: 6 Finish binding event prediction: 58.2s Refine read distribution from 61 binding events. --------------------------- Events discovered Significant: 108 Insignificant: 102 Filtered: 1 Finish binding event prediction: 52.1s --------------------------- Events discovered Significant: 36 Insignificant: 15 Filtered: 0 Refine read distribution from 98 binding events. Finish binding event prediction: 27.1s Refine read distribution from 21 binding events. --------------------------- Events discovered Significant: 69 Insignificant: 2 Filtered: 8 Finish binding event prediction: 3.5m Refine read distribution from 37 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 39 Insignificant: 2 Filtered: 6 Finish binding event prediction: 3.4m Refine read distribution from 18 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 122 Insignificant: 81 Filtered: 0 Finish binding event prediction: 1.2m Refine read distribution from 91 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 21 Filtered: 9 Finish binding event prediction: 3.5m Running with 1 threads ... --------------------------- Events discovered Significant: 59 Insignificant: 22 Filtered: 0 Finish binding event prediction: 43.1s Refine read distribution from 39 binding events. --------------------------- Events discovered Significant: 11 Insignificant: 0 Filtered: 3 Finish binding event prediction: 3.7m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 135 Insignificant: 35 Filtered: 1 Finish binding event prediction: 1.3m Refine read distribution from 94 binding events. --------------------------- Events discovered Significant: 226 Insignificant: 13 Filtered: 10 Finish binding event prediction: 57.1s Refine read distribution from 99 binding events. --------------------------- Events discovered Significant: 140 Insignificant: 50 Filtered: 0 Finish binding event prediction: 52.1s Refine read distribution from 79 binding events. --------------------------- Events discovered Significant: 111 Insignificant: 44 Filtered: 0 Finish binding event prediction: 1.2m Refine read distribution from 74 binding events. --------------------------- Events discovered Significant: 33 Insignificant: 17 Filtered: 0 Finish binding event prediction: 32.1s Refine read distribution from 15 binding events. --------------------------- Events discovered Significant: 83 Insignificant: 36 Filtered: 1 Finish binding event prediction: 58.2s Refine read distribution from 55 binding events. --------------------------- Events discovered Significant: 150 Insignificant: 3 Filtered: 11 Finish binding event prediction: 1.1m Refine read distribution from 55 binding events. --------------------------- Events discovered Significant: 39 Insignificant: 0 Filtered: 10 Finish binding event prediction: 3.9m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 100 Insignificant: 34 Filtered: 3 Finish binding event prediction: 56.1s Refine read distribution from 63 binding events. --------------------------- Events discovered Significant: 81 Insignificant: 18 Filtered: 15 Finish binding event prediction: 1.1m Refine read distribution from 37 binding events. --------------------------- Events discovered Significant: 199 Insignificant: 18 Filtered: 1 Finish binding event prediction: 49.2s Refine read distribution from 184 binding events. --------------------------- Events discovered Significant: 43 Insignificant: 1 Filtered: 10 Finish binding event prediction: 4.3m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 8 Insignificant: 20 Filtered: 9 Finish binding event prediction: 1.6m --------------------------- Events discovered Significant: 51 Insignificant: 26 Filtered: 1 Finish binding event prediction: 50.1s Refine read distribution from 45 binding events. --------------------------- Events discovered Significant: 268 Insignificant: 21 Filtered: 4 Finish binding event prediction: 1.7m Refine read distribution from 119 binding events. --------------------------- Events discovered Significant: 101 Insignificant: 17 Filtered: 7 Finish binding event prediction: 1.2m Refine read distribution from 53 binding events. --------------------------- Events discovered Significant: 199 Insignificant: 0 Filtered: 1 Finish binding event prediction: 49.1s Refine read distribution from 191 binding events. --------------------------- Events discovered Significant: 39 Insignificant: 0 Filtered: 9 Finish binding event prediction: 4.7m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 21 Filtered: 9 Finish binding event prediction: 1.7m --------------------------- Events discovered Significant: 200 Insignificant: 0 Filtered: 3 Finish binding event prediction: 49.1s Refine read distribution from 187 binding events. --------------------------- Events discovered Significant: 199 Insignificant: 14 Filtered: 3 Finish binding event prediction: 1.4m Refine read distribution from 181 binding events. ============================================== 2025-02-21 21:37:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_30C_rep2.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/SigH_30C_rep2.1x36mers.unique.GPS Original read count stats: _IP Bases: 209881 HitCounts: 783247.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 41 reads. ============================================== 2025-02-21 21:37:22 The genome is segmented into 8198 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_30C_rep2.SE.a.bam --out 13-E.coli-SigH-GSE60667/SigH_30C_rep2.SE.a.GPS Original read count stats: _IP Bases: 241297 HitCounts: 972770.0 ============================================== 2025-02-21 21:37:23 ============================================== 2025-02-21 21:37:23 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_30C_rep1.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/SigH_30C_rep1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 53 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_42C_rep1.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/SigH_42C_rep1.1x36mers.unique.GPS The genome is segmented into 8376 regions for analysis. Original read count stats: _IP Bases: 502630 HitCounts: 1164140.0 Running with 1 threads ... Original read count stats: _IP Bases: 518443 HitCounts: 1165275.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 90 reads. ============================================== 2025-02-21 21:37:24 At Poisson p-value 1.0e-03, in a 301bp window, expect 93 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_42C_rep1.SE.a.bam --out 13-E.coli-SigH-GSE60667/SigH_42C_rep1.SE.a.GPS ============================================== 2025-02-21 21:37:25 The genome is segmented into 8121 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_30C_rep1.SE.a.bam --out 13-E.coli-SigH-GSE60667/SigH_30C_rep1.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 572078 HitCounts: 1386680.0 Original read count stats: _IP Bases: 559314 HitCounts: 1408673.0 The genome is segmented into 8165 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 110 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 109 reads. The genome is segmented into 8325 regions for analysis. Running with 1 threads ... The genome is segmented into 8286 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:37:29 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc2_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 1211564 HitCounts: 4834683.0 ============================================== 2025-02-21 21:37:30 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc1_ChIPexo.1x36mers.unique.GPS ============================================== 2025-02-21 21:37:30 Original read count stats: _IP Bases: 1746897 HitCounts: 3892383.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc2_ChIPexo.SE.a.GPS ============================================== 2025-02-21 21:37:31 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep1.SE.a.bam --out 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep1.SE.a.GPS Original read count stats: ============================================== 2025-02-21 21:37:31_IP Bases: 1752821 HitCounts: 4369271.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc1_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 1425613 HitCounts: 4612456.0 ============================================== 2025-02-21 21:37:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep1.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1790537 HitCounts: 4585003.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 336 reads. Original read count stats: _IP Bases: 1309542 HitCounts: 2446813.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 286 reads. The genome is segmented into 8263 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:37:33 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep2.SE.a.bam --out 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 318 reads. Original read count stats: _IP Bases: 1521678 HitCounts: 5489183.0 The genome is segmented into 7998 regions for analysis. Running with 1 threads ... The genome is segmented into 8215 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 334 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 229 reads. The genome is segmented into 8138 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 385 reads. ============================================== 2025-02-21 21:37:35 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc2_ChIPexo.1x36mers.unique.GPS The genome is segmented into 8236 regions for analysis. Original read count stats: _IP Bases: 1610631 HitCounts: 3491921.0 Running with 1 threads ... The genome is segmented into 8074 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:37:36 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep2.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1404555 HitCounts: 2834972.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 254 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 437 reads. The genome is segmented into 8220 regions for analysis. Running with 1 threads ... The genome is segmented into 8050 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 257 reads. The genome is segmented into 8065 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:37:41 ============================================== 2025-02-21 21:37:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc2_ChIPexo.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc1_ChIPexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 1068257 HitCounts: 9824664.0 Original read count stats: _IP Bases: 1563229 HitCounts: 1.1097442E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 251 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 406 reads. The genome is segmented into 8081 regions for analysis. Running with 1 threads ... The genome is segmented into 8089 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:37:51 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 12-E.coli-cysB-metJ-GSE122320/cysB_taur_2_ChIPexo.PE.a.bam --out 12-E.coli-cysB-metJ-GSE122320/cysB_taur_2_ChIPexo.PE.a.GPS Original read count stats: _IP Bases: 2054929 HitCounts: 1.273821E7 ============================================== 2025-02-21 21:37:53 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc2_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 1202264 HitCounts: 1.5698825E7 ============================================== 2025-02-21 21:37:56 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 12-E.coli-cysB-metJ-GSE122320/metJ_meio_2_ChIPexo.PE.a.bam --out 12-E.coli-cysB-metJ-GSE122320/metJ_meio_2_ChIPexo.PE.a.GPS Original read count stats: _IP Bases: 4000280 HitCounts: 1.3723754E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 845 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 597 reads. ============================================== 2025-02-21 21:37:59 The genome is segmented into 8717 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 12-E.coli-cysB-metJ-GSE122320/metJ_meio_1_ChIPexo.PE.a.bam --out 12-E.coli-cysB-metJ-GSE122320/metJ_meio_1_ChIPexo.PE.a.GPS Running with 1 threads ... The genome is segmented into 8231 regions for analysis. ============================================== 2025-02-21 21:37:59 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc1_ChIPexo.SE.a.GPS Original read count stats: _IP Bases: 1714830 HitCounts: 1.8162704E7 Original read count stats: _IP Bases: 4211725 HitCounts: 1.5186838E7 ============================================== 2025-02-21 21:38:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 12-E.coli-cysB-metJ-GSE122320/cysB_taur_1_ChIPexo.PE.a.bam --out 12-E.coli-cysB-metJ-GSE122320/cysB_taur_1_ChIPexo.PE.a.GPS Original read count stats: _IP Bases: 2202941 HitCounts: 1.6697324E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 819 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 1087 reads. The genome is segmented into 8245 regions for analysis. Running with 1 threads ... The genome is segmented into 8653 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 1060 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 1193 reads. The genome is segmented into 8728 regions for analysis. Running with 1 threads ... The genome is segmented into 8681 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 847 Insignificant: 1 Filtered: 103 Finish binding event prediction: 1.2m Refine read distribution from 524 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 756 Insignificant: 13 Filtered: 155 Finish binding event prediction: 1.2m Refine read distribution from 520 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 919 Insignificant: 1 Filtered: 197 Finish binding event prediction: 1.8m Refine read distribution from 641 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 996 Insignificant: 206 Filtered: 6 Finish binding event prediction: 41.1s Refine read distribution from 804 binding events. --------------------------- Events discovered Significant: 26 Insignificant: 41 Filtered: 9 Finish binding event prediction: 1.8m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 919 Insignificant: 11 Filtered: 202 Finish binding event prediction: 2.1m Refine read distribution from 666 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 960 Insignificant: 0 Filtered: 192 Finish binding event prediction: 2.2m Refine read distribution from 674 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1349 Insignificant: 417 Filtered: 2 Finish binding event prediction: 30.2s Refine read distribution from 1092 binding events. --------------------------- Events discovered Significant: 844 Insignificant: 263 Filtered: 6 Finish binding event prediction: 1.1m Refine read distribution from 641 binding events. --------------------------- Events discovered Significant: 60 Insignificant: 55 Filtered: 16 Finish binding event prediction: 2.0m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 432 Insignificant: 1 Filtered: 129 Finish binding event prediction: 2.4m Refine read distribution from 299 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1379 Insignificant: 439 Filtered: 4 Finish binding event prediction: 36.2s Refine read distribution from 1082 binding events. --------------------------- Events discovered Significant: 74 Insignificant: 55 Filtered: 2 Finish binding event prediction: 59.2s Refine read distribution from 32 binding events. --------------------------- Events discovered Significant: 122 Insignificant: 1 Filtered: 25 Finish binding event prediction: 2.8m Refine read distribution from 42 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 46 Insignificant: 41 Filtered: 14 Finish binding event prediction: 2.4m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 14 Insignificant: 12 Filtered: 8 Finish binding event prediction: 3.1m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 12 Insignificant: 4 Filtered: 5 Finish binding event prediction: 3.1m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 370 Insignificant: 11 Filtered: 124 Finish binding event prediction: 3.1m Refine read distribution from 201 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1170 Insignificant: 448 Filtered: 51 Finish binding event prediction: 1.3m Refine read distribution from 909 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 20 Filtered: 0 Finish binding event prediction: 2.9m Running with 1 threads ... --------------------------- Events discovered Significant: 855 Insignificant: 7 Filtered: 213 Finish binding event prediction: 3.5m Refine read distribution from 652 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 128 Insignificant: 45 Filtered: 0 Finish binding event prediction: 1.0m Refine read distribution from 83 binding events. --------------------------- Events discovered Significant: 384 Insignificant: 22 Filtered: 128 Finish binding event prediction: 3.4m Refine read distribution from 219 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 14 Insignificant: 0 Filtered: 4 Finish binding event prediction: 3.5m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 14 Insignificant: 0 Filtered: 4 Finish binding event prediction: 3.9m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 208 Insignificant: 21 Filtered: 2 Finish binding event prediction: 55.1s Refine read distribution from 100 binding events. --------------------------- Events discovered Significant: 73 Insignificant: 14 Filtered: 0 Finish binding event prediction: 47.2s Refine read distribution from 67 binding events. --------------------------- Events discovered Significant: 112 Insignificant: 32 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 60 binding events. --------------------------- Events discovered Significant: 986 Insignificant: 330 Filtered: 43 --------------------------- Events discovered Significant: 1173 Insignificant: 440 Filtered: 7 Finish binding event prediction: 1.6m Finish binding event prediction: 41.2s Refine read distribution from 706 binding events. Refine read distribution from 926 binding events. --------------------------- Events discovered Significant: 71 Insignificant: 36 Filtered: 0 Finish binding event prediction: 58.1s Refine read distribution from 51 binding events. --------------------------- Events discovered Significant: 72 Insignificant: 3 Filtered: 21 Finish binding event prediction: 3.9m Refine read distribution from 32 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 6 Filtered: 1 Finish binding event prediction: 3.6m Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 2 Filtered: 2 Finish binding event prediction: 3.6m Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 15 Filtered: 1 Finish binding event prediction: 3.7m Running with 1 threads ... --------------------------- Events discovered Significant: 42 Insignificant: 7 Filtered: 0 Finish binding event prediction: 46.1s Refine read distribution from 42 binding events. --------------------------- Events discovered Significant: 391 Insignificant: 2 Filtered: 119 Finish binding event prediction: 4.4m Refine read distribution from 248 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 20 Filtered: 0 Finish binding event prediction: 1.2m --------------------------- Events discovered Significant: 46 Insignificant: 30 Filtered: 0 Finish binding event prediction: 58.1s Refine read distribution from 42 binding events. --------------------------- Events discovered Significant: 143 Insignificant: 8 Filtered: 3 Finish binding event prediction: 54.6s Refine read distribution from 68 binding events. --------------------------- Events discovered Significant: 707 Insignificant: 277 Filtered: 45 Finish binding event prediction: 2.0m Refine read distribution from 491 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 15 Filtered: 1 Finish binding event prediction: 1.3m --------------------------- Events discovered Significant: 985 Insignificant: 317 Filtered: 30 Finish binding event prediction: 1.6m Refine read distribution from 689 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 6 Filtered: 1 Finish binding event prediction: 1.9m --------------------------- Events discovered Significant: 4 Insignificant: 2 Filtered: 2 Finish binding event prediction: 2.0m --------------------------- Events discovered Significant: 661 Insignificant: 281 Filtered: 56 Finish binding event prediction: 3.5m Refine read distribution from 473 binding events. ============================================== 2025-02-21 21:49:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_42C_rep2.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/SigH_42C_rep2.1x36mers.unique.GPS Original read count stats: _IP Bases: 292571 HitCounts: 1028084.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 63 reads. The genome is segmented into 8245 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:50:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_42C_rep2.SE.a.bam --out 13-E.coli-SigH-GSE60667/SigH_42C_rep2.SE.a.GPS Original read count stats: _IP Bases: 330253 HitCounts: 1253451.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 77 reads. The genome is segmented into 8427 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:50:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR2_Chipexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 214243 HitCounts: 2296872.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 35 reads. The genome is segmented into 8508 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:50:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR2_Chipexo.SE.a.GPS ============================================== 2025-02-21 21:50:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR2_Chipexo.SE.a.GPS Original read count stats: _IP Bases: 239441 HitCounts: 2626261.0 ============================================== 2025-02-21 21:50:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR1_Chipexo.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 42 reads. ============================================== 2025-02-21 21:50:08 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_2.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 2357226 HitCounts: 4201743.0 ============================================== 2025-02-21 21:50:08 Original read count stats: _IP Bases: 2374561 HitCounts: 4213036.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_1.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_1.1x36mers.unique.GPS The genome is segmented into 8716 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:50:09 ============================================== 2025-02-21 21:50:09 Original read count stats: _IP Bases: 2660419 HitCounts: 3886369.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_1.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_1.SE.a.GPS Original read count stats: _IP Bases: 827343 HitCounts: 4985011.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_2.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_2.SE.a.GPS ============================================== 2025-02-21 21:50:09 Original read count stats: _IP Bases: 2280649 HitCounts: 5093285.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE1_Chipexo.SE.a.GPS Original read count stats: _IP Bases: 2820191 HitCounts: 5038373.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 165 reads. Original read count stats: _IP Bases: 2182657 HitCounts: 3924083.0 The genome is segmented into 8228 regions for analysis. ============================================== 2025-02-21 21:50:10 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE2_Chipexo.SE.a.GPS Running with 1 threads ... ============================================== 2025-02-21 21:50:11 At Poisson p-value 1.0e-03, in a 301bp window, expect 355 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_2.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_2.SE.a.GPS Original read count stats: _IP Bases: 2175771 HitCounts: 4272864.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 357 reads. The genome is segmented into 8254 regions for analysis. Original read count stats: _IP Bases: 848694 HitCounts: 6029784.0 Running with 1 threads ... The genome is segmented into 8252 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 351 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 438 reads. ============================================== 2025-02-21 21:50:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_1.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_1.1x36mers.unique.GPS The genome is segmented into 8429 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 337 reads. Running with 1 threads ... ============================================== 2025-02-21 21:50:13 At Poisson p-value 1.0e-03, in a 301bp window, expect 250 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_1.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_1.SE.a.GPS ============================================== 2025-02-21 21:50:13 The genome is segmented into 8212 regions for analysis. Original read count stats: _IP Bases: 2127751 HitCounts: 3349430.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_2.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 447 reads. Running with 1 threads ... The genome is segmented into 8308 regions for analysis. Running with 1 threads ... The genome is segmented into 8405 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 937867 HitCounts: 6864887.0 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 346 reads. _IP Bases: 377374 HitCounts: 3987404.0 ============================================== 2025-02-21 21:50:14 ============================================== 2025-02-21 21:50:14 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_1.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR1_Chipexo.1x36mers.unique.GPS The genome is segmented into 8372 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 21:50:14 Original read count stats: _IP Bases: 453159 HitCounts: 4051920.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE1_Chipexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 90 reads. The genome is segmented into 8248 regions for analysis. Original read count stats: _IP Bases: 1683890 HitCounts: 3491565.0 Running with 1 threads ... The genome is segmented into 8549 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2067892 HitCounts: 3442736.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 107 reads. The genome is segmented into 8440 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 295 reads. ============================================== 2025-02-21 21:50:16 ============================================== 2025-02-21 21:50:16 At Poisson p-value 1.0e-03, in a 301bp window, expect 285 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_2.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR2_Chipexo.1x36mers.unique.GPS ============================================== 2025-02-21 21:50:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_1.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_1.SE.a.GPS ============================================== 2025-02-21 21:50:16 The genome is segmented into 8267 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB1_Chipexo.1x36mers.unique.GPS ============================================== 2025-02-21 21:50:16 The genome is segmented into 8396 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_2.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_2.1x36mers.unique.GPS Running with 1 threads ... Original read count stats: _IP Bases: 463610 HitCounts: 8799722.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 273 reads. Original read count stats: _IP Bases: 545227 HitCounts: 8969180.0 Original read count stats: _IP Bases: 2217182 HitCounts: 3606084.0 Original read count stats: _IP Bases: 743251 HitCounts: 4363490.0 ============================================== 2025-02-21 21:50:17 Original read count stats: _IP Bases: 2216015 HitCounts: 3387230.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR1_Chipexo.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 297 reads. Original read count stats: _IP Bases: 1799002 HitCounts: 3924880.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 142 reads. The genome is segmented into 8163 regions for analysis. Running with 1 threads ... The genome is segmented into 8233 regions for analysis. Running with 1 threads ... The genome is segmented into 8251 regions for analysis. ============================================== 2025-02-21 21:50:19 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR1_Chipexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 310 reads. ============================================== 2025-02-21 21:50:19 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE2_Chipexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 2233352 HitCounts: 3617240.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 374 reads. The genome is segmented into 8108 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 398 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 307 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 306 reads. Running with 1 threads ... Original read count stats: _IP Bases: 2037009 HitCounts: 3677942.0 The genome is segmented into 8592 regions for analysis. The genome is segmented into 8712 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8400 regions for analysis. Running with 1 threads ... The genome is segmented into 8144 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 311 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 301 reads. The genome is segmented into 8087 regions for analysis. Running with 1 threads ... The genome is segmented into 8073 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 72 Insignificant: 0 Filtered: 10 Finish binding event prediction: 1.3m Refine read distribution from 26 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1023 Insignificant: 0 Filtered: 140 Finish binding event prediction: 1.7m Refine read distribution from 681 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 84 Insignificant: 66 Filtered: 9 Finish binding event prediction: 1.6m Refine read distribution from 27 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 77 Insignificant: 49 Filtered: 10 Finish binding event prediction: 1.9m Refine read distribution from 25 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1090 Insignificant: 313 Filtered: 6 Finish binding event prediction: 38.2s Refine read distribution from 825 binding events. --------------------------- Events discovered Significant: 126 Insignificant: 9 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 87 binding events. --------------------------- Events discovered Significant: 64 Insignificant: 3 Filtered: 16 Finish binding event prediction: 2.5m Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 275 Insignificant: 10 Filtered: 40 Finish binding event prediction: 2.4m Refine read distribution from 101 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 91 Insignificant: 33 Filtered: 17 Finish binding event prediction: 2.5m Refine read distribution from 26 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 134 Insignificant: 68 Filtered: 4 Finish binding event prediction: 55.1s Refine read distribution from 76 binding events. --------------------------- Events discovered Significant: 935 Insignificant: 2 Filtered: 175 Finish binding event prediction: 2.8m Refine read distribution from 606 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 150 Insignificant: 18 Filtered: 1 Finish binding event prediction: 23.1s Refine read distribution from 103 binding events. --------------------------- Events discovered Significant: 93 Insignificant: 32 Filtered: 21 Finish binding event prediction: 3.2m Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 155 Insignificant: 64 Filtered: 2 Finish binding event prediction: 1.2m Refine read distribution from 91 binding events. --------------------------- Events discovered Significant: 409 Insignificant: 59 Filtered: 5 Finish binding event prediction: 47.1s Refine read distribution from 210 binding events. --------------------------- Events discovered Significant: 10 Insignificant: 0 Filtered: 3 Finish binding event prediction: 3.2m Refine read distribution from 2 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 311 Insignificant: 8 Filtered: 35 Finish binding event prediction: 3.3m Refine read distribution from 104 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 215 Insignificant: 46 Filtered: 10 Finish binding event prediction: 52.1s Refine read distribution from 142 binding events. --------------------------- Events discovered Significant: 938 Insignificant: 358 Filtered: 29 Finish binding event prediction: 54.2s Refine read distribution from 690 binding events. --------------------------- Events discovered Significant: 130 Insignificant: 1 Filtered: 35 Finish binding event prediction: 3.8m Refine read distribution from 61 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 2 Finish binding event prediction: 3.7m Running with 1 threads ... --------------------------- Events discovered Significant: 10 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.9m Refine read distribution from 4 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 121 Insignificant: 3 Filtered: 37 Finish binding event prediction: 3.9m Refine read distribution from 58 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 42 Insignificant: 5 Filtered: 8 Finish binding event prediction: 45.1s Refine read distribution from 17 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 9 Filtered: 4 Finish binding event prediction: 4.2m Running with 1 threads ... --------------------------- Events discovered Significant: 199 Insignificant: 55 Filtered: 7 Finish binding event prediction: 1.1m Refine read distribution from 124 binding events. --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 4.4m Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 4 Filtered: 2 Finish binding event prediction: 4.4m Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.4m Running with 1 threads ... --------------------------- Events discovered Significant: 315 Insignificant: 51 Filtered: 1 Finish binding event prediction: 45.1s Refine read distribution from 208 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 310 Insignificant: 33 Filtered: 1 Finish binding event prediction: 45.2s Refine read distribution from 195 binding events. --------------------------- Events discovered Significant: 38 Insignificant: 7 Filtered: 0 Finish binding event prediction: 1.0m Refine read distribution from 32 binding events. --------------------------- Events discovered Significant: 426 Insignificant: 45 Filtered: 3 Finish binding event prediction: 1.6m Refine read distribution from 220 binding events. --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 1 Finish binding event prediction: 4.9m Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 2 Filtered: 1 Finish binding event prediction: 4.9m Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 5.1m Running with 1 threads ... --------------------------- Events discovered Significant: 8 Insignificant: 0 Filtered: 1 Finish binding event prediction: 4.9m Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 5.5m Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 9 Filtered: 4 Finish binding event prediction: 1.3m No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 2 Finish binding event prediction: 2.1m --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 2.3m --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 1 Finish binding event prediction: 1.9m --------------------------- Events discovered Significant: 3 Insignificant: 4 Filtered: 2 Finish binding event prediction: 2.6m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.0m No valid binding event was found. --------------------------- Events discovered Significant: 4 Insignificant: 2 Filtered: 1 Finish binding event prediction: 2.6m --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 2.2m --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 2.9m --------------------------- Events discovered Significant: 8 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.5m No valid binding event was found. No valid binding event was found. ============================================== 2025-02-21 22:00:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR1_Chipexo.1x36mers.unique.GPS ============================================== 2025-02-21 22:00:35 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB1_Chipexo.SE.a.GPS Original read count stats: _IP Bases: 1482104 HitCounts: 3904373.0 Original read count stats: _IP Bases: 2350672 HitCounts: 3947684.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 272 reads. ============================================== 2025-02-21 22:00:37 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB2_Chipexo.1x36mers.unique.GPS Original read count stats: _IP Bases: 2864798 HitCounts: 4836427.0 The genome is segmented into 8310 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 352 reads. The genome is segmented into 8288 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:00:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB2_Chipexo.SE.a.GPS Original read count stats: _IP Bases: 3031212 HitCounts: 5725144.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 420 reads. The genome is segmented into 8211 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 488 reads. The genome is segmented into 8368 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 20 Insignificant: 0 Filtered: 5 Finish binding event prediction: 3.0m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 20 Filtered: 5 Finish binding event prediction: 31.1s --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.3m Running with 1 threads ... No valid binding event was found. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.1m ============================================== 2025-02-21 22:08:23 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_1.1x36mers.unique.GPS ============================================== 2025-02-21 22:08:23 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1283146 HitCounts: 1530907.0 ============================================== 2025-02-21 22:08:24 Original read count stats: _IP Bases: 1268950 HitCounts: 1516292.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_1.SE.a.GPS ============================================== 2025-02-21 22:08:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_2.SE.a.GPS Original read count stats: _IP Bases: 1332088 HitCounts: 1740661.0 Original read count stats: _IP Bases: 1317068 HitCounts: 1723711.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 151 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 150 reads. The genome is segmented into 8165 regions for analysis. Running with 1 threads ... The genome is segmented into 8177 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 168 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 166 reads. The genome is segmented into 8345 regions for analysis. Running with 1 threads ... The genome is segmented into 8356 regions for analysis. ============================================== 2025-02-21 22:08:26 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_1.1x36mers.unique.GPS ============================================== 2025-02-21 22:08:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 16-E.coli-ydhB-GSE166465/ydhB_1.1x36mers.unique.bam --out 16-E.coli-ydhB-GSE166465/ydhB_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 542365 HitCounts: 4668361.0 ============================================== 2025-02-21 22:08:27 ============================================== 2025-02-21 22:08:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 75 reads. Original read count stats: _IP Bases: 760697 HitCounts: 5506418.0 The genome is segmented into 8167 regions for analysis. Original read count stats: Running with 1 threads ... _IP Bases: 1352124 HitCounts: 4315258.0 ============================================== 2025-02-21 22:08:28 Original read count stats: _IP Bases: 1336599 HitCounts: 4197429.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_1.SE.a.GPS ============================================== 2025-02-21 22:08:28 At Poisson p-value 1.0e-03, in a 301bp window, expect 170 reads. ============================================== 2025-02-21 22:08:28 Original read count stats: Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_2.SE.a.GPS _IP Bases: 581095 HitCounts: 5254679.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1552810 HitCounts: 4896400.0 ============================================== 2025-02-21 22:08:29 At Poisson p-value 1.0e-03, in a 301bp window, expect 98 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR1_Chipexo.SE.a.GPS Original read count stats: _IP Bases: 1537564 HitCounts: 4758369.0 The genome is segmented into 8340 regions for analysis. Running with 1 threads ... The genome is segmented into 8374 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:08:30 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 16-E.coli-ydhB-GSE166465/ydhB_2.1x36mers.unique.bam --out 16-E.coli-ydhB-GSE166465/ydhB_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1614636 HitCounts: 7034704.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 267 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 262 reads. Original read count stats: _IP Bases: 817565 HitCounts: 6981979.0 The genome is segmented into 8517 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:08:31 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_2.1x36mers.unique.GPS ============================================== 2025-02-21 22:08:31 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR2_Chipexo.SE.a.GPS Original read count stats: _IP Bases: 592410 HitCounts: 5673812.0 The genome is segmented into 8344 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:08:31 At Poisson p-value 1.0e-03, in a 301bp window, expect 307 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR2_Chipexo.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 203 reads. Original read count stats: _IP Bases: 1145536 HitCounts: 7296145.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 301 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 90 reads. Original read count stats: _IP Bases: 1025804 HitCounts: 3892202.0 The genome is segmented into 8315 regions for analysis. The genome is segmented into 8402 regions for analysis. ============================================== 2025-02-21 22:08:32 Running with 1 threads ... ============================================== 2025-02-21 22:08:32 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_2.1x36mers.unique.GPS The genome is segmented into 8113 regions for analysis. Running with 1 threads ... The genome is segmented into 8242 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:08:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 633966 HitCounts: 6405331.0 ============================================== 2025-02-21 22:08:33 At Poisson p-value 1.0e-03, in a 301bp window, expect 501 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 201 reads. The genome is segmented into 8474 regions for analysis. Original read count stats: _IP Bases: 2513342 HitCounts: 3912182.0 Original read count stats: _IP Bases: 2472536 HitCounts: 4060551.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 122 reads. Original read count stats: _IP Bases: 2498372 HitCounts: 4169448.0 ============================================== 2025-02-21 22:08:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_1.SE.a.GPS The genome is segmented into 8315 regions for analysis. Running with 1 threads ... The genome is segmented into 8270 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 443 reads. Original read count stats: _IP Bases: 2479530 HitCounts: 4435047.0 The genome is segmented into 8452 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 356 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 357 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 374 reads. The genome is segmented into 8408 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 377 reads. The genome is segmented into 8015 regions for analysis. The genome is segmented into 8241 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8176 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:08:43 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 16-E.coli-ydhB-GSE166465/ydhB_1.SE.a.bam --out 16-E.coli-ydhB-GSE166465/ydhB_1.SE.a.GPS Original read count stats: _IP Bases: 874000 HitCounts: 1.2217449E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 577 reads. ============================================== 2025-02-21 22:08:49 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 16-E.coli-ydhB-GSE166465/ydhB_2.SE.a.bam --out 16-E.coli-ydhB-GSE166465/ydhB_2.SE.a.GPS The genome is segmented into 8491 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 934058 HitCounts: 1.5781896E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 727 reads. The genome is segmented into 8456 regions for analysis. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 39 Insignificant: 13 Filtered: 13 Finish binding event prediction: 1.5m Refine read distribution from 33 binding events. Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 31 Insignificant: 13 Filtered: 6 Finish binding event prediction: 1.8m Refine read distribution from 23 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 38 Insignificant: 43 Filtered: 15 Finish binding event prediction: 1.6m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 37 Insignificant: 56 Filtered: 16 Finish binding event prediction: 1.7m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 83 Insignificant: 50 Filtered: 10 Finish binding event prediction: 30.1s Refine read distribution from 56 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.4m Running with 1 threads ... --------------------------- Events discovered Significant: 50 Insignificant: 1 Filtered: 15 Finish binding event prediction: 2.4m Refine read distribution from 30 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.4m Running with 1 threads ... --------------------------- Events discovered Significant: 63 Insignificant: 1 Filtered: 21 Finish binding event prediction: 2.5m Refine read distribution from 31 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 167 Insignificant: 2 Filtered: 39 Finish binding event prediction: 2.6m Refine read distribution from 57 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 88 Insignificant: 43 Filtered: 1 Finish binding event prediction: 47.2s Refine read distribution from 49 binding events. --------------------------- Events discovered Significant: 6 Insignificant: 37 Filtered: 5 Finish binding event prediction: 2.6m Running with 1 threads ... --------------------------- Events discovered Significant: 58 Insignificant: 1 Filtered: 19 Finish binding event prediction: 2.6m Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.8m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.8m Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 124 Insignificant: 44 Filtered: 0 Finish binding event prediction: 51.1s Refine read distribution from 68 binding events. --------------------------- Events discovered Significant: 33 Insignificant: 0 Filtered: 11 Finish binding event prediction: 2.8m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 47 Insignificant: 1 Filtered: 16 Finish binding event prediction: 2.9m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 36.1s --------------------------- Events discovered Significant: 2 Insignificant: 24 Filtered: 3 Finish binding event prediction: 3.0m Running with 1 threads ... --------------------------- Events discovered Significant: 104 Insignificant: 59 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 59 binding events. --------------------------- Events discovered Significant: 162 Insignificant: 0 Filtered: 34 Finish binding event prediction: 3.1m Refine read distribution from 50 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 2 Filtered: 2 Finish binding event prediction: 3.5m Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 37 Filtered: 5 Finish binding event prediction: 52.1s --------------------------- Events discovered Significant: 297 Insignificant: 22 Filtered: 2 Finish binding event prediction: 58.1s Refine read distribution from 144 binding events. --------------------------- Events discovered Significant: 552 Insignificant: 89 Filtered: 6 Finish binding event prediction: 1.2m Refine read distribution from 451 binding events. --------------------------- Events discovered Significant: 68 Insignificant: 6 Filtered: 17 Finish binding event prediction: 54.1s Refine read distribution from 18 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.6m --------------------------- Events discovered Significant: 2 Insignificant: 24 Filtered: 3 Finish binding event prediction: 55.3s --------------------------- Events discovered Significant: 594 Insignificant: 95 Filtered: 7 Finish binding event prediction: 1.5m Refine read distribution from 470 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.3m --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 1 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 306 Insignificant: 19 Filtered: 0 Finish binding event prediction: 1.1m Refine read distribution from 166 binding events. --------------------------- Events discovered Significant: 570 Insignificant: 59 Filtered: 4 Finish binding event prediction: 1.6m Refine read distribution from 470 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 2 Filtered: 2 Finish binding event prediction: 1.2m --------------------------- Events discovered Significant: 576 Insignificant: 64 Filtered: 8 Finish binding event prediction: 1.8m Refine read distribution from 471 binding events. --------------------------- Events discovered Significant: 12 Insignificant: 0 Filtered: 4 Finish binding event prediction: 5.3m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 5 Filtered: 3 Finish binding event prediction: 5.5m Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 2 Finish binding event prediction: 5.5m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 6.4m Running with 1 threads ... ============================================== 2025-02-21 22:15:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_1.SE.a.GPS ============================================== 2025-02-21 22:15:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_2.1x36mers.unique.GPS ============================================== 2025-02-21 22:15:40 Original read count stats: _IP Bases: 905381 HitCounts: 4213645.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_1.1x36mers.unique.GPS ============================================== 2025-02-21 22:15:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_2.SE.a.GPS Original read count stats: _IP Bases: 928922 HitCounts: 4267421.0 Original read count stats: _IP Bases: 909271 HitCounts: 4239459.0 Original read count stats: _IP Bases: 924610 HitCounts: 4241004.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 310 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 321 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 317 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 314 reads. The genome is segmented into 8479 regions for analysis. Running with 1 threads ... The genome is segmented into 8212 regions for analysis. Running with 1 threads ... The genome is segmented into 8335 regions for analysis. Running with 1 threads ... The genome is segmented into 8535 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:15:54 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1886937 HitCounts: 1.021139E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 459 reads. The genome is segmented into 7982 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 218 Insignificant: 108 Filtered: 0 Finish binding event prediction: 2.1m Refine read distribution from 186 binding events. --------------------------- Events discovered Significant: 11 Insignificant: 4 Filtered: 4 Finish binding event prediction: 2.1m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 13 Insignificant: 5 Filtered: 5 Finish binding event prediction: 2.3m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 2 Finish binding event prediction: 3.9m --------------------------- Events discovered Significant: 12 Insignificant: 9 Filtered: 6 Finish binding event prediction: 2.4m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 14 Insignificant: 7 Filtered: 6 Finish binding event prediction: 3.0m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 5 Filtered: 3 Finish binding event prediction: 4.9m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.9m Running with 1 threads ... --------------------------- Events discovered Significant: 456 Insignificant: 66 Filtered: 1 Finish binding event prediction: 2.2m Refine read distribution from 296 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 5.6m --------------------------- Events discovered Significant: 478 Insignificant: 63 Filtered: 7 Finish binding event prediction: 2.7m Refine read distribution from 284 binding events. --------------------------- Events discovered Significant: 474 Insignificant: 60 Filtered: 6 Finish binding event prediction: 2.4m Refine read distribution from 289 binding events. --------------------------- Events discovered Significant: 468 Insignificant: 62 Filtered: 1 Finish binding event prediction: 3.3m Refine read distribution from 318 binding events. ============================================== 2025-02-21 22:21:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_2.1x36mers.unique.GPS ============================================== 2025-02-21 22:21:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1836371 HitCounts: 2756191.0 Original read count stats: _IP Bases: 469734 HitCounts: 1519851.0 ============================================== 2025-02-21 22:21:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_2.SE.a.GPS ============================================== 2025-02-21 22:21:16 At Poisson p-value 1.0e-03, in a 301bp window, expect 74 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1981907 HitCounts: 3289556.0 The genome is segmented into 8411 regions for analysis. Original read count stats: _IP Bases: 520730 HitCounts: 1775756.0 Running with 1 threads ... ============================================== 2025-02-21 22:21:17 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 242 reads. ============================================== 2025-02-21 22:21:17 At Poisson p-value 1.0e-03, in a 301bp window, expect 84 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1080795 HitCounts: 3678513.0 The genome is segmented into 8374 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1193361 HitCounts: 3816542.0 ============================================== 2025-02-21 22:21:18 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_2.1x36mers.unique.GPS ============================================== 2025-02-21 22:21:18 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_1.SE.a.GPS The genome is segmented into 8045 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1473906 HitCounts: 2033900.0 Original read count stats: _IP Bases: 1170828 HitCounts: 4037353.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 284 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 197 reads. The genome is segmented into 8201 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 208 reads. ============================================== 2025-02-21 22:21:20 At Poisson p-value 1.0e-03, in a 301bp window, expect 184 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_2.SE.a.GPS The genome is segmented into 8311 regions for analysis. Running with 1 threads ... Original read count stats: The genome is segmented into 8322 regions for analysis. _IP Bases: 1290184 HitCounts: 4201094.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 218 reads. The genome is segmented into 8030 regions for analysis. Running with 1 threads ... The genome is segmented into 8491 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:21:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 231 reads. Original read count stats: _IP Bases: 2759347 HitCounts: 5546316.0 The genome is segmented into 8493 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:21:23 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_1.SE.a.GPS Original read count stats: _IP Bases: 585682 HitCounts: 2697824.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 146 reads. ============================================== 2025-02-21 22:21:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_2.SE.a.GPS Original read count stats: _IP Bases: 1604927 HitCounts: 2432215.0 The genome is segmented into 8565 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:21:26 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 445 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 216 reads. The genome is segmented into 7962 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2932537 HitCounts: 6611735.0 The genome is segmented into 8198 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 522 reads. The genome is segmented into 8110 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:21:37 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_1.SE.a.GPS Original read count stats: _IP Bases: 2028079 HitCounts: 1.182491E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 554 reads. The genome is segmented into 8157 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.7m --------------------------- Events discovered Significant: 50 Insignificant: 46 Filtered: 10 Finish binding event prediction: 1.8m Refine read distribution from 26 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 278 Insignificant: 1 Filtered: 90 Finish binding event prediction: 1.9m Refine read distribution from 267 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 52 Insignificant: 0 Filtered: 17 Finish binding event prediction: 2.3m Refine read distribution from 42 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.3m Running with 1 threads ... --------------------------- Events discovered Significant: 299 Insignificant: 1 Filtered: 96 Finish binding event prediction: 2.7m Refine read distribution from 285 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 138 Insignificant: 17 Filtered: 3 Finish binding event prediction: 29.1s Refine read distribution from 95 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 108 Insignificant: 48 Filtered: 6 Finish binding event prediction: 1.0m Refine read distribution from 71 binding events. --------------------------- Events discovered Significant: 1051 Insignificant: 228 Filtered: 6 Finish binding event prediction: 1.1m Refine read distribution from 908 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 2 Filtered: 0 Finish binding event prediction: 3.2m Running with 1 threads ... --------------------------- Events discovered Significant: 294 Insignificant: 0 Filtered: 94 Finish binding event prediction: 3.2m Refine read distribution from 286 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 55 Insignificant: 0 Filtered: 18 Finish binding event prediction: 3.4m Refine read distribution from 49 binding events. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 8 Insignificant: 2 Filtered: 3 Finish binding event prediction: 3.2m Running with 1 threads ... --------------------------- Events discovered Significant: 149 Insignificant: 16 Filtered: 0 Finish binding event prediction: 25.1s Refine read distribution from 97 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.4m --------------------------- Events discovered Significant: 1079 Insignificant: 231 Filtered: 5 Finish binding event prediction: 1.2m Refine read distribution from 935 binding events. --------------------------- Events discovered Significant: 1101 Insignificant: 203 Filtered: 3 Finish binding event prediction: 59.2s Refine read distribution from 951 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 0 Insignificant: 2 Filtered: 0 Finish binding event prediction: 5.1m Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 2 Filtered: 0 Finish binding event prediction: 2.2m No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 8 Insignificant: 2 Filtered: 3 Finish binding event prediction: 1.9m --------------------------- Events discovered Significant: 308 Insignificant: 0 Filtered: 98 Finish binding event prediction: 5.7m Refine read distribution from 298 binding events. Running with 1 threads ... No valid binding event was found. ============================================== 2025-02-21 22:27:33 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 727246 HitCounts: 1330197.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 96 reads. The genome is segmented into 8235 regions for analysis. ============================================== 2025-02-21 22:27:35 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1093038 HitCounts: 1752582.0 ============================================== 2025-02-21 22:27:36 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 143 reads. ============================================== 2025-02-21 22:27:36 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_1.SE.a.GPS Original read count stats: _IP Bases: 1147001 HitCounts: 2041145.0 The genome is segmented into 8065 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 792223 HitCounts: 1838681.0 ============================================== 2025-02-21 22:27:37 ============================================== 2025-02-21 22:27:37 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_1.1x36mers.unique.GPS ============================================== 2025-02-21 22:27:38 Original read count stats: _IP Bases: 1240141 HitCounts: 2065973.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_2.SE.a.GPS Original read count stats: _IP Bases: 961923 HitCounts: 1955313.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 165 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 136 reads. Original read count stats: _IP Bases: 536739 HitCounts: 2343485.0 The genome is segmented into 8418 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 137 reads. The genome is segmented into 8262 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 168 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 133 reads. The genome is segmented into 8104 regions for analysis. Running with 1 threads ... The genome is segmented into 8594 regions for analysis. The genome is segmented into 8035 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-21 22:27:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_1.SE.a.GPS Original read count stats: _IP Bases: 1292688 HitCounts: 2397527.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 192 reads. ============================================== 2025-02-21 22:27:43 The genome is segmented into 8227 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_2.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 1031055 HitCounts: 2704001.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 193 reads. The genome is segmented into 8303 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 1130 Insignificant: 229 Filtered: 5 Finish binding event prediction: 1.8m Refine read distribution from 969 binding events. --------------------------- Events discovered Significant: 0 Insignificant: 2 Filtered: 0 Finish binding event prediction: 2.4m --------------------------- Events discovered Significant: 32 Insignificant: 20 Filtered: 8 Finish binding event prediction: 2.4m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 19 Insignificant: 1 Filtered: 6 Finish binding event prediction: 2.5m Refine read distribution from 19 binding events. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 19 Insignificant: 0 Filtered: 4 Finish binding event prediction: 2.7m Refine read distribution from 15 binding events. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 27 Insignificant: 27 Filtered: 9 Finish binding event prediction: 2.9m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.0m Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 91 Insignificant: 32 Filtered: 1 Finish binding event prediction: 49.1s Refine read distribution from 63 binding events. --------------------------- Events discovered Significant: 79 Insignificant: 2 Filtered: 1 Finish binding event prediction: 35.1s Refine read distribution from 58 binding events. --------------------------- Events discovered Significant: 6 Insignificant: 1 Filtered: 0 Finish binding event prediction: 3.3m Running with 1 threads ... --------------------------- Events discovered Significant: 64 Insignificant: 51 Filtered: 11 Finish binding event prediction: 3.3m Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 78 Insignificant: 3 Filtered: 0 Finish binding event prediction: 1.3m Refine read distribution from 62 binding events. No valid binding event was found. --------------------------- Events discovered Significant: 78 Insignificant: 26 Filtered: 0 Finish binding event prediction: 56.2s Refine read distribution from 48 binding events. --------------------------- Events discovered Significant: 112 Insignificant: 50 Filtered: 2 Finish binding event prediction: 40.1s Refine read distribution from 76 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 1.2m No valid binding event was found. --------------------------- Events discovered Significant: 6 Insignificant: 1 Filtered: 0 Finish binding event prediction: 1.2m ============================================== 2025-02-21 22:36:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 582502 HitCounts: 1410081.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 89 reads. The genome is segmented into 8298 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:36:09 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_2.1x36mers.unique.GPS ============================================== 2025-02-21 22:36:10 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_2.SE.a.GPS ============================================== 2025-02-21 22:36:10 ============================================== 2025-02-21 22:36:10 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_2.SE.a.GPS Original read count stats: _IP Bases: 925178 HitCounts: 3599521.0 Original read count stats: _IP Bases: 837761 HitCounts: 3203985.0 Original read count stats: _IP Bases: 646953 HitCounts: 1921735.0 Original read count stats: _IP Bases: 966395 HitCounts: 3758165.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 130 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 188 reads. The genome is segmented into 8465 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:36:12 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_1.SE.a.GPS The genome is segmented into 8419 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1101243 HitCounts: 4769684.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 286 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 297 reads. ============================================== 2025-02-21 22:36:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_1.1x36mers.unique.GPS ============================================== 2025-02-21 22:36:14 The genome is segmented into 8164 regions for analysis. The genome is segmented into 8473 regions for analysis. ============================================== 2025-02-21 22:36:14 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_2.1x36mers.unique.GPS ============================================== 2025-02-21 22:36:14 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/narL_2.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/narL_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_2.1x36mers.unique.GPS ============================================== 2025-02-21 22:36:14 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/narL_1.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/narL_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1052195 HitCounts: 4563536.0 ============================================== 2025-02-21 22:36:14 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_2.SE.a.GPS Original read count stats: _IP Bases: 772560 HitCounts: 2410847.0 Original read count stats: _IP Bases: 2116429 HitCounts: 4703088.0 Original read count stats: _IP Bases: 2092940 HitCounts: 4913782.0 Original read count stats: _IP Bases: 2203293 HitCounts: 4934203.0 Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 130 reads. ============================================== 2025-02-21 22:36:15_IP Bases: 2100328 HitCounts: 5349698.0 ============================================== 2025-02-21 22:36:15 At Poisson p-value 1.0e-03, in a 301bp window, expect 365 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/narL_1.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/narL_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 347 reads. Original read count stats: _IP Bases: 2136906 HitCounts: 5574342.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 365 reads. Original read count stats: _IP Bases: 2344058 HitCounts: 5548944.0 ============================================== 2025-02-21 22:36:17 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_1.SE.a.GPS The genome is segmented into 8683 regions for analysis. The genome is segmented into 8258 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 351 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 384 reads. Original read count stats: _IP Bases: 2143412 HitCounts: 6061388.0 ============================================== 2025-02-21 22:36:18 The genome is segmented into 7991 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_1.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_1.1x36mers.unique.GPS Running with 1 threads ... The genome is segmented into 7968 regions for analysis. The genome is segmented into 8396 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8097 regions for analysis. Original read count stats: _IP Bases: 1632857 HitCounts: 4020316.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 408 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 410 reads. The genome is segmented into 8265 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 418 reads. Running with 1 threads ... The genome is segmented into 8122 regions for analysis. ============================================== 2025-02-21 22:36:21 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/narL_2.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/narL_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 291 reads. Original read count stats: _IP Bases: 2254669 HitCounts: 5293574.0 The genome is segmented into 8068 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 444 reads. Running with 1 threads ... The genome is segmented into 8251 regions for analysis. Running with 1 threads ... The genome is segmented into 8192 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 390 reads. ============================================== 2025-02-21 22:36:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_1.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_1.1x36mers.unique.GPS The genome is segmented into 8152 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 290754 HitCounts: 9938906.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 49 reads. The genome is segmented into 8434 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:36:28 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_2.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_2.1x36mers.unique.GPS ============================================== 2025-02-21 22:36:28 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_1.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_1.SE.a.GPS Original read count stats: _IP Bases: 626797 HitCounts: 8303695.0 ============================================== 2025-02-21 22:36:28 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_2.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1779004 HitCounts: 7842874.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 111 reads. Original read count stats: _IP Bases: 1713126 HitCounts: 3726589.0 The genome is segmented into 8210 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:36:31 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_2.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 287 reads. Original read count stats: _IP Bases: 731902 HitCounts: 1.2111681E7 The genome is segmented into 8211 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 563 reads. The genome is segmented into 8355 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 317 reads. Running with 1 threads ... The genome is segmented into 8358 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:36:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_1.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_1.SE.a.GPS Original read count stats: _IP Bases: 363734 HitCounts: 1.432915E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 206 reads. The genome is segmented into 8599 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 116 Insignificant: 1 Filtered: 23 Finish binding event prediction: 1.2m Refine read distribution from 58 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 8 Filtered: 5 Finish binding event prediction: 1.8m Running with 1 threads ... --------------------------- Events discovered Significant: 65 Insignificant: 73 Filtered: 28 Finish binding event prediction: 1.5m Refine read distribution from 17 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 200 Insignificant: 48 Filtered: 0 Finish binding event prediction: 43.1s Refine read distribution from 105 binding events. --------------------------- Events discovered Significant: 96 Insignificant: 1 Filtered: 22 Finish binding event prediction: 1.9m Refine read distribution from 37 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 121 Insignificant: 1 Filtered: 14 Finish binding event prediction: 2.6m Refine read distribution from 26 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 20 Insignificant: 6 Filtered: 7 Finish binding event prediction: 2.6m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 7 Filtered: 4 Finish binding event prediction: 2.7m Running with 1 threads ... --------------------------- Events discovered Significant: 95 Insignificant: 37 Filtered: 21 Finish binding event prediction: 2.9m Refine read distribution from 31 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 174 Insignificant: 18 Filtered: 2 Finish binding event prediction: 45.1s Refine read distribution from 86 binding events. --------------------------- Events discovered Significant: 117 Insignificant: 0 Filtered: 14 Finish binding event prediction: 3.0m Refine read distribution from 32 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 170 Insignificant: 24 Filtered: 2 Finish binding event prediction: 33.1s Refine read distribution from 121 binding events. --------------------------- Events discovered Significant: 44 Insignificant: 55 Filtered: 11 Finish binding event prediction: 2.8m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 93 Insignificant: 68 Filtered: 26 Finish binding event prediction: 1.3m Refine read distribution from 38 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.2m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.4m Running with 1 threads ... --------------------------- Events discovered Significant: 16 Insignificant: 12 Filtered: 7 Finish binding event prediction: 3.5m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 7 Filtered: 4 Finish binding event prediction: 55.1s --------------------------- Events discovered Significant: 165 Insignificant: 8 Filtered: 2 Finish binding event prediction: 41.7s Refine read distribution from 120 binding events. --------------------------- Events discovered Significant: 27 Insignificant: 35 Filtered: 10 Finish binding event prediction: 3.5m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 153 Insignificant: 65 Filtered: 2 Finish binding event prediction: 59.1s Refine read distribution from 106 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 8 Filtered: 5 Finish binding event prediction: 2.1m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.9m Running with 1 threads ... --------------------------- Events discovered Significant: 82 Insignificant: 34 Filtered: 18 Finish binding event prediction: 4.0m Refine read distribution from 27 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 105 Insignificant: 44 Filtered: 0 Finish binding event prediction: 58.1s Refine read distribution from 66 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.1m Running with 1 threads ... --------------------------- Events discovered Significant: 47 Insignificant: 2 Filtered: 14 Finish binding event prediction: 4.4m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 156 Insignificant: 52 Filtered: 1 Finish binding event prediction: 36.1s Refine read distribution from 112 binding events. --------------------------- Events discovered Significant: 40 Insignificant: 1 Filtered: 12 Finish binding event prediction: 4.5m Refine read distribution from 40 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 529 Insignificant: 76 Filtered: 4 Finish binding event prediction: 2.2m Refine read distribution from 311 binding events. --------------------------- Events discovered Significant: 80 Insignificant: 34 Filtered: 1 Finish binding event prediction: 1.2m Refine read distribution from 44 binding events. --------------------------- Events discovered Significant: 36 Insignificant: 0 Filtered: 11 Finish binding event prediction: 4.9m --------------------------- Events discovered Significant: 58 Insignificant: 0 Filtered: 11 Refine read distribution from 25 binding events. Finish binding event prediction: 5.1m Running with 1 threads ... Refine read distribution from 55 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.0m --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.3m --------------------------- Events discovered Significant: 215 Insignificant: 107 Filtered: 1 Finish binding event prediction: 1.3m Refine read distribution from 197 binding events. --------------------------- Events discovered Significant: 109 Insignificant: 13 Filtered: 3 Finish binding event prediction: 1.3m Refine read distribution from 65 binding events. --------------------------- Events discovered Significant: 52 Insignificant: 0 Filtered: 10 Finish binding event prediction: 5.8m Refine read distribution from 49 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 33 Insignificant: 0 Filtered: 10 Finish binding event prediction: 5.9m Refine read distribution from 30 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 92 Insignificant: 11 Filtered: 5 Finish binding event prediction: 55.2s Refine read distribution from 51 binding events. --------------------------- Events discovered Significant: 498 Insignificant: 75 Filtered: 12 Finish binding event prediction: 2.8m Refine read distribution from 272 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.5m --------------------------- Events discovered Significant: 248 Insignificant: 94 Filtered: 2 Finish binding event prediction: 1.6m Refine read distribution from 227 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.7m --------------------------- Events discovered Significant: 218 Insignificant: 115 Filtered: 2 Finish binding event prediction: 1.4m Refine read distribution from 202 binding events. --------------------------- Events discovered Significant: 204 Insignificant: 109 Filtered: 1 Finish binding event prediction: 1.5m Refine read distribution from 183 binding events. ============================================== 2025-02-21 22:48:38 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-21 22:48:39 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 19-E.coli-ZraR-GSE181993/ZraR_1.1x36mers.unique.bam --out 19-E.coli-ZraR-GSE181993/ZraR_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1341389 HitCounts: 3672629.0 ============================================== 2025-02-21 22:48:39 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1531665 HitCounts: 4243110.0 ============================================== 2025-02-21 22:48:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1401694 HitCounts: 4048408.0 ============================================== 2025-02-21 22:48:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 2663537 HitCounts: 3892301.0 ============================================== 2025-02-21 22:48:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1618403 HitCounts: 4739985.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 275 reads. Original read count stats: _IP Bases: 894308 HitCounts: 4740332.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 286 reads. ============================================== 2025-02-21 22:48:41 ============================================== 2025-02-21 22:48:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_2.SE.a.GPS The genome is segmented into 8557 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:48:42 Original read count stats: _IP Bases: 1393698 HitCounts: 5157484.0 The genome is segmented into 8183 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_2.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 1622652 HitCounts: 5166553.0 ============================================== 2025-02-21 22:48:42 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 192 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 295 reads. Original read count stats: _IP Bases: 2835132 HitCounts: 5104303.0 ============================================== 2025-02-21 22:48:43 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 1673120 HitCounts: 5250822.0 ============================================== 2025-02-21 22:48:43 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_1.SE.a.GPS The genome is segmented into 8289 regions for analysis. The genome is segmented into 8529 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-21 22:48:44 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 352 reads. Original read count stats: _IP Bases: 2293136 HitCounts: 5165780.0 Original read count stats: _IP Bases: 1675720 HitCounts: 5701076.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 351 reads. Original read count stats: _IP Bases: 1451407 HitCounts: 5629371.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 357 reads. The genome is segmented into 8211 regions for analysis. Running with 1 threads ... The genome is segmented into 8510 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 365 reads. Running with 1 threads ... The genome is segmented into 8716 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:48:46 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 19-E.coli-ZraR-GSE181993/ZraR_2.SE.a.bam --out 19-E.coli-ZraR-GSE181993/ZraR_2.SE.a.GPS ============================================== 2025-02-21 22:48:46 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_2.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 382 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 451 reads. Original read count stats: _IP Bases: 1191078 HitCounts: 8059265.0 The genome is segmented into 8688 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1859952 HitCounts: 7174248.0 ============================================== 2025-02-21 22:48:47 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 19-E.coli-ZraR-GSE181993/ZraR_1.SE.a.bam --out 19-E.coli-ZraR-GSE181993/ZraR_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 443 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 378 reads. The genome is segmented into 8382 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 395 reads. Running with 1 threads ... Original read count stats: _IP Bases: 1674295 HitCounts: 7791351.0 The genome is segmented into 8432 regions for analysis. The genome is segmented into 8678 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:48:48 The genome is segmented into 8480 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 19-E.coli-ZraR-GSE181993/ZraR_2.1x36mers.unique.bam --out 19-E.coli-ZraR-GSE181993/ZraR_2.1x36mers.unique.GPS Running with 1 threads ... The genome is segmented into 8652 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1063480 HitCounts: 4219336.0 ============================================== 2025-02-21 22:48:50 At Poisson p-value 1.0e-03, in a 301bp window, expect 210 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 467 reads. Original read count stats: _IP Bases: 1019855 HitCounts: 8412773.0 The genome is segmented into 8370 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 534 reads. The genome is segmented into 8209 regions for analysis. Running with 1 threads ... The genome is segmented into 8341 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 530 reads. The genome is segmented into 8345 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 426 reads. The genome is segmented into 8440 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:48:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1019615 HitCounts: 4679799.0 ============================================== 2025-02-21 22:49:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 215 reads. Original read count stats: _IP Bases: 2129793 HitCounts: 3353120.0 The genome is segmented into 8259 regions for analysis. ============================================== 2025-02-21 22:49:02 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 401373 HitCounts: 6455486.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 296 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 95 reads. The genome is segmented into 8437 regions for analysis. Running with 1 threads ... The genome is segmented into 8254 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:49:08 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 1150465 HitCounts: 8393367.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 458 reads. The genome is segmented into 8425 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:49:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 500913 HitCounts: 1.6479901E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 637 reads. The genome is segmented into 8590 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 47 Insignificant: 32 Filtered: 7 Finish binding event prediction: 1.8m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 29 Insignificant: 35 Filtered: 9 Finish binding event prediction: 2.1m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 22 Insignificant: 25 Filtered: 11 Finish binding event prediction: 2.2m Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 37 Insignificant: 51 Filtered: 13 Finish binding event prediction: 1.7m Refine read distribution from 17 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 89 Insignificant: 24 Filtered: 2 Finish binding event prediction: 48.1s Refine read distribution from 61 binding events. --------------------------- Events discovered Significant: 163 Insignificant: 1 Filtered: 53 Finish binding event prediction: 2.7m Refine read distribution from 134 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 246 Insignificant: 1 Filtered: 27 Finish binding event prediction: 2.5m Refine read distribution from 43 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 117 Insignificant: 34 Filtered: 0 Finish binding event prediction: 42.1s Refine read distribution from 87 binding events. --------------------------- Events discovered Significant: 172 Insignificant: 0 Filtered: 57 Finish binding event prediction: 2.9m Refine read distribution from 147 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 36 Insignificant: 31 Filtered: 9 Finish binding event prediction: 2.5m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 81 Insignificant: 7 Filtered: 8 Finish binding event prediction: 3.0m Refine read distribution from 30 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 75 Insignificant: 0 Filtered: 17 Finish binding event prediction: 3.1m Refine read distribution from 31 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 45 Insignificant: 0 Filtered: 10 Finish binding event prediction: 3.3m Refine read distribution from 24 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 100 Insignificant: 23 Filtered: 4 Finish binding event prediction: 59.5s Refine read distribution from 55 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 21 Filtered: 2 Finish binding event prediction: 3.3m Running with 1 threads ... --------------------------- Events discovered Significant: 25 Insignificant: 22 Filtered: 10 Finish binding event prediction: 3.3m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 176 Insignificant: 0 Filtered: 58 Finish binding event prediction: 3.5m Refine read distribution from 143 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 381 Insignificant: 1 Filtered: 89 Finish binding event prediction: 3.7m Refine read distribution from 313 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 61 Insignificant: 5 Filtered: 5 Finish binding event prediction: 3.5m Refine read distribution from 27 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.8m Running with 1 threads ... --------------------------- Events discovered Significant: 84 Insignificant: 21 Filtered: 1 Finish binding event prediction: 53.2s Refine read distribution from 55 binding events. --------------------------- Events discovered Significant: 123 Insignificant: 21 Filtered: 3 Finish binding event prediction: 55.1s Refine read distribution from 86 binding events. --------------------------- Events discovered Significant: 98 Insignificant: 13 Filtered: 13 Finish binding event prediction: 50.1s Refine read distribution from 51 binding events. --------------------------- Events discovered Significant: 180 Insignificant: 13 Filtered: 2 Finish binding event prediction: 52.1s Refine read distribution from 104 binding events. --------------------------- Events discovered Significant: 78 Insignificant: 24 Filtered: 0 Finish binding event prediction: 42.2s Refine read distribution from 49 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.7m Running with 1 threads ... --------------------------- Events discovered Significant: 166 Insignificant: 0 Filtered: 52 Finish binding event prediction: 4.1m Refine read distribution from 145 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 69 Insignificant: 36 Filtered: 0 Finish binding event prediction: 1.7m Refine read distribution from 41 binding events. --------------------------- Events discovered Significant: 203 Insignificant: 25 Filtered: 6 Finish binding event prediction: 1.5m Refine read distribution from 69 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 21 Filtered: 2 Finish binding event prediction: 1.4m --------------------------- Events discovered Significant: 98 Insignificant: 20 Filtered: 3 Finish binding event prediction: 1.0m Refine read distribution from 79 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 341 Insignificant: 14 Filtered: 51 Finish binding event prediction: 5.2m Refine read distribution from 202 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 333 Insignificant: 18 Filtered: 66 Finish binding event prediction: 5.3m Refine read distribution from 223 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 385 Insignificant: 1 Filtered: 83 Finish binding event prediction: 5.4m Refine read distribution from 309 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1341 Insignificant: 200 Filtered: 10 Finish binding event prediction: 2.6m Refine read distribution from 959 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 1 Filtered: 1 Finish binding event prediction: 1.9m --------------------------- Events discovered Significant: 1332 Insignificant: 224 Filtered: 8 Finish binding event prediction: 3.1m Refine read distribution from 962 binding events. --------------------------- Events discovered Significant: 788 Insignificant: 119 Filtered: 3 Finish binding event prediction: 2.2m Refine read distribution from 639 binding events. --------------------------- Events discovered Significant: 1373 Insignificant: 212 Filtered: 5 Finish binding event prediction: 2.4m Refine read distribution from 967 binding events. --------------------------- Events discovered Significant: 1299 Insignificant: 217 Filtered: 8 Finish binding event prediction: 2.5m Refine read distribution from 954 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 1 Finish binding event prediction: 2.6m --------------------------- Events discovered Significant: 801 Insignificant: 107 Filtered: 1 Finish binding event prediction: 1.9m Refine read distribution from 649 binding events. --------------------------- Events discovered Significant: 679 Insignificant: 124 Filtered: 2 Finish binding event prediction: 2.4m Refine read distribution from 531 binding events. --------------------------- Events discovered Significant: 696 Insignificant: 134 Filtered: 1 Finish binding event prediction: 2.5m Refine read distribution from 547 binding events. No valid binding event was found. ============================================== 2025-02-21 22:58:19 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-21 22:58:20 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1953471 HitCounts: 3998354.0 Original read count stats: _IP Bases: 2370720 HitCounts: 4318058.0 ============================================== 2025-02-21 22:58:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-21 22:58:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 322 reads. Original read count stats: _IP Bases: 464470 HitCounts: 5526371.0 Original read count stats: _IP Bases: 2227898 HitCounts: 4296963.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 99 reads. The genome is segmented into 8353 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 365 reads. Running with 1 threads ... The genome is segmented into 8335 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:58:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_2.1x36mers.unique.GPS The genome is segmented into 8258 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:58:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 356 reads. Original read count stats: _IP Bases: 3222569 HitCounts: 5322203.0 Original read count stats: The genome is segmented into 8308 regions for analysis. _IP Bases: 2540585 HitCounts: 6814164.0 Running with 1 threads ... ============================================== 2025-02-21 22:58:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 2253826 HitCounts: 5543604.0 ============================================== 2025-02-21 22:58:29 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_2.SE.a.GPS ============================================== 2025-02-21 22:58:30 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 468 reads. Original read count stats: _IP Bases: 2113095 HitCounts: 7206027.0 The genome is segmented into 8187 regions for analysis. Original read count stats: _IP Bases: 2393964 HitCounts: 7516732.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 565 reads. ============================================== 2025-02-21 22:58:31 The genome is segmented into 8427 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 459 reads. ============================================== 2025-02-21 22:58:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_2.SE.a.GPS The genome is segmented into 8489 regions for analysis. Original read count stats: _IP Bases: 1849788 HitCounts: 3660778.0 Running with 1 threads ... Original read count stats: _IP Bases: 3404983 HitCounts: 7271123.0 ============================================== 2025-02-21 22:58:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 567 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 295 reads. Original read count stats: _IP Bases: 2089370 HitCounts: 3870081.0 The genome is segmented into 8513 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 605 reads. The genome is segmented into 8325 regions for analysis. Running with 1 threads ... The genome is segmented into 8456 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 323 reads. The genome is segmented into 8318 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 22:58:39 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 567869 HitCounts: 1.3596035E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 625 reads. The genome is segmented into 8364 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 555 reads. The genome is segmented into 8504 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 28 Insignificant: 64 Filtered: 13 Finish binding event prediction: 1.4m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 191 Insignificant: 1 Filtered: 32 Finish binding event prediction: 1.9m Refine read distribution from 47 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 206 Insignificant: 15 Filtered: 6 Finish binding event prediction: 36.1s Refine read distribution from 61 binding events. --------------------------- Events discovered Significant: 73 Insignificant: 39 Filtered: 0 Finish binding event prediction: 1.0m Refine read distribution from 37 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 13 Filtered: 2 Finish binding event prediction: 3.0m Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 39 Filtered: 1 Finish binding event prediction: 3.2m Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 18 Filtered: 3 Finish binding event prediction: 3.6m Running with 1 threads ... --------------------------- Events discovered Significant: 18 Insignificant: 3 Filtered: 6 Finish binding event prediction: 4.0m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 12 Filtered: 4 Finish binding event prediction: 3.9m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 13 Filtered: 2 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 22 Insignificant: 11 Filtered: 8 Finish binding event prediction: 45.1s Refine read distribution from 16 binding events. --------------------------- Events discovered Significant: 6 Insignificant: 39 Filtered: 1 Finish binding event prediction: 1.6m --------------------------- Events discovered Significant: 9 Insignificant: 2 Filtered: 3 Finish binding event prediction: 5.0m Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 18 Filtered: 3 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 5.3m Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 12 Filtered: 4 Finish binding event prediction: 2.3m --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 6.6m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 5 Filtered: 2 Finish binding event prediction: 6.5m Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 1 Finish binding event prediction: 6.9m Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 2 Filtered: 2 Finish binding event prediction: 7.2m Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 2 Filtered: 3 Finish binding event prediction: 3.1m --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.2m --------------------------- Events discovered Significant: 2 Insignificant: 5 Filtered: 2 Finish binding event prediction: 3.4m ============================================== 2025-02-21 23:08:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 2008676 HitCounts: 5379932.0 ============================================== 2025-02-21 23:08:42 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-21 23:08:42 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 2079380 HitCounts: 6185748.0 Original read count stats: _IP Bases: 2095222 HitCounts: 4989098.0 ============================================== 2025-02-21 23:08:43 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 433 reads. Original read count stats: _IP Bases: 2136191 HitCounts: 5341767.0 The genome is segmented into 8478 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 370 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 410 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 384 reads. The genome is segmented into 7973 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 23:08:47 The genome is segmented into 8255 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_2.SE.a.GPS Running with 1 threads ... The genome is segmented into 7998 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2300274 HitCounts: 7324153.0 ============================================== 2025-02-21 23:08:49 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 2241350 HitCounts: 8518481.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 524 reads. The genome is segmented into 8168 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 569 reads. The genome is segmented into 8118 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 1 Finish binding event prediction: 4.2m --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.7m --------------------------- Events discovered Significant: 2 Insignificant: 13 Filtered: 4 Finish binding event prediction: 2.2m Running with 1 threads ... --------------------------- Events discovered Significant: 14 Insignificant: 22 Filtered: 3 Finish binding event prediction: 2.9m Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 16 Insignificant: 20 Filtered: 8 Finish binding event prediction: 3.0m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 2 Filtered: 2 Finish binding event prediction: 6.5m --------------------------- Events discovered Significant: 2 Insignificant: 13 Filtered: 4 Finish binding event prediction: 1.4m --------------------------- Events discovered Significant: 52 Insignificant: 16 Filtered: 0 Finish binding event prediction: 43.2s Refine read distribution from 32 binding events. --------------------------- Events discovered Significant: 44 Insignificant: 19 Filtered: 0 Finish binding event prediction: 44.1s Refine read distribution from 23 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.9m Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 2 Finish binding event prediction: 4.0m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.5m Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 2.3m --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 2 Finish binding event prediction: 2.4m --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.2m ============================================== 2025-02-21 23:18:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 2049853 HitCounts: 4877443.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 360 reads. The genome is segmented into 8245 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 23:18:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-21 23:18:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 1182488 HitCounts: 6724907.0 Original read count stats: _IP Bases: 2251947 HitCounts: 7703728.0 ============================================== 2025-02-21 23:18:29 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 297 reads. Original read count stats: _IP Bases: 2205187 HitCounts: 7654432.0 The genome is segmented into 8122 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 555 reads. The genome is segmented into 8410 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 548 reads. The genome is segmented into 8407 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 18 Insignificant: 21 Filtered: 6 Finish binding event prediction: 3.5m Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 46 Insignificant: 15 Filtered: 0 Finish binding event prediction: 43.2s Refine read distribution from 29 binding events. --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 2 Finish binding event prediction: 4.3m Running with 1 threads ... --------------------------- Events discovered Significant: 18 Insignificant: 22 Filtered: 5 Finish binding event prediction: 4.5m Refine read distribution from 6 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 45 Insignificant: 14 Filtered: 0 Finish binding event prediction: 57.2s Refine read distribution from 26 binding events. --------------------------- Events discovered Significant: 86 Insignificant: 0 Filtered: 16 Finish binding event prediction: 5.7m Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 182 Insignificant: 5 Filtered: 2 Finish binding event prediction: 58.1s Refine read distribution from 169 binding events. --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 2 Finish binding event prediction: 2.6m ============================================== 2025-02-21 23:29:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1122680 HitCounts: 5692719.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 262 reads. ============================================== 2025-02-21 23:29:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_2.SE.a.GPS The genome is segmented into 8180 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1248816 HitCounts: 6954058.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 347 reads. The genome is segmented into 8330 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 23:29:19 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 1312431 HitCounts: 8135169.0 ============================================== 2025-02-21 23:29:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 790657 HitCounts: 4969791.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 392 reads. The genome is segmented into 8280 regions for analysis. Running with 1 threads ... ============================================== 2025-02-21 23:29:23 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 175 reads. Original read count stats: _IP Bases: 910217 HitCounts: 1.0653228E7 The genome is segmented into 8261 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 520 reads. The genome is segmented into 8412 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 54 Insignificant: 50 Filtered: 13 Finish binding event prediction: 1.7m Refine read distribution from 25 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 140 Insignificant: 53 Filtered: 1 Finish binding event prediction: 1.1m Refine read distribution from 100 binding events. --------------------------- Events discovered Significant: 155 Insignificant: 1 Filtered: 27 Finish binding event prediction: 3.3m Refine read distribution from 75 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 88 Insignificant: 0 Filtered: 16 Finish binding event prediction: 3.7m Refine read distribution from 32 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 87 Insignificant: 12 Filtered: 20 Finish binding event prediction: 3.9m Refine read distribution from 30 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 81 Insignificant: 16 Filtered: 18 Finish binding event prediction: 4.0m Refine read distribution from 34 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 193 Insignificant: 9 Filtered: 3 Finish binding event prediction: 41.1s Refine read distribution from 168 binding events. --------------------------- Events discovered Significant: 289 Insignificant: 63 Filtered: 1 Finish binding event prediction: 1.1m Refine read distribution from 191 binding events. --------------------------- Events discovered Significant: 192 Insignificant: 31 Filtered: 3 Finish binding event prediction: 47.1s Refine read distribution from 159 binding events. --------------------------- Events discovered Significant: 179 Insignificant: 29 Filtered: 2 Finish binding event prediction: 1.0m Refine read distribution from 155 binding events. ============================================== 2025-02-21 23:39:54 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 3031451 HitCounts: 4745234.0 ============================================== 2025-02-21 23:39:57 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 424 reads. Original read count stats: _IP Bases: 3473831 HitCounts: 6371262.0 The genome is segmented into 8235 regions for analysis. ============================================== 2025-02-21 23:40:00 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 3667827 HitCounts: 7765399.0 ============================================== 2025-02-21 23:40:02 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 905254 HitCounts: 4704325.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 551 reads. ============================================== 2025-02-21 23:40:03 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 195 reads. Original read count stats: _IP Bases: 1030186 HitCounts: 1.0224687E7 The genome is segmented into 8245 regions for analysis. Running with 1 threads ... The genome is segmented into 8350 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 664 reads. The genome is segmented into 8525 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 538 reads. The genome is segmented into 8396 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 123 Insignificant: 4 Filtered: 23 Finish binding event prediction: 2.4m Refine read distribution from 55 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 46 Insignificant: 34 Filtered: 9 Finish binding event prediction: 2.8m Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 273 Insignificant: 38 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 202 binding events. --------------------------- Events discovered Significant: 135 Insignificant: 56 Filtered: 1 Finish binding event prediction: 43.1s Refine read distribution from 103 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 4.6m Running with 1 threads ... --------------------------- Events discovered Significant: 12 Insignificant: 0 Filtered: 4 Finish binding event prediction: 5.1m Refine read distribution from 1 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 11 Insignificant: 0 Filtered: 3 Finish binding event prediction: 5.4m Refine read distribution from 2 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 14 Insignificant: 2 Filtered: 5 Finish binding event prediction: 55.1s Refine read distribution from 6 binding events. --------------------------- Events discovered Significant: 28 Insignificant: 0 Filtered: 6 Finish binding event prediction: 40.1s Refine read distribution from 13 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 2.4m ============================================== 2025-02-21 23:50:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 759418 HitCounts: 5492266.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 169 reads. ============================================== 2025-02-21 23:50:43 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_2.SE.a.GPS The genome is segmented into 8333 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 3219770 HitCounts: 5865320.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 513 reads. The genome is segmented into 8408 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 164 Insignificant: 2 Filtered: 38 Finish binding event prediction: 2.3m Refine read distribution from 59 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 294 Insignificant: 20 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 158 binding events. --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 3 Finish binding event prediction: 5.1m Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 3 Finish binding event prediction: 2.2m ============================================== 2025-02-22 00:00:54 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1443196 HitCounts: 2513089.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 204 reads. The genome is segmented into 8187 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:00:58 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 2988974 HitCounts: 5401419.0 ============================================== 2025-02-22 00:00:59 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:01:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 843802 HitCounts: 6263812.0 Original read count stats: _IP Bases: 816155 HitCounts: 6963095.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 207 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 201 reads. The genome is segmented into 8320 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 461 reads. ============================================== 2025-02-22 00:01:02 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:01:03 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_2.1x36mers.unique.GPS The genome is segmented into 8304 regions for analysis. Running with 1 threads ... Original read count stats: Original read count stats: _IP Bases: 2064319 HitCounts: 6642853.0 _IP Bases: 918381 HitCounts: 7226287.0 ============================================== 2025-02-22 00:01:04 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_2.SE.a.GPS The genome is segmented into 8222 regions for analysis. ============================================== 2025-02-22 00:01:04 Running with 1 threads ... Original read count stats: _IP Bases: 3175337 HitCounts: 7639307.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 291911 HitCounts: 4967131.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 239 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 64 reads. ============================================== 2025-02-22 00:01:08 At Poisson p-value 1.0e-03, in a 301bp window, expect 436 reads. ============================================== 2025-02-22 00:01:06 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_2.1x36mers.unique.GPS The genome is segmented into 8521 regions for analysis. Running with 1 threads ... The genome is segmented into 8289 regions for analysis. Original read count stats: Original read count stats: ============================================== 2025-02-22 00:01:12 The genome is segmented into 8246 regions for analysis. _IP Bases: 384684 HitCounts: 5110523.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 639 reads. ============================================== 2025-02-22 00:01:12_IP Bases: 1591466 HitCounts: 3768693.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_1.SE.a.GPS Running with 1 threads ... Running with 1 threads ... Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 79 reads. The genome is segmented into 8404 regions for analysis. Original read count stats: _IP Bases: 877187 HitCounts: 1.2400471E7 ============================================== 2025-02-22 00:01:14_IP Bases: 2224842 HitCounts: 1.0968279E7 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_1.SE.a.GPS Running with 1 threads ... ============================================== 2025-02-22 00:01:14 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_2.SE.a.GPS The genome is segmented into 8450 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 383488 HitCounts: 1.3975146E7 Original read count stats: _IP Bases: 482037 HitCounts: 1.3523404E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 307 reads. The genome is segmented into 8358 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 586 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 527 reads. The genome is segmented into 8484 regions for analysis. The genome is segmented into 8608 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 547 reads. The genome is segmented into 8685 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 714 reads. ============================================== 2025-02-22 00:01:20 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_2.SE.a.GPS The genome is segmented into 8390 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 937554 HitCounts: 1.6021871E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 738 reads. The genome is segmented into 8458 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:01:29 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 968170 HitCounts: 1.8594108E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 933 reads. The genome is segmented into 8449 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:01:39 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 1045667 HitCounts: 2.176312E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 1075 reads. The genome is segmented into 8441 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 34 Insignificant: 57 Filtered: 10 Finish binding event prediction: 1.3m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 142 Insignificant: 16 Filtered: 32 Finish binding event prediction: 1.4m Refine read distribution from 35 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 208 Insignificant: 7 Filtered: 25 Finish binding event prediction: 1.7m Refine read distribution from 43 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 157 Insignificant: 2 Filtered: 33 Finish binding event prediction: 2.0m Refine read distribution from 57 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 27 Insignificant: 60 Filtered: 6 Finish binding event prediction: 2.0m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 49 Insignificant: 54 Filtered: 13 Finish binding event prediction: 2.1m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 45 Insignificant: 52 Filtered: 15 Finish binding event prediction: 2.4m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.9m Running with 1 threads ... --------------------------- Events discovered Significant: 184 Insignificant: 29 Filtered: 1 Finish binding event prediction: 1.2m Refine read distribution from 78 binding events. --------------------------- Events discovered Significant: 56 Insignificant: 37 Filtered: 1 Finish binding event prediction: 38.2s Refine read distribution from 30 binding events. --------------------------- Events discovered Significant: 53 Insignificant: 42 Filtered: 1 Finish binding event prediction: 1.3m Refine read distribution from 24 binding events. --------------------------- Events discovered Significant: 286 Insignificant: 24 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 163 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 23 Filtered: 1 Finish binding event prediction: 3.0m Running with 1 threads ... --------------------------- Events discovered Significant: 186 Insignificant: 30 Filtered: 5 Finish binding event prediction: 1.5m Refine read distribution from 59 binding events. --------------------------- Events discovered Significant: 47 Insignificant: 53 Filtered: 5 Finish binding event prediction: 2.8m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 44 Insignificant: 60 Filtered: 8 Finish binding event prediction: 2.6m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 113 Insignificant: 50 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 62 binding events. --------------------------- Events discovered Significant: 171 Insignificant: 2 Filtered: 33 Finish binding event prediction: 3.5m Refine read distribution from 40 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 174 Insignificant: 3 Filtered: 38 Finish binding event prediction: 3.7m Refine read distribution from 35 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 129 Insignificant: 46 Filtered: 0 Finish binding event prediction: 59.2s Refine read distribution from 84 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 23 Filtered: 1 Finish binding event prediction: 58.2s --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 0 Insignificant: 12 Filtered: 0 Finish binding event prediction: 4.2m Running with 1 threads ... --------------------------- Events discovered Significant: 88 Insignificant: 39 Filtered: 0 Finish binding event prediction: 1.1m Refine read distribution from 52 binding events. --------------------------- Events discovered Significant: 20 Insignificant: 26 Filtered: 6 Finish binding event prediction: 4.2m Refine read distribution from 6 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 228 Insignificant: 11 Filtered: 8 Finish binding event prediction: 57.1s Refine read distribution from 73 binding events. --------------------------- Events discovered Significant: 91 Insignificant: 38 Filtered: 1 Finish binding event prediction: 1.4m Refine read distribution from 45 binding events. --------------------------- Events discovered Significant: 246 Insignificant: 11 Filtered: 5 Finish binding event prediction: 1.4m Refine read distribution from 98 binding events. --------------------------- Events discovered Significant: 9 Insignificant: 1 Filtered: 3 Finish binding event prediction: 5.0m Running with 1 threads ... --------------------------- Events discovered Significant: 50 Insignificant: 15 Filtered: 1 Finish binding event prediction: 58.2s Refine read distribution from 26 binding events. --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 5.5m Running with 1 threads ... --------------------------- Events discovered Significant: 0 Insignificant: 12 Filtered: 0 Finish binding event prediction: 2.1m ============================================== 2025-02-22 00:09:20 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-22 00:09:20 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1907290 HitCounts: 2544961.0 ============================================== 2025-02-22 00:09:21 Original read count stats: _IP Bases: 2809979 HitCounts: 4913559.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:09:22 Original read count stats: _IP Bases: 2069035 HitCounts: 2805746.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:09:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 237 reads. Original read count stats: _IP Bases: 975537 HitCounts: 5416839.0 Original read count stats: _IP Bases: 954794 HitCounts: 5465371.0 The genome is segmented into 8235 regions for analysis. ============================================== 2025-02-22 00:09:23 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_2.SE.a.GPS Running with 1 threads ... ============================================== 2025-02-22 00:09:23 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-22 00:09:23 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 2993521 HitCounts: 6148374.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 260 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 251 reads. Original read count stats: _IP Bases: 2760577 HitCounts: 5952426.0 Original read count stats: _IP Bases: 2334074 HitCounts: 6252928.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 250 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 420 reads. ============================================== 2025-02-22 00:09:24 The genome is segmented into 8265 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_2.1x36mers.unique.GPS Running with 1 threads ... The genome is segmented into 8291 regions for analysis. Running with 1 threads ... The genome is segmented into 8228 regions for analysis. The genome is segmented into 8159 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 2069132 HitCounts: 6881702.0 ============================================== 2025-02-22 00:09:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_2.SE.a.GPS ============================================== 2025-02-22 00:09:26 ============================================== 2025-02-22 00:09:26 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 2060339 HitCounts: 3326636.0 Original read count stats: _IP Bases: 2227173 HitCounts: 3657724.0 Original read count stats: _IP Bases: 2164640 HitCounts: 4016475.0 ============================================== 2025-02-22 00:09:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 465 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 522 reads. Original read count stats: At Poisson p-value 1.0e-03, in a 301bp window, expect 446 reads. _IP Bases: 2942618 HitCounts: 6832102.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 517 reads. ============================================== 2025-02-22 00:09:28 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_2.SE.a.GPS The genome is segmented into 8324 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 303 reads. The genome is segmented into 8492 regions for analysis. Running with 1 threads ... The genome is segmented into 8389 regions for analysis. Running with 1 threads ... The genome is segmented into 8246 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 335 reads. Original read count stats: _IP Bases: 2930579 HitCounts: 7459665.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 332 reads. Running with 1 threads ... The genome is segmented into 8070 regions for analysis. Running with 1 threads ... The genome is segmented into 8380 regions for analysis. The genome is segmented into 8315 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-22 00:09:31 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_1.SE.a.GPS ============================================== 2025-02-22 00:09:31 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 1100564 HitCounts: 9593307.0 ============================================== 2025-02-22 00:09:32 Original read count stats: _IP Bases: 3114941 HitCounts: 8580558.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 522 reads. Original read count stats: _IP Bases: 1079615 HitCounts: 9875080.0 The genome is segmented into 8088 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 574 reads. ============================================== 2025-02-22 00:09:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_2.SE.a.GPS The genome is segmented into 8211 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2230983 HitCounts: 1.1508791E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 524 reads. The genome is segmented into 8418 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 542 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 645 reads. The genome is segmented into 8427 regions for analysis. The genome is segmented into 8261 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 746 reads. The genome is segmented into 8402 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 1 Filtered: 3 Finish binding event prediction: 3.8m --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.8m --------------------------- Events discovered Significant: 80 Insignificant: 16 Filtered: 21 Finish binding event prediction: 2.2m Refine read distribution from 52 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 88 Insignificant: 4 Filtered: 15 Finish binding event prediction: 3.0m Refine read distribution from 39 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.1m Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 3 Filtered: 2 Finish binding event prediction: 3.1m Running with 1 threads ... --------------------------- Events discovered Significant: 147 Insignificant: 25 Filtered: 5 Finish binding event prediction: 1.2m Refine read distribution from 115 binding events. --------------------------- Events discovered Significant: 43 Insignificant: 35 Filtered: 16 Finish binding event prediction: 3.5m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 4 Filtered: 3 Finish binding event prediction: 3.8m Running with 1 threads ... --------------------------- Events discovered Significant: 142 Insignificant: 20 Filtered: 3 Finish binding event prediction: 1.2m Refine read distribution from 111 binding events. No valid binding event was found. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 19 Insignificant: 24 Filtered: 7 Finish binding event prediction: 4.1m Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 47 Insignificant: 38 Filtered: 18 Finish binding event prediction: 4.2m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 11 Insignificant: 1 Filtered: 4 Finish binding event prediction: 4.4m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 3 Filtered: 2 Finish binding event prediction: 1.6m --------------------------- Events discovered Significant: 97 Insignificant: 29 Filtered: 1 Finish binding event prediction: 1.2m Refine read distribution from 68 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 5.1m Running with 1 threads ... --------------------------- Events discovered Significant: 49 Insignificant: 2 Filtered: 1 Finish binding event prediction: 42.2s Refine read distribution from 35 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 2.1m --------------------------- Events discovered Significant: 49 Insignificant: 17 Filtered: 0 Finish binding event prediction: 58.2s Refine read distribution from 26 binding events. --------------------------- Events discovered Significant: 10 Insignificant: 6 Filtered: 3 Finish binding event prediction: 5.2m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 11 Insignificant: 1 Filtered: 4 Finish binding event prediction: 5.3m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 4 Filtered: 3 Finish binding event prediction: 1.6m --------------------------- Events discovered Significant: 103 Insignificant: 28 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 74 binding events. --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 5.5m Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 3 Filtered: 2 Finish binding event prediction: 6.0m Running with 1 threads ... --------------------------- Events discovered Significant: 32 Insignificant: 6 Filtered: 0 Finish binding event prediction: 48.2s Refine read distribution from 26 binding events. --------------------------- Events discovered Significant: 31 Insignificant: 7 Filtered: 1 Finish binding event prediction: 48.1s Refine read distribution from 27 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 0 Filtered: 1 Finish binding event prediction: 6.2m Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 6.4m Running with 1 threads ... No valid binding event was found. No valid binding event was found. --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 3.3m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.8m --------------------------- Events discovered Significant: 6 Insignificant: 3 Filtered: 2 Finish binding event prediction: 3.4m --------------------------- Events discovered Significant: 5 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.5m --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.8m ============================================== 2025-02-22 00:20:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 2394079 HitCounts: 3904971.0 ============================================== 2025-02-22 00:20:16 ============================================== 2025-02-22 00:20:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 1924569 HitCounts: 4353424.0 Original read count stats: _IP Bases: 2606664 HitCounts: 5174404.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 343 reads. ============================================== 2025-02-22 00:20:18 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1771424 HitCounts: 3016404.0 ============================================== 2025-02-22 00:20:19 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 368 reads. The genome is segmented into 8316 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 420 reads. The genome is segmented into 8511 regions for analysis. Original read count stats: _IP Bases: 2562485 HitCounts: 5263361.0 Running with 1 threads ... The genome is segmented into 8147 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:20:20 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 259 reads. The genome is segmented into 8346 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2786318 HitCounts: 6977195.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 454 reads. The genome is segmented into 8483 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 565 reads. The genome is segmented into 8304 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:20:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 2590001 HitCounts: 4858536.0 ============================================== 2025-02-22 00:20:33 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:20:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 2725026 HitCounts: 4851740.0 ============================================== 2025-02-22 00:20:34 Original read count stats: _IP Bases: 2289635 HitCounts: 4841273.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-22 00:20:35 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-22 00:20:35 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-22 00:20:35 Original read count stats: _IP Bases: 3146596 HitCounts: 5352823.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 3056511 HitCounts: 4795808.0 ============================================== 2025-02-22 00:20:36 Original read count stats: _IP Bases: 2689013 HitCounts: 5582365.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 403 reads. ============================================== 2025-02-22 00:20:36 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 3014736 HitCounts: 5177269.0 Original read count stats: _IP Bases: 471979 HitCounts: 5915317.0 ============================================== 2025-02-22 00:20:37 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 2239255 HitCounts: 5980687.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 99 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 386 reads. ============================================== 2025-02-22 00:20:37 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_2.1x36mers.unique.GPS ============================================== 2025-02-22 00:20:37 The genome is segmented into 8330 regions for analysis. The genome is segmented into 8190 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 620279 HitCounts: 6513850.0 Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 411 reads. Original read count stats: _IP Bases: 860289 HitCounts: 6835099.0 Original read count stats: _IP Bases: 2572737 HitCounts: 5632376.0 ============================================== 2025-02-22 00:20:38 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_2.SE.a.GPS ============================================== 2025-02-22 00:20:38 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 140 reads. ============================================== 2025-02-22 00:20:38 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_2.SE.a.GPS The genome is segmented into 8248 regions for analysis. Running with 1 threads ... The genome is segmented into 8309 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:20:39 Original read count stats: _IP Bases: 3334713 HitCounts: 6489363.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 2904512 HitCounts: 5833212.0 Original read count stats: _IP Bases: 2770337 HitCounts: 6765117.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 215 reads. The genome is segmented into 8183 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 451 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 467 reads. The genome is segmented into 8347 regions for analysis. ============================================== 2025-02-22 00:20:40 ============================================== 2025-02-22 00:20:40 At Poisson p-value 1.0e-03, in a 301bp window, expect 425 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_1.SE.a.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 3240889 HitCounts: 5686883.0 The genome is segmented into 8190 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:20:40 Original read count stats: _IP Bases: 556501 HitCounts: 7975945.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_1.1x36mers.unique.GPS The genome is segmented into 8135 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 460 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 472 reads. Original read count stats: _IP Bases: 2750841 HitCounts: 7043756.0 Original read count stats: _IP Bases: 441401 HitCounts: 3764103.0 ============================================== 2025-02-22 00:20:41 ============================================== 2025-02-22 00:20:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:20:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_2.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 443 reads. The genome is segmented into 8332 regions for analysis. The genome is segmented into 8336 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 2072892 HitCounts: 4188854.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 102 reads. The genome is segmented into 8169 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:20:42 At Poisson p-value 1.0e-03, in a 301bp window, expect 207 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 2462479 HitCounts: 7247385.0 Original read count stats: _IP Bases: 2864072 HitCounts: 8042448.0 The genome is segmented into 8434 regions for analysis. Running with 1 threads ... The genome is segmented into 8505 regions for analysis. ============================================== 2025-02-22 00:20:42 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_1.1x36mers.unique.GPS Running with 1 threads ... Original read count stats: _IP Bases: 720579 HitCounts: 8883232.0 The genome is segmented into 8132 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2831975 HitCounts: 4249272.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 491 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 559 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 331 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 276 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 560 reads. The genome is segmented into 8354 regions for analysis. Running with 1 threads ... The genome is segmented into 8459 regions for analysis. Running with 1 threads ... The genome is segmented into 8187 regions for analysis. The genome is segmented into 8357 regions for analysis. Running with 1 threads ... Running with 1 threads ... The genome is segmented into 8313 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 555 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 499 reads. The genome is segmented into 8300 regions for analysis. Running with 1 threads ... The genome is segmented into 8340 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 579 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 382 reads. The genome is segmented into 8426 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 641 reads. The genome is segmented into 8151 regions for analysis. Running with 1 threads ... The genome is segmented into 8352 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:20:57 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 901866 HitCounts: 1.4750543E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 299 reads. The genome is segmented into 8284 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:21:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 984688 HitCounts: 1.8378499E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 873 reads. The genome is segmented into 8503 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:21:57 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 1028077 HitCounts: 3.9191654E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 1576 reads. The genome is segmented into 8439 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:22:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 452679 HitCounts: 4045064.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 106 reads. The genome is segmented into 8440 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:22:17 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 257785 HitCounts: 4136652.0 ============================================== 2025-02-22 00:22:17 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 65 reads. The genome is segmented into 8531 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 548133 HitCounts: 9086539.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 403 reads. The genome is segmented into 8594 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:22:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 546315 HitCounts: 1.2045912E7 ============================================== 2025-02-22 00:22:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 349608 HitCounts: 1.3037946E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 616 reads. The genome is segmented into 8616 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 571 reads. The genome is segmented into 8670 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 199 Insignificant: 6 Filtered: 35 Finish binding event prediction: 2.0m Refine read distribution from 63 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 33 Insignificant: 48 Filtered: 12 Finish binding event prediction: 1.6m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 132 Insignificant: 59 Filtered: 19 Finish binding event prediction: 2.2m Refine read distribution from 55 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 145 Insignificant: 1 Filtered: 33 Finish binding event prediction: 2.7m Refine read distribution from 42 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 16 Filtered: 5 Finish binding event prediction: 3.1m Running with 1 threads ... --------------------------- Events discovered Significant: 125 Insignificant: 56 Filtered: 30 Finish binding event prediction: 2.7m Refine read distribution from 51 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 2 Finish binding event prediction: 3.0m Running with 1 threads ... --------------------------- Events discovered Significant: 271 Insignificant: 4 Filtered: 33 Finish binding event prediction: 2.8m Refine read distribution from 44 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 201 Insignificant: 2 Filtered: 35 Finish binding event prediction: 2.6m Refine read distribution from 52 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 104 Insignificant: 35 Filtered: 0 Finish binding event prediction: 55.1s Refine read distribution from 57 binding events. --------------------------- Events discovered Significant: 306 Insignificant: 3 Filtered: 24 Finish binding event prediction: 1.5m Refine read distribution from 53 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 260 Insignificant: 85 Filtered: 0 Finish binding event prediction: 51.1s Refine read distribution from 170 binding events. --------------------------- Events discovered Significant: 340 Insignificant: 37 Filtered: 2 Finish binding event prediction: 1.3m Refine read distribution from 196 binding events. --------------------------- Events discovered Significant: 60 Insignificant: 61 Filtered: 22 Finish binding event prediction: 1.4m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 15 Filtered: 2 Finish binding event prediction: 3.3m Running with 1 threads ... --------------------------- Events discovered Significant: 81 Insignificant: 72 Filtered: 8 Finish binding event prediction: 1.6m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 192 Insignificant: 3 Filtered: 37 Finish binding event prediction: 3.7m Refine read distribution from 74 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 233 Insignificant: 75 Filtered: 1 Finish binding event prediction: 1.0m Refine read distribution from 163 binding events. --------------------------- Events discovered Significant: 43 Insignificant: 63 Filtered: 17 Finish binding event prediction: 1.9m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 4.1m Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 11 Filtered: 1 Finish binding event prediction: 3.9m Running with 1 threads ... --------------------------- Events discovered Significant: 221 Insignificant: 14 Filtered: 2 Finish binding event prediction: 1.3m Refine read distribution from 99 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 16 Filtered: 5 Finish binding event prediction: 1.3m --------------------------- Events discovered Significant: 2 Insignificant: 25 Filtered: 7 Finish binding event prediction: 4.0m Running with 1 threads ... --------------------------- Events discovered Significant: 14 Insignificant: 1 Filtered: 5 Finish binding event prediction: 4.1m --------------------------- Events discovered Significant: 283 Insignificant: 10 Filtered: 39 Refine read distribution from 4 binding events. Finish binding event prediction: 2.5m Running with 1 threads ... Refine read distribution from 101 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 4.6m Running with 1 threads ... --------------------------- Events discovered Significant: 283 Insignificant: 15 Filtered: 2 Finish binding event prediction: 1.3m Refine read distribution from 125 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 11 Filtered: 4 Finish binding event prediction: 4.2m Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 2 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.3m Running with 1 threads ... --------------------------- Events discovered Significant: 38 Insignificant: 68 Filtered: 11 Finish binding event prediction: 2.8m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 1 Filtered: 1 Finish binding event prediction: 4.4m Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 2 Filtered: 1 Finish binding event prediction: 4.8m Running with 1 threads ... --------------------------- Events discovered Significant: 93 Insignificant: 41 Filtered: 1 Finish binding event prediction: 51.1s Refine read distribution from 62 binding events. --------------------------- Events discovered Significant: 81 Insignificant: 37 Filtered: 0 Finish binding event prediction: 1.5m Refine read distribution from 48 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.8m Running with 1 threads ... --------------------------- Events discovered Significant: 22 Insignificant: 4 Filtered: 7 Finish binding event prediction: 47.2s Refine read distribution from 11 binding events. --------------------------- Events discovered Significant: 287 Insignificant: 18 Filtered: 6 Finish binding event prediction: 1.8m Refine read distribution from 98 binding events. --------------------------- Events discovered Significant: 333 Insignificant: 57 Filtered: 0 Finish binding event prediction: 1.3m Refine read distribution from 201 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 11 Filtered: 3 Finish binding event prediction: 4.8m Running with 1 threads ... --------------------------- Events discovered Significant: 148 Insignificant: 66 Filtered: 1 Finish binding event prediction: 1.7m Refine read distribution from 97 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 302 Insignificant: 22 Filtered: 5 Finish binding event prediction: 2.2m Refine read distribution from 109 binding events. --------------------------- Events discovered Significant: 406 Insignificant: 57 Filtered: 6 Finish binding event prediction: 1.0m Refine read distribution from 202 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 15 Filtered: 2 Finish binding event prediction: 2.0m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 5.4m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 25 Filtered: 7 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 10 Insignificant: 1 Filtered: 3 Finish binding event prediction: 5.6m Refine read distribution from 6 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 102 Insignificant: 46 Filtered: 0 Finish binding event prediction: 1.4m Refine read distribution from 59 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 2.1m --------------------------- Events discovered Significant: 5 Insignificant: 3 Filtered: 2 Finish binding event prediction: 29.2s --------------------------- Events discovered Significant: 12 Insignificant: 1 Filtered: 4 Finish binding event prediction: 6.3m Refine read distribution from 4 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 6.3m Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 6.6m Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 11 Filtered: 4 Finish binding event prediction: 2.4m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 6.7m Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 11 Filtered: 1 Finish binding event prediction: 2.8m --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.7m --------------------------- Events discovered Significant: 7 Insignificant: 6 Filtered: 3 Finish binding event prediction: 42.1s --------------------------- Events discovered Significant: 5 Insignificant: 4 Filtered: 3 Finish binding event prediction: 7.0m Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 2 Filtered: 1 Finish binding event prediction: 2.9m --------------------------- Events discovered Significant: 1 Insignificant: 11 Filtered: 3 Finish binding event prediction: 2.6m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.3m --------------------------- Events discovered Significant: 2 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.5m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.2m --------------------------- Events discovered Significant: 11 Insignificant: 0 Filtered: 3 Finish binding event prediction: 8.1m No valid binding event was found. ============================================== 2025-02-22 00:29:12 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1968046 HitCounts: 5481011.0 ============================================== 2025-02-22 00:29:14 ============================================== 2025-02-22 00:29:14 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 376910 HitCounts: 3980197.0 Original read count stats: _IP Bases: 1605878 HitCounts: 6106335.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 90 reads. ============================================== 2025-02-22 00:29:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_1.1x36mers.unique.GPS The genome is segmented into 8543 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 385 reads. Running with 1 threads ... Original read count stats: ============================================== 2025-02-22 00:29:16_IP Bases: 797568 HitCounts: 6989487.0 ============================================== 2025-02-22 00:29:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_2.1x36mers.unique.GPS The genome is segmented into 8204 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_2.1x36mers.unique.GPS Running with 1 threads ... Original read count stats: Original read count stats: _IP Bases: 804059 HitCounts: 7421408.0 _IP Bases: 1488402 HitCounts: 6742863.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 323 reads. ============================================== 2025-02-22 00:29:17 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_1.SE.a.GPS ============================================== 2025-02-22 00:29:18 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 913067 HitCounts: 7552335.0 Original read count stats: _IP Bases: 466311 HitCounts: 8920212.0 The genome is segmented into 8069 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 277 reads. ============================================== 2025-02-22 00:29:19 At Poisson p-value 1.0e-03, in a 301bp window, expect 319 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_2.SE.a.GPS ============================================== 2025-02-22 00:29:19 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_2.SE.a.GPS Original read count stats: _IP Bases: 920710 HitCounts: 8063244.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 288 reads. Original read count stats: _IP Bases: 654785 HitCounts: 8279064.0 The genome is segmented into 8372 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:29:20 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_1.SE.a.GPS The genome is segmented into 8365 regions for analysis. Running with 1 threads ... The genome is segmented into 8065 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1753507 HitCounts: 8189330.0 ============================================== 2025-02-22 00:29:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 322 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 379 reads. ============================================== 2025-02-22 00:29:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_2.SE.a.GPS The genome is segmented into 8708 regions for analysis. The genome is segmented into 8544 regions for analysis. Original read count stats: Running with 1 threads ... _IP Bases: 565857 HitCounts: 9369885.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 304 reads. Original read count stats: _IP Bases: 1630466 HitCounts: 8843712.0 The genome is segmented into 8474 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 338 reads. The genome is segmented into 8539 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 464 reads. ============================================== 2025-02-22 00:29:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_1.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 342 reads. The genome is segmented into 8204 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:29:24 Original read count stats: _IP Bases: 466036 HitCounts: 5064924.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_2.1x36mers.unique.GPS The genome is segmented into 8547 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 458 reads. Original read count stats: _IP Bases: 551649 HitCounts: 4882493.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 97 reads. The genome is segmented into 8252 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 106 reads. The genome is segmented into 8328 regions for analysis. Running with 1 threads ... The genome is segmented into 8401 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.1m ============================================== 2025-02-22 00:30:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_1.SE.a.GPS ============================================== 2025-02-22 00:30:32 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 2961705 HitCounts: 5101014.0 Original read count stats: _IP Bases: 826342 HitCounts: 4979790.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 165 reads. ============================================== 2025-02-22 00:30:34 ============================================== 2025-02-22 00:30:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_2.SE.a.GPS The genome is segmented into 8228 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 852135 HitCounts: 6107258.0 Original read count stats: _IP Bases: 1666235 HitCounts: 2067685.0 ============================================== 2025-02-22 00:30:35 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:30:35 ============================================== 2025-02-22 00:30:36 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 740577 HitCounts: 5151060.0 Original read count stats: _IP Bases: 2110906 HitCounts: 5656377.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 450 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 253 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 198 reads. ============================================== 2025-02-22 00:30:37 Original read count stats: _IP Bases: 3160771 HitCounts: 5742973.0 ============================================== 2025-02-22 00:30:37 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_1.SE.a.GPS ============================================== 2025-02-22 00:30:37 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_2.SE.a.GPS The genome is segmented into 8410 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 157 reads. Running with 1 threads ... ============================================== 2025-02-22 00:30:37 The genome is segmented into 8267 regions for analysis. The genome is segmented into 8188 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_1.1x36mers.unique.GPS Running with 1 threads ... Original read count stats: _IP Bases: 1806230 HitCounts: 2487884.0 Original read count stats: Running with 1 threads ... _IP Bases: 941493 HitCounts: 6950530.0 The genome is segmented into 8316 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 449369 HitCounts: 3463305.0 Original read count stats: _IP Bases: 3351352 HitCounts: 7288614.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 99 reads. ============================================== 2025-02-22 00:30:39 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_2.1x36mers.unique.GPS The genome is segmented into 8441 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:30:39 Original read count stats: _IP Bases: 742261 HitCounts: 4357971.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 289 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 410 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 235 reads. Original read count stats: The genome is segmented into 8398 regions for analysis. _IP Bases: 1980889 HitCounts: 2555030.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 142 reads. The genome is segmented into 8383 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:30:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_1.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:30:40 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 490 reads. Original read count stats: _IP Bases: 636117 HitCounts: 9548724.0 The genome is segmented into 8242 regions for analysis. The genome is segmented into 8204 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 1344031 HitCounts: 6725849.0 ============================================== 2025-02-22 00:30:41 The genome is segmented into 8144 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_1.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 100 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 241 reads. Original read count stats: _IP Bases: 854781 HitCounts: 7655358.0 ============================================== 2025-02-22 00:30:42 ============================================== 2025-02-22 00:30:42 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2A1.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2A1.1x36mers.unique.GPS The genome is segmented into 8157 regions for analysis. The genome is segmented into 8205 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 685565 HitCounts: 3363701.0 Original read count stats: _IP Bases: 276835 HitCounts: 9756631.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 41 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 615 reads. ============================================== 2025-02-22 00:30:44 The genome is segmented into 8384 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 126 reads. ============================================== 2025-02-22 00:30:44 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2A1.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2A1.SE.a.GPS The genome is segmented into 8318 regions for analysis. Running with 1 threads ... Original read count stats: ============================================== 2025-02-22 00:30:44_IP Bases: 2130689 HitCounts: 3077070.0 Original read count stats: _IP Bases: 311629 HitCounts: 1.0997578E7 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_1.SE.a.GPS The genome is segmented into 8302 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 398 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 314 reads. ============================================== 2025-02-22 00:30:45 At Poisson p-value 1.0e-03, in a 301bp window, expect 54 reads. ============================================== 2025-02-22 00:30:45 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_1.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 554955 HitCounts: 9829692.0 The genome is segmented into 8339 regions for analysis. Running with 1 threads ... The genome is segmented into 8566 regions for analysis. Running with 1 threads ... The genome is segmented into 8475 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 706868 HitCounts: 1.082474E7 Original read count stats: _IP Bases: 1209369 HitCounts: 4179052.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 145 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 221 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 286 reads. The genome is segmented into 8330 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:30:47 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_2.SE.a.GPS ============================================== 2025-02-22 00:30:48 The genome is segmented into 8362 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:30:48 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_1.SE.a.GPS Original read count stats: _IP Bases: 2274847 HitCounts: 1.0487437E7 The genome is segmented into 8197 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 2127271 HitCounts: 9963407.0 Original read count stats: _IP Bases: 2778481 HitCounts: 4188234.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 498 reads. The genome is segmented into 8584 regions for analysis. ============================================== 2025-02-22 00:30:50 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 1327066 HitCounts: 1.2793148E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 374 reads. --------------------------- Events discovered Significant: 86 Insignificant: 70 Filtered: 10 Finish binding event prediction: 1.5m Refine read distribution from 28 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 34 Insignificant: 49 Filtered: 10 Finish binding event prediction: 1.5m Refine read distribution from 13 binding events. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 679 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 726 reads. The genome is segmented into 8089 regions for analysis. Running with 1 threads ... The genome is segmented into 8347 regions for analysis. The genome is segmented into 8344 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-22 00:30:55 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 736 reads. Original read count stats: _IP Bases: 794971 HitCounts: 4973064.0 --------------------------- Events discovered Significant: 70 Insignificant: 7 Filtered: 24 Finish binding event prediction: 1.5m Refine read distribution from 39 binding events. Running with 1 threads ... The genome is segmented into 8252 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 235 reads. --------------------------- Events discovered Significant: 0 Insignificant: 1 Filtered: 0 Finish binding event prediction: 3.9m The genome is segmented into 8451 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 3.8m --------------------------- Events discovered Significant: 133 Insignificant: 28 Filtered: 0 Finish binding event prediction: 21.1s Refine read distribution from 94 binding events. --------------------------- Events discovered Significant: 57 Insignificant: 49 Filtered: 12 Finish binding event prediction: 2.2m Refine read distribution from 21 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 4 Filtered: 3 Finish binding event prediction: 3.8m --------------------------- Events discovered Significant: 119 Insignificant: 10 Filtered: 27 Finish binding event prediction: 2.2m Refine read distribution from 45 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 5 Insignificant: 0 Filtered: 0 Finish binding event prediction: 59.1s Running with 1 threads ... --------------------------- Events discovered Significant: 127 Insignificant: 80 Filtered: 7 Finish binding event prediction: 53.1s Refine read distribution from 60 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 0 Filtered: 0 Finish binding event prediction: 11.1s --------------------------- Events discovered Significant: 308 Insignificant: 9 Filtered: 37 Finish binding event prediction: 2.6m Refine read distribution from 104 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 24 Insignificant: 48 Filtered: 22 Finish binding event prediction: 1.2m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 4.7m No valid binding event was found. --------------------------- Events discovered Significant: 13 Insignificant: 14 Filtered: 6 Finish binding event prediction: 2.8m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 102 Insignificant: 35 Filtered: 0 Finish binding event prediction: 42.1s Refine read distribution from 63 binding events. --------------------------- Events discovered Significant: 83 Insignificant: 40 Filtered: 5 Finish binding event prediction: 1.4m Refine read distribution from 41 binding events. --------------------------- Events discovered Significant: 124 Insignificant: 6 Filtered: 36 Finish binding event prediction: 1.7m Refine read distribution from 57 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 95 Insignificant: 36 Filtered: 20 Finish binding event prediction: 1.8m Refine read distribution from 25 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.7m Running with 1 threads ... --------------------------- Events discovered Significant: 78 Insignificant: 14 Filtered: 0 Finish binding event prediction: 27.1s Refine read distribution from 51 binding events. --------------------------- Events discovered Significant: 179 Insignificant: 37 Filtered: 2 Finish binding event prediction: 47.6s Refine read distribution from 101 binding events. --------------------------- Events discovered Significant: 18 Insignificant: 17 Filtered: 6 Finish binding event prediction: 3.1m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 77 Insignificant: 61 Filtered: 14 Finish binding event prediction: 1.7m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 3.4m Running with 1 threads ... --------------------------- Events discovered Significant: 52 Insignificant: 17 Filtered: 0 Finish binding event prediction: 39.1s Refine read distribution from 34 binding events. --------------------------- Events discovered Significant: 50 Insignificant: 29 Filtered: 20 Finish binding event prediction: 2.1m Refine read distribution from 5 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 30.1s --------------------------- Events discovered Significant: 129 Insignificant: 1 Filtered: 20 Finish binding event prediction: 2.3m Refine read distribution from 57 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 92 Insignificant: 41 Filtered: 22 Finish binding event prediction: 2.3m Refine read distribution from 28 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 409 Insignificant: 53 Filtered: 3 Finish binding event prediction: 1.1m Refine read distribution from 214 binding events. --------------------------- Events discovered Significant: 66 Insignificant: 18 Filtered: 0 Finish binding event prediction: 38.1s Refine read distribution from 46 binding events. --------------------------- Events discovered Significant: 276 Insignificant: 3 Filtered: 35 Finish binding event prediction: 2.5m Refine read distribution from 51 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 23 Insignificant: 30 Filtered: 5 Finish binding event prediction: 2.4m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 25 Insignificant: 29 Filtered: 9 Finish binding event prediction: 2.3m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 325 Insignificant: 46 Filtered: 1 Finish binding event prediction: 50.1s Refine read distribution from 218 binding events. --------------------------- Events discovered Significant: 175 Insignificant: 9 Filtered: 21 Finish binding event prediction: 4.0m Refine read distribution from 87 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 212 Insignificant: 74 Filtered: 3 Finish binding event prediction: 57.2s Refine read distribution from 136 binding events. --------------------------- Events discovered Significant: 60 Insignificant: 30 Filtered: 0 Finish binding event prediction: 29.1s Refine read distribution from 29 binding events. --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 2 Finish binding event prediction: 4.1m Running with 1 threads ... --------------------------- Events discovered Significant: 177 Insignificant: 13 Filtered: 14 Finish binding event prediction: 4.0m Refine read distribution from 79 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 19 Insignificant: 1 Filtered: 6 Finish binding event prediction: 2.9m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 101 Insignificant: 38 Filtered: 18 Finish binding event prediction: 2.9m Refine read distribution from 43 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 57 Insignificant: 25 Filtered: 0 Finish binding event prediction: 39.1s Refine read distribution from 30 binding events. --------------------------- Events discovered Significant: 302 Insignificant: 42 Filtered: 1 Finish binding event prediction: 50.1s Refine read distribution from 189 binding events. --------------------------- Events discovered Significant: 302 Insignificant: 31 Filtered: 6 Finish binding event prediction: 45.1s Refine read distribution from 109 binding events. --------------------------- Events discovered Significant: 96 Insignificant: 11 Filtered: 35 Finish binding event prediction: 2.9m Refine read distribution from 12 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 87 Insignificant: 22 Filtered: 0 Finish binding event prediction: 46.1s Refine read distribution from 58 binding events. --------------------------- Events discovered Significant: 245 Insignificant: 72 Filtered: 3 Finish binding event prediction: 1.0m Refine read distribution from 177 binding events. --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 2 Finish binding event prediction: 1.4m No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 212 Insignificant: 87 Filtered: 2 Finish binding event prediction: 50.1s Refine read distribution from 188 binding events. --------------------------- Events discovered Significant: 133 Insignificant: 1 Filtered: 35 Finish binding event prediction: 3.7m Refine read distribution from 61 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 85 Insignificant: 24 Filtered: 20 Finish binding event prediction: 3.3m Refine read distribution from 33 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 46 Insignificant: 12 Filtered: 2 Finish binding event prediction: 42.1s Refine read distribution from 34 binding events. --------------------------- Events discovered Significant: 178 Insignificant: 6 Filtered: 18 Finish binding event prediction: 5.1m Refine read distribution from 86 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 207 Insignificant: 77 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 177 binding events. --------------------------- Events discovered Significant: 115 Insignificant: 43 Filtered: 4 Finish binding event prediction: 2.0m Refine read distribution from 58 binding events. No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 166 Insignificant: 7 Filtered: 17 Finish binding event prediction: 5.3m Refine read distribution from 80 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 27 Insignificant: 1 Filtered: 8 Finish binding event prediction: 5.3m Refine read distribution from 21 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 218 Insignificant: 78 Filtered: 2 Finish binding event prediction: 56.1s Refine read distribution from 141 binding events. --------------------------- Events discovered Significant: 20 Insignificant: 33 Filtered: 10 Finish binding event prediction: 3.8m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 2 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 171 Insignificant: 2 Filtered: 35 Finish binding event prediction: 4.2m Refine read distribution from 85 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.2m Running with 1 threads ... --------------------------- Events discovered Significant: 202 Insignificant: 91 Filtered: 7 Finish binding event prediction: 45.1s Refine read distribution from 131 binding events. --------------------------- Events discovered Significant: 310 Insignificant: 62 Filtered: 1 Finish binding event prediction: 49.1s Refine read distribution from 213 binding events. --------------------------- Events discovered Significant: 217 Insignificant: 65 Filtered: 2 Finish binding event prediction: 43.1s Refine read distribution from 201 binding events. --------------------------- Events discovered Significant: 74 Insignificant: 18 Filtered: 0 Finish binding event prediction: 41.2s Refine read distribution from 52 binding events. --------------------------- Events discovered Significant: 224 Insignificant: 64 Filtered: 3 Finish binding event prediction: 55.1s Refine read distribution from 204 binding events. --------------------------- Events discovered Significant: 78 Insignificant: 10 Filtered: 1 Finish binding event prediction: 59.1s Refine read distribution from 55 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 4.9m Running with 1 threads ... --------------------------- Events discovered Significant: 346 Insignificant: 60 Filtered: 0 Finish binding event prediction: 1.2m Refine read distribution from 239 binding events. --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 5.4m Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 5.3m Running with 1 threads ... --------------------------- Events discovered Significant: 32 Insignificant: 0 Filtered: 7 Finish binding event prediction: 5.5m Refine read distribution from 22 binding events. Running with 1 threads ... No valid binding event was found. --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.4m --------------------------- Events discovered Significant: 244 Insignificant: 34 Filtered: 24 Finish binding event prediction: 2.8m Refine read distribution from 129 binding events. --------------------------- Events discovered Significant: 68 Insignificant: 11 Filtered: 4 Finish binding event prediction: 47.2s Refine read distribution from 42 binding events. No valid binding event was found. No valid binding event was found. Running with 1 threads ... No valid binding event was found. Running with 1 threads ... --------------------------- Events discovered Significant: 2 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.5m --------------------------- Events discovered Significant: 4 Insignificant: 1 Filtered: 1 Finish binding event prediction: 3.2m --------------------------- Events discovered Significant: 4 Insignificant: 0 Filtered: 1 Finish binding event prediction: 3.0m No valid binding event was found. ============================================== 2025-02-22 00:41:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 147695 HitCounts: 1063562.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 33 reads. ============================================== 2025-02-22 00:41:05 The genome is segmented into 8087 regions for analysis. Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:41:06 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 519057 HitCounts: 1193050.0 ============================================== 2025-02-22 00:41:06 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_1.SE.a.GPS Original read count stats: _IP Bases: 537466 HitCounts: 1237879.0 Original read count stats: _IP Bases: 550114 HitCounts: 1244085.0 ============================================== 2025-02-22 00:41:06 At Poisson p-value 1.0e-03, in a 301bp window, expect 84 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 87 reads. Original read count stats: _IP Bases: 210564 HitCounts: 1555994.0 The genome is segmented into 8462 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 88 reads. The genome is segmented into 8490 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 45 reads. Running with 1 threads ... The genome is segmented into 8652 regions for analysis. The genome is segmented into 8545 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-22 00:41:08 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5A10.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5A10.1x36mers.unique.GPS Original read count stats: _IP Bases: 114803 HitCounts: 2511340.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 20 reads. The genome is segmented into 8645 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:41:10 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_2.SE.a.GPS Original read count stats: _IP Bases: 567995 HitCounts: 1288140.0 ============================================== 2025-02-22 00:41:10 ============================================== 2025-02-22 00:41:11 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:41:11 ============================================== 2025-02-22 00:41:11 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5A10.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5A10.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 91 reads. Original read count stats: _IP Bases: 208032 HitCounts: 2470496.0 ============================================== 2025-02-22 00:41:11 Original read count stats: _IP Bases: 127720 HitCounts: 2786283.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 712384 HitCounts: 1494591.0 Original read count stats: _IP Bases: 724829 HitCounts: 1523511.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 22 reads. The genome is segmented into 8671 regions for analysis. Running with 1 threads ... The genome is segmented into 8858 regions for analysis. Original read count stats: _IP Bases: 742110 HitCounts: 1542286.0 Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 126 reads. ============================================== 2025-02-22 00:41:12 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_M2.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_M2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 107 reads. ============================================== 2025-02-22 00:41:12 At Poisson p-value 1.0e-03, in a 301bp window, expect 108 reads. The genome is segmented into 7480 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2C4.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2C4.1x36mers.unique.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 111 reads. The genome is segmented into 8389 regions for analysis. Original read count stats: _IP Bases: 156866 HitCounts: 6278261.0 Running with 1 threads ... Original read count stats: _IP Bases: 1813453 HitCounts: 2919876.0 The genome is segmented into 8539 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 25 reads. Running with 1 threads ... ============================================== 2025-02-22 00:41:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4A3.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4A3.1x36mers.unique.GPS The genome is segmented into 8575 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:41:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2C4.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2C4.SE.a.GPS Original read count stats: _IP Bases: 145009 HitCounts: 6444763.0 The genome is segmented into 8395 regions for analysis. Original read count stats: Running with 1 threads ... _IP Bases: 178293 HitCounts: 7104045.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 24 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 30 reads. The genome is segmented into 8598 regions for analysis. Running with 1 threads ... The genome is segmented into 8753 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 264 reads. ============================================== 2025-02-22 00:41:15 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4A3.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4A3.SE.a.GPS Original read count stats: _IP Bases: 165808 HitCounts: 7350691.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 29 reads. ============================================== 2025-02-22 00:41:16 ============================================== 2025-02-22 00:41:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2B6.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2B6.1x36mers.unique.GPS The genome is segmented into 8798 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_M2.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_M2.SE.a.GPS Running with 1 threads ... The genome is segmented into 8246 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:41:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4A1.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4A1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1389334 HitCounts: 8331264.0 Original read count stats: _IP Bases: 1946952 HitCounts: 3308046.0 Original read count stats: _IP Bases: 287692 HitCounts: 8129856.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 41 reads. ============================================== 2025-02-22 00:41:17 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5G8.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5G8.1x36mers.unique.GPS The genome is segmented into 8435 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:41:18 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5B6.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5B6.1x36mers.unique.GPS Original read count stats: _IP Bases: 220431 HitCounts: 7508069.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 33 reads. ============================================== 2025-02-22 00:41:18 Original read count stats: _IP Bases: 129134 HitCounts: 8252072.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 360 reads. The genome is segmented into 8531 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 22 reads. ============================================== 2025-02-22 00:41:18 Original read count stats: _IP Bases: 275088 HitCounts: 3541908.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4A1.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4A1.SE.a.GPS The genome is segmented into 8624 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 296 reads. Running with 1 threads ... Original read count stats: _IP Bases: 329388 HitCounts: 9512563.0 The genome is segmented into 8407 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:41:19 The genome is segmented into 8139 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5G8.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5G8.SE.a.GPS Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 53 reads. ============================================== 2025-02-22 00:41:20 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2B6.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2B6.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 173 reads. The genome is segmented into 8611 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 251020 HitCounts: 8521110.0 The genome is segmented into 8628 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:41:20 At Poisson p-value 1.0e-03, in a 301bp window, expect 42 reads. Original read count stats: ============================================== 2025-02-22 00:41:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_7B10.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_7B10.1x36mers.unique.GPS ============================================== 2025-02-22 00:41:21 ============================================== 2025-02-22 00:41:21_IP Bases: 1516471 HitCounts: 9518752.0 ============================================== 2025-02-22 00:41:21 ============================================== 2025-02-22 00:41:22 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4D6.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4D6.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2D6.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2D6.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5B9.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5B9.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_M4.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_M4.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5B6.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5B6.SE.a.GPS ============================================== 2025-02-22 00:41:22 Original read count stats: The genome is segmented into 8693 regions for analysis. Original read count stats: _IP Bases: 417328 HitCounts: 1.039868E7 Original read count stats: _IP Bases: 599100 HitCounts: 1.0067819E7 ============================================== 2025-02-22 00:41:23 Original read count stats: _IP Bases: 208002 HitCounts: 4654936.0 _IP Bases: 399555 HitCounts: 9214127.0 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_8B2.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_8B2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5B9.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5B9.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 31 reads. ============================================== 2025-02-22 00:41:24 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_7B10.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_7B10.SE.a.GPS Original read count stats: _IP Bases: 146474 HitCounts: 9194710.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 56 reads. The genome is segmented into 8476 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 61 reads. Running with 1 threads ... Original read count stats: _IP Bases: 448613 HitCounts: 1.0410012E7 ============================================== 2025-02-22 00:41:24 At Poisson p-value 1.0e-03, in a 301bp window, expect 26 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2D6.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2D6.SE.a.GPS Original read count stats: The genome is segmented into 8290 regions for analysis. _IP Bases: 391474 HitCounts: 1.058095E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 109 reads. The genome is segmented into 8261 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 3950846 HitCounts: 8499004.0 The genome is segmented into 8829 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 676295 HitCounts: 1.1784235E7 The genome is segmented into 8309 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 75 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 57 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 444 reads. Original read count stats: _IP Bases: 466240 HitCounts: 1.1744E7 The genome is segmented into 8480 regions for analysis. ============================================== 2025-02-22 00:41:25 The genome is segmented into 8295 regions for analysis. Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_M4.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_M4.SE.a.GPS The genome is segmented into 8305 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 85 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 179 reads. The genome is segmented into 8434 regions for analysis. --------------------------- Events discovered Significant: 23 Insignificant: 0 Filtered: 0 Finish binding event prediction: 17.1s Refine read distribution from 9 binding events. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 4143008 HitCounts: 1.0028549E7 ============================================== 2025-02-22 00:41:26 The genome is segmented into 8454 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4D6.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4D6.SE.a.GPS ============================================== 2025-02-22 00:41:26 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_8B2.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_8B2.SE.a.GPS Original read count stats: _IP Bases: 237298 HitCounts: 5314314.0 ============================================== 2025-02-22 00:41:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5F9.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5F9.1x36mers.unique.GPS Original read count stats: _IP Bases: 438847 HitCounts: 1.1954406E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 40 reads. The genome is segmented into 8671 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 263858 HitCounts: 1.1960133E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 79 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 39 reads. The genome is segmented into 8413 regions for analysis. The genome is segmented into 8473 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-22 00:41:30 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2.SE.a.GPS Original read count stats: _IP Bases: 1438729 HitCounts: 1.3776992E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 716 reads. ============================================== 2025-02-22 00:41:31 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5F9.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5F9.SE.a.GPS Original read count stats: _IP Bases: 298245 HitCounts: 1.3534434E7 At Poisson p-value 1.0e-03, in a 301bp window, expect 50 reads. The genome is segmented into 8621 regions for analysis. Running with 1 threads ... The genome is segmented into 8331 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 0 Finish binding event prediction: 20.1s Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 841 reads. The genome is segmented into 8498 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 10 Insignificant: 0 Filtered: 1 Finish binding event prediction: 17.1s Refine read distribution from 4 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 0 Finish binding event prediction: 23.1s Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 801 reads. The genome is segmented into 8425 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 21 Insignificant: 2 Filtered: 0 Finish binding event prediction: 32.1s Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 20 Insignificant: 2 Filtered: 0 Finish binding event prediction: 18.0s Refine read distribution from 15 binding events. --------------------------- Events discovered Significant: 9 Insignificant: 0 Filtered: 0 Finish binding event prediction: 19.0s --------------------------- Events discovered Significant: 21 Insignificant: 10 Filtered: 0 Finish binding event prediction: 10.0s Refine read distribution from 21 binding events. --------------------------- Events discovered Significant: 12 Insignificant: 5 Filtered: 0 Finish binding event prediction: 19.0s Refine read distribution from 10 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 1 Finish binding event prediction: 37.1s Running with 1 threads ... --------------------------- Events discovered Significant: 39 Insignificant: 6 Filtered: 13 Finish binding event prediction: 34.1s Refine read distribution from 26 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 0 Finish binding event prediction: 23.1s --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 36.1s Running with 1 threads ... --------------------------- Events discovered Significant: 38 Insignificant: 28 Filtered: 19 Finish binding event prediction: 47.1s Refine read distribution from 24 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 21 Insignificant: 8 Filtered: 6 Finish binding event prediction: 49.1s Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 29 Insignificant: 22 Filtered: 0 Finish binding event prediction: 8.1s Refine read distribution from 27 binding events. --------------------------- Events discovered Significant: 5 Insignificant: 1 Filtered: 1 Finish binding event prediction: 18.0s No valid binding event was found. --------------------------- Events discovered Significant: 35 Insignificant: 15 Filtered: 0 Finish binding event prediction: 17.1s Refine read distribution from 26 binding events. --------------------------- Events discovered Significant: 14 Insignificant: 0 Filtered: 3 Finish binding event prediction: 59.1s Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 313 Insignificant: 1 Filtered: 29 Finish binding event prediction: 1.4m Refine read distribution from 83 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 32 Insignificant: 12 Filtered: 14 Finish binding event prediction: 1.1m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 32.0s --------------------------- Events discovered Significant: 30 Insignificant: 21 Filtered: 0 Finish binding event prediction: 31.1s Refine read distribution from 22 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 1.3m Running with 1 threads ... --------------------------- Events discovered Significant: 109 Insignificant: 83 Filtered: 20 Finish binding event prediction: 1.3m Refine read distribution from 25 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 294 Insignificant: 4 Filtered: 18 Finish binding event prediction: 1.6m Refine read distribution from 73 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 34 Insignificant: 17 Filtered: 17 Finish binding event prediction: 1.2m Refine read distribution from 21 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 23 Insignificant: 25 Filtered: 14 Finish binding event prediction: 1.3m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.3m Running with 1 threads ... --------------------------- Events discovered Significant: 109 Insignificant: 0 Filtered: 35 Finish binding event prediction: 1.6m Refine read distribution from 85 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.4m Running with 1 threads ... --------------------------- Events discovered Significant: 43 Insignificant: 20 Filtered: 0 Finish binding event prediction: 10.1s Refine read distribution from 32 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 17.2s --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 1.5m Running with 1 threads ... --------------------------- Events discovered Significant: 57 Insignificant: 27 Filtered: 0 Finish binding event prediction: 23.1s Refine read distribution from 35 binding events. --------------------------- Events discovered Significant: 308 Insignificant: 40 Filtered: 2 Finish binding event prediction: 27.1s Refine read distribution from 160 binding events. --------------------------- Events discovered Significant: 61 Insignificant: 1 Filtered: 16 Finish binding event prediction: 1.8m Refine read distribution from 38 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 31 Insignificant: 45 Filtered: 12 Finish binding event prediction: 1.6m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 69 Insignificant: 6 Filtered: 16 Finish binding event prediction: 2.0m Refine read distribution from 38 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 17 Insignificant: 31 Filtered: 7 Finish binding event prediction: 1.8m Refine read distribution from 15 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 46 Insignificant: 21 Filtered: 21 --------------------------- Events discovered Significant: 16 Insignificant: 13 Filtered: 0 Finish binding event prediction: 1.8m Finish binding event prediction: 51.1s Refine read distribution from 9 binding events. Refine read distribution from 7 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 7 Insignificant: 0 Filtered: 0 Finish binding event prediction: 35.1s --------------------------- Events discovered Significant: 6 Insignificant: 0 Filtered: 0 Finish binding event prediction: 30.0s --------------------------- Events discovered Significant: 66 Insignificant: 18 Filtered: 0 Finish binding event prediction: 40.1s Refine read distribution from 38 binding events. --------------------------- Events discovered Significant: 37 Insignificant: 16 Filtered: 17 Finish binding event prediction: 2.0m Refine read distribution from 25 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 0 Finish binding event prediction: 35.1s --------------------------- Events discovered Significant: 29 Insignificant: 0 Filtered: 9 Finish binding event prediction: 2.2m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 57 Insignificant: 22 Filtered: 0 Finish binding event prediction: 24.1s Refine read distribution from 43 binding events. --------------------------- Events discovered Significant: 49 Insignificant: 13 Filtered: 0 Finish binding event prediction: 23.1s Refine read distribution from 34 binding events. --------------------------- Events discovered Significant: 48 Insignificant: 23 Filtered: 0 Finish binding event prediction: 17.1s Refine read distribution from 37 binding events. --------------------------- Events discovered Significant: 227 Insignificant: 31 Filtered: 2 Finish binding event prediction: 39.1s Refine read distribution from 205 binding events. --------------------------- Events discovered Significant: 265 Insignificant: 27 Filtered: 4 Finish binding event prediction: 1.2m Refine read distribution from 142 binding events. --------------------------- Events discovered Significant: 689 Insignificant: 64 Filtered: 1 --------------------------- Events discovered Significant: 65 Insignificant: 8 Filtered: 22 Finish binding event prediction: 1.1m Finish binding event prediction: 2.3m Refine read distribution from 22 binding events. Running with 1 threads ... Refine read distribution from 629 binding events. --------------------------- Events discovered Significant: 144 Insignificant: 48 Filtered: 2 Finish binding event prediction: 48.1s Refine read distribution from 65 binding events. --------------------------- Events discovered Significant: 98 Insignificant: 10 Filtered: 35 Finish binding event prediction: 2.4m Refine read distribution from 22 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 71 Insignificant: 24 Filtered: 0 Finish binding event prediction: 15.1s Refine read distribution from 44 binding events. --------------------------- Events discovered Significant: 32 Insignificant: 0 Filtered: 10 Finish binding event prediction: 2.7m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 71 Insignificant: 2 Filtered: 19 Finish binding event prediction: 3.0m Refine read distribution from 46 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 119 Insignificant: 73 Filtered: 27 Finish binding event prediction: 3.0m Refine read distribution from 28 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 202 Insignificant: 18 Filtered: 1 Finish binding event prediction: 1.3m --------------------------- Events discovered Significant: 298 Insignificant: 4 Filtered: 5 Refine read distribution from 178 binding events. Finish binding event prediction: 48.2s Refine read distribution from 205 binding events. --------------------------- Events discovered Significant: 16 Insignificant: 22 Filtered: 12 Finish binding event prediction: 3.0m Refine read distribution from 11 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 107 Insignificant: 57 Filtered: 17 Finish binding event prediction: 1.9m Refine read distribution from 65 binding events. --------------------------- Events discovered Significant: 157 Insignificant: 10 Filtered: 3 Finish binding event prediction: 26.2s Refine read distribution from 79 binding events. --------------------------- Events discovered Significant: 17 Insignificant: 0 Filtered: 5 Finish binding event prediction: 3.5m Refine read distribution from 8 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 124 Insignificant: 0 Filtered: 35 Finish binding event prediction: 3.6m Refine read distribution from 88 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 121 Insignificant: 54 Filtered: 9 Finish binding event prediction: 44.1s Refine read distribution from 66 binding events. --------------------------- Events discovered Significant: 76 Insignificant: 3 Filtered: 20 Finish binding event prediction: 3.8m Refine read distribution from 43 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 128 Insignificant: 0 Filtered: 40 Finish binding event prediction: 3.8m Refine read distribution from 99 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 241 Insignificant: 6 Filtered: 2 Finish binding event prediction: 1.1m Refine read distribution from 210 binding events. --------------------------- Events discovered Significant: 17 Insignificant: 0 Filtered: 5 Finish binding event prediction: 3.9m Refine read distribution from 10 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 276 Insignificant: 20 Filtered: 2 Finish binding event prediction: 52.1s Refine read distribution from 213 binding events. --------------------------- Events discovered Significant: 109 Insignificant: 0 Filtered: 4 Finish binding event prediction: 42.1s Refine read distribution from 46 binding events. --------------------------- Events discovered Significant: 254 Insignificant: 8 Filtered: 4 Finish binding event prediction: 34.1s Refine read distribution from 230 binding events. --------------------------- Events discovered Significant: 102 Insignificant: 1 Filtered: 3 Finish binding event prediction: 40.1s Refine read distribution from 55 binding events. --------------------------- Events discovered Significant: 721 Insignificant: 55 Filtered: 1 Finish binding event prediction: 1.0m Refine read distribution from 640 binding events. --------------------------- Events discovered Significant: 679 Insignificant: 40 Filtered: 3 Finish binding event prediction: 1.3m Refine read distribution from 614 binding events. --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 4.9m Running with 1 threads ... --------------------------- Events discovered Significant: 223 Insignificant: 38 Filtered: 35 Finish binding event prediction: 2.6m Refine read distribution from 122 binding events. --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 6.1m Running with 1 threads ... --------------------------- Events discovered Significant: 3 Insignificant: 0 Filtered: 1 Finish binding event prediction: 2.5m --------------------------- Events discovered Significant: 1 Insignificant: 0 Filtered: 0 Finish binding event prediction: 4.6m ============================================== 2025-02-22 00:53:58 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 725823 HitCounts: 1052672.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 96 reads. ============================================== 2025-02-22 00:54:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_2.1x36mers.unique.GPS ============================================== 2025-02-22 00:54:00 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_2.SE.a.GPS The genome is segmented into 8494 regions for analysis. Original read count stats: _IP Bases: 864902 HitCounts: 1334816.0 Running with 1 threads ... ============================================== 2025-02-22 00:54:01 ============================================== 2025-02-22 00:54:01 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_2.SE.a.GPS Original read count stats: _IP Bases: 892240 HitCounts: 1403363.0 Original read count stats: _IP Bases: 755863 HitCounts: 1575242.0 Original read count stats: _IP Bases: 751154 HitCounts: 1107032.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 115 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 120 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 100 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 113 reads. The genome is segmented into 8650 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:54:02 The genome is segmented into 8639 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_2.SE.a.GPS Running with 1 threads ... The genome is segmented into 8544 regions for analysis. The genome is segmented into 8464 regions for analysis. Running with 1 threads ... Running with 1 threads ... Original read count stats: _IP Bases: 404037 HitCounts: 3533324.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 115 reads. ============================================== 2025-02-22 00:54:04 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_1.1x36mers.unique.GPS The genome is segmented into 8585 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 103598 HitCounts: 2497958.0 ============================================== 2025-02-22 00:54:04 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_2.1x36mers.unique.GPS ============================================== 2025-02-22 00:54:04 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_2.SE.a.GPS Original read count stats: _IP Bases: 131625 HitCounts: 2622151.0 Original read count stats: _IP Bases: 152727 HitCounts: 2812355.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 60 reads. ============================================== 2025-02-22 00:54:05 ============================================== 2025-02-22 00:54:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_1.SE.a.GPS The genome is segmented into 7487 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_2.1x36mers.unique.GPS Running with 1 threads ... ============================================== 2025-02-22 00:54:05 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 122017 HitCounts: 2669570.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 65 reads. Original read count stats: _IP Bases: 465352 HitCounts: 2004733.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 70 reads. ============================================== 2025-02-22 00:54:05 The genome is segmented into 8380 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_1.1x36mers.unique.GPS Running with 1 threads ... The genome is segmented into 8543 regions for analysis. Original read count stats: _IP Bases: 1184791 HitCounts: 4300293.0 Running with 1 threads ... Original read count stats: _IP Bases: 32839 HitCounts: 2500185.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 64 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 13 reads. The genome is segmented into 7374 regions for analysis. The genome is segmented into 2284 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-22 00:54:06 At Poisson p-value 1.0e-03, in a 301bp window, expect 92 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_2.1x36mers.unique.GPS ============================================== 2025-02-22 00:54:06 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_2.1x36mers.unique.GPS ============================================== 2025-02-22 00:54:06 The genome is segmented into 8421 regions for analysis. Original read count stats: _IP Bases: 89026 HitCounts: 2127757.0 ============================================== 2025-02-22 00:54:06 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:54:07 Original read count stats: _IP Bases: 469116 HitCounts: 2416531.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 22 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_2.1x36mers.unique.GPS ============================================== 2025-02-22 00:54:07 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_2.SE.a.GPS The genome is segmented into 7884 regions for analysis. ============================================== 2025-02-22 00:54:07 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_1.SE.a.GPS Original read count stats: Original read count stats: _IP Bases: 1390672 HitCounts: 4888022.0 _IP Bases: 1356886 HitCounts: 4840673.0 Original read count stats: _IP Bases: 503551 HitCounts: 2528048.0 Original read count stats: _IP Bases: 1403600 HitCounts: 4123570.0 Original read count stats: _IP Bases: 52887 HitCounts: 4643043.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 112 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 35 reads. ============================================== 2025-02-22 00:54:08 At Poisson p-value 1.0e-03, in a 301bp window, expect 290 reads. The genome is segmented into 1050 regions for analysis. ============================================== 2025-02-22 00:54:08 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_1.1x36mers.unique.GPS Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 119 reads. Original read count stats: _IP Bases: 625350 HitCounts: 2650724.0 The genome is segmented into 8396 regions for analysis. ============================================== 2025-02-22 00:54:08 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_2.1x36mers.unique.GPS ============================================== 2025-02-22 00:54:08 Original read count stats: _IP Bases: 1232969 HitCounts: 5596422.0 The genome is segmented into 8615 regions for analysis. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_2.SE.a.GPS Running with 1 threads ... Original read count stats: _IP Bases: 384213 HitCounts: 2231588.0 The genome is segmented into 8352 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 524330 HitCounts: 2532401.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 137 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 284 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 314 reads. ============================================== 2025-02-22 00:54:10 At Poisson p-value 1.0e-03, in a 301bp window, expect 85 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 327 reads. ============================================== 2025-02-22 00:54:10 The genome is segmented into 8357 regions for analysis. ============================================== 2025-02-22 00:54:10 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_1.1x36mers.unique.GPS Running with 1 threads ... The genome is segmented into 8532 regions for analysis. The genome is segmented into 8375 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:54:10 At Poisson p-value 1.0e-03, in a 301bp window, expect 132 reads. ============================================== 2025-02-22 00:54:10 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_2.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_1.SE.a.GPS Original read count stats: _IP Bases: 505484 HitCounts: 2878937.0 ============================================== 2025-02-22 00:54:10 Original read count stats: _IP Bases: 1450149 HitCounts: 5757885.0 Original read count stats: _IP Bases: 1411476 HitCounts: 4931122.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_1.SE.a.GPS The genome is segmented into 8618 regions for analysis. ============================================== 2025-02-22 00:54:11 The genome is segmented into 8494 regions for analysis. ============================================== 2025-02-22 00:54:11 Running with 1 threads ... Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_1.1x36mers.unique.GPS ============================================== 2025-02-22 00:54:11 Original read count stats: _IP Bases: 1182779 HitCounts: 5215102.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_1.1x36mers.unique.GPS The genome is segmented into 8294 regions for analysis. Original read count stats: _IP Bases: 1403477 HitCounts: 6442082.0 Running with 1 threads ... ============================================== 2025-02-22 00:54:11 ============================================== 2025-02-22 00:54:11 Original read count stats: _IP Bases: 517323 HitCounts: 2837900.0 Original read count stats: _IP Bases: 1436452 HitCounts: 6820786.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_2.SE.a.GPS ============================================== 2025-02-22 00:54:11 Original read count stats: _IP Bases: 169142 HitCounts: 2585054.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_1.SE.a.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 1313894 HitCounts: 5200693.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 127 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 350 reads. Original read count stats: _IP Bases: 429467 HitCounts: 2571724.0 Original read count stats: _IP Bases: 542620 HitCounts: 3017843.0 Original read count stats: _IP Bases: 1522155 HitCounts: 5863153.0 The genome is segmented into 8380 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 61 reads. Running with 1 threads ... The genome is segmented into 8534 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 140 reads. The genome is segmented into 8611 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:54:12 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_2.SE.a.GPS The genome is segmented into 8612 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 106 reads. Running with 1 threads ... ============================================== 2025-02-22 00:54:13 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 136 reads. ============================================== 2025-02-22 00:54:13 Original read count stats: _IP Bases: 1222750 HitCounts: 6738796.0 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_1.SE.a.GPS The genome is segmented into 8575 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 312 reads. Running with 1 threads ... The genome is segmented into 8532 regions for analysis. Running with 1 threads ... Original read count stats: _IP Bases: 1450262 HitCounts: 6406893.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 355 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 317 reads. Original read count stats: _IP Bases: 1352522 HitCounts: 6715028.0 The genome is segmented into 8646 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:54:14 The genome is segmented into 8482 regions for analysis. ============================================== 2025-02-22 00:54:14 At Poisson p-value 1.0e-03, in a 301bp window, expect 328 reads. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 398 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_1.1x36mers.unique.GPS Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_1.SE.a.GPS ============================================== 2025-02-22 00:54:14 At Poisson p-value 1.0e-03, in a 301bp window, expect 394 reads. Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 197128 HitCounts: 2954162.0 The genome is segmented into 8434 regions for analysis. Original read count stats: _IP Bases: 160531 HitCounts: 2977178.0 Running with 1 threads ... The genome is segmented into 8443 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 359 reads. The genome is segmented into 8421 regions for analysis. The genome is segmented into 8683 regions for analysis. Original read count stats: _IP Bases: 362985 HitCounts: 3182015.0 Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 62 reads. At Poisson p-value 1.0e-03, in a 301bp window, expect 74 reads. ============================================== 2025-02-22 00:54:16 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_1.SE.a.GPS The genome is segmented into 8535 regions for analysis. The genome is segmented into 8805 regions for analysis. Running with 1 threads ... Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 95 reads. The genome is segmented into 8410 regions for analysis. ============================================== 2025-02-22 00:54:16 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_1.SE.a.GPS Original read count stats: _IP Bases: 1559847 HitCounts: 7592534.0 The genome is segmented into 8376 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 371 reads. Running with 1 threads ... Original read count stats: _IP Bases: 183313 HitCounts: 3260068.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 366 reads. The genome is segmented into 8612 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 382 reads. The genome is segmented into 8638 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 70 reads. The genome is segmented into 8609 regions for analysis. The genome is segmented into 8738 regions for analysis. Running with 1 threads ... Running with 1 threads ... ============================================== 2025-02-22 00:54:19 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_2.SE.a.GPS Original read count stats: _IP Bases: 114463 HitCounts: 3631357.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 36 reads. The genome is segmented into 7567 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 421 reads. The genome is segmented into 8595 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:54:25 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_1.1x36mers.unique.GPS Original read count stats: _IP Bases: 456732 HitCounts: 2239488.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 96 reads. The genome is segmented into 8418 regions for analysis. Running with 1 threads ... ============================================== 2025-02-22 00:54:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_2.1x36mers.unique.GPS Original read count stats: _IP Bases: 568146 HitCounts: 2362376.0 ============================================== 2025-02-22 00:54:27 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 124 reads. Original read count stats: _IP Bases: 602200 HitCounts: 2488977.0 ============================================== 2025-02-22 00:54:28 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_1.1x36mers.unique.GPS The genome is segmented into 8376 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 132 reads. Original read count stats: _IP Bases: 407209 HitCounts: 2534539.0 Running with 1 threads ... The genome is segmented into 8522 regions for analysis. ============================================== 2025-02-22 00:54:29 Running with 1 threads ... Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_1.SE.a.GPS ============================================== 2025-02-22 00:54:29 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_1.SE.a.GPS ============================================== 2025-02-22 00:54:30 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_2.SE.a.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 106 reads. Original read count stats: _IP Bases: 442568 HitCounts: 2668839.0 Original read count stats: _IP Bases: 659345 HitCounts: 2784058.0 Original read count stats: _IP Bases: 508043 HitCounts: 3053198.0 The genome is segmented into 8409 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 116 reads. ============================================== 2025-02-22 00:54:31 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_2.1x36mers.unique.GPS At Poisson p-value 1.0e-03, in a 301bp window, expect 131 reads. The genome is segmented into 8614 regions for analysis. At Poisson p-value 1.0e-03, in a 301bp window, expect 145 reads. Original read count stats: _IP Bases: 467639 HitCounts: 2871187.0 Running with 1 threads ... The genome is segmented into 8512 regions for analysis. Running with 1 threads ... The genome is segmented into 8536 regions for analysis. Running with 1 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 118 reads. The genome is segmented into 8377 regions for analysis. Running with 1 threads ... --------------------------- Events discovered Significant: 79 Insignificant: 1 Filtered: 14 Finish binding event prediction: 59.1s Refine read distribution from 23 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 82 Insignificant: 3 Filtered: 6 Finish binding event prediction: 28.0s Refine read distribution from 33 binding events. --------------------------- Events discovered Significant: 65 Insignificant: 0 Filtered: 21 Finish binding event prediction: 1.7m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 107 Insignificant: 53 Filtered: 43 Finish binding event prediction: 1.6m Refine read distribution from 32 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 337 Insignificant: 2 Filtered: 70 Finish binding event prediction: 1.7m Refine read distribution from 254 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 425 Insignificant: 12 Filtered: 58 Finish binding event prediction: 1.6m Refine read distribution from 246 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 30 Insignificant: 0 Filtered: 9 Finish binding event prediction: 2.1m Refine read distribution from 30 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 158 Insignificant: 82 Filtered: 67 Finish binding event prediction: 2.2m Refine read distribution from 20 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 131 Insignificant: 0 Filtered: 37 Finish binding event prediction: 2.3m Refine read distribution from 13 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 132 Insignificant: 3 Filtered: 33 Finish binding event prediction: 2.4m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 130 Insignificant: 0 Filtered: 34 Finish binding event prediction: 2.4m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 62 Insignificant: 2 Filtered: 3 Finish binding event prediction: 38.1s Refine read distribution from 39 binding events. --------------------------- Events discovered Significant: 97 Insignificant: 19 Filtered: 6 Finish binding event prediction: 35.1s Refine read distribution from 66 binding events. --------------------------- Events discovered Significant: 164 Insignificant: 31 Filtered: 45 Finish binding event prediction: 2.3m --------------------------- Events discovered Significant: 108 Insignificant: 0 Filtered: 34 Refine read distribution from 109 binding events. Finish binding event prediction: 2.5m Running with 1 threads ... Refine read distribution from 84 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 479 Insignificant: 12 Filtered: 84 Finish binding event prediction: 2.4m Refine read distribution from 327 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 438 Insignificant: 6 Filtered: 57 Finish binding event prediction: 2.1m Refine read distribution from 243 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 36 Insignificant: 0 Filtered: 11 Finish binding event prediction: 2.6m Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 29 Insignificant: 0 Filtered: 9 Finish binding event prediction: 2.7m Refine read distribution from 29 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 340 Insignificant: 3 Filtered: 63 --------------------------- Events discovered Significant: 423 Insignificant: 6 Filtered: 83 Finish binding event prediction: 2.3m Finish binding event prediction: 2.7m Refine read distribution from 232 binding events. Refine read distribution from 297 binding events. Running with 1 threads ... Running with 1 threads ... --------------------------- Events discovered Significant: 37 Insignificant: 0 Filtered: 12 Finish binding event prediction: 3.0m Refine read distribution from 37 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 337 Insignificant: 3 Filtered: 78 Finish binding event prediction: 2.9m Refine read distribution from 249 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 92 Insignificant: 26 Filtered: 1 Finish binding event prediction: 35.1s Refine read distribution from 58 binding events. --------------------------- Events discovered Significant: 165 Insignificant: 10 Filtered: 0 Finish binding event prediction: 57.1s Refine read distribution from 164 binding events. --------------------------- Events discovered Significant: 96 Insignificant: 0 Filtered: 19 Finish binding event prediction: 2.9m Refine read distribution from 16 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 556 Insignificant: 125 Filtered: 9 Finish binding event prediction: 1.1m Refine read distribution from 476 binding events. --------------------------- Events discovered Significant: 387 Insignificant: 116 Filtered: 8 Finish binding event prediction: 1.1m Refine read distribution from 298 binding events. --------------------------- Events discovered Significant: 239 Insignificant: 2 Filtered: 48 Finish binding event prediction: 3.1m Refine read distribution from 156 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 504 Insignificant: 1 Filtered: 46 Finish binding event prediction: 2.8m Refine read distribution from 265 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 128 Insignificant: 14 Filtered: 36 Finish binding event prediction: 3.1m Refine read distribution from 19 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 171 Insignificant: 17 Filtered: 7 Finish binding event prediction: 1.0m Refine read distribution from 30 binding events. --------------------------- Events discovered Significant: 158 Insignificant: 1 Filtered: 37 Finish binding event prediction: 3.3m Refine read distribution from 17 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 404 Insignificant: 0 Filtered: 92 Finish binding event prediction: 3.2m Refine read distribution from 299 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 346 Insignificant: 3 Filtered: 54 Finish binding event prediction: 3.2m Refine read distribution from 212 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 195 Insignificant: 10 Filtered: 0 Finish binding event prediction: 42.1s Refine read distribution from 186 binding events. --------------------------- Events discovered Significant: 823 Insignificant: 0 Filtered: 124 Finish binding event prediction: 3.4m Refine read distribution from 572 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 175 Insignificant: 30 Filtered: 44 Finish binding event prediction: 3.4m Refine read distribution from 123 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 222 Insignificant: 79 Filtered: 8 Finish binding event prediction: 1.0m Refine read distribution from 176 binding events. --------------------------- Events discovered Significant: 166 Insignificant: 13 Filtered: 42 Finish binding event prediction: 3.3m Refine read distribution from 27 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 129 Insignificant: 0 Filtered: 26 Finish binding event prediction: 3.4m Refine read distribution from 14 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 175 Insignificant: 1 Filtered: 0 Finish binding event prediction: 39.1s Refine read distribution from 172 binding events. --------------------------- Events discovered Significant: 241 Insignificant: 0 Filtered: 45 Finish binding event prediction: 3.2m Refine read distribution from 154 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 656 Insignificant: 73 Filtered: 4 Finish binding event prediction: 1.1m Refine read distribution from 593 binding events. --------------------------- Events discovered Significant: 405 Insignificant: 1 Filtered: 83 Finish binding event prediction: 3.4m Refine read distribution from 287 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 696 Insignificant: 1 Filtered: 131 Finish binding event prediction: 3.5m Refine read distribution from 480 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 156 Insignificant: 9 Filtered: 39 Finish binding event prediction: 3.8m Refine read distribution from 36 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 214 Insignificant: 5 Filtered: 0 Finish binding event prediction: 1.2m Refine read distribution from 204 binding events. --------------------------- Events discovered Significant: 371 Insignificant: 111 Filtered: 16 Finish binding event prediction: 1.3m Refine read distribution from 297 binding events. --------------------------- Events discovered Significant: 68 Insignificant: 16 Filtered: 3 Finish binding event prediction: 1.5m Refine read distribution from 34 binding events. --------------------------- Events discovered Significant: 402 Insignificant: 0 Filtered: 73 Finish binding event prediction: 3.5m Refine read distribution from 262 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 697 Insignificant: 0 Filtered: 124 Finish binding event prediction: 3.8m Refine read distribution from 465 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 780 Insignificant: 0 Filtered: 124 Finish binding event prediction: 3.9m Refine read distribution from 536 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 540 Insignificant: 164 Filtered: 15 Finish binding event prediction: 1.3m Refine read distribution from 455 binding events. --------------------------- Events discovered Significant: 531 Insignificant: 180 Filtered: 15 Finish binding event prediction: 1.6m Refine read distribution from 455 binding events. --------------------------- Events discovered Significant: 320 Insignificant: 67 Filtered: 8 Finish binding event prediction: 55.1s Refine read distribution from 279 binding events. --------------------------- Events discovered Significant: 128 Insignificant: 0 Filtered: 27 Finish binding event prediction: 4.0m Refine read distribution from 9 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 116 Insignificant: 1 Filtered: 28 Finish binding event prediction: 3.9m Refine read distribution from 23 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 149 Insignificant: 4 Filtered: 29 Finish binding event prediction: 4.0m Refine read distribution from 23 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 734 Insignificant: 1 Filtered: 123 Finish binding event prediction: 4.1m Refine read distribution from 512 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 70 Insignificant: 25 Filtered: 3 Finish binding event prediction: 56.1s Refine read distribution from 49 binding events. --------------------------- Events discovered Significant: 548 Insignificant: 141 Filtered: 9 Finish binding event prediction: 1.6m Refine read distribution from 481 binding events. --------------------------- Events discovered Significant: 94 Insignificant: 13 Filtered: 2 Finish binding event prediction: 57.1s Refine read distribution from 62 binding events. --------------------------- Events discovered Significant: 431 Insignificant: 0 Filtered: 54 Finish binding event prediction: 4.0m Refine read distribution from 257 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 131 Insignificant: 23 Filtered: 4 Finish binding event prediction: 1.4m Refine read distribution from 87 binding events. --------------------------- Events discovered Significant: 670 Insignificant: 0 Filtered: 105 Finish binding event prediction: 4.5m Refine read distribution from 448 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 407 Insignificant: 110 Filtered: 12 Finish binding event prediction: 1.5m Refine read distribution from 330 binding events. --------------------------- Events discovered Significant: 77 Insignificant: 14 Filtered: 2 Finish binding event prediction: 1.7m Refine read distribution from 39 binding events. --------------------------- Events discovered Significant: 716 Insignificant: 83 Filtered: 4 Finish binding event prediction: 1.8m Refine read distribution from 600 binding events. --------------------------- Events discovered Significant: 257 Insignificant: 80 Filtered: 5 Finish binding event prediction: 1.3m Refine read distribution from 204 binding events. --------------------------- Events discovered Significant: 120 Insignificant: 26 Filtered: 3 Finish binding event prediction: 59.1s Refine read distribution from 82 binding events. --------------------------- Events discovered Significant: 619 Insignificant: 3 Filtered: 109 Finish binding event prediction: 4.6m Refine read distribution from 394 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 80 Insignificant: 2 Filtered: 3 Finish binding event prediction: 1.3m Refine read distribution from 44 binding events. --------------------------- Events discovered Significant: 387 Insignificant: 0 Filtered: 68 Finish binding event prediction: 4.8m --------------------------- Events discovered Significant: 585 Insignificant: 104 Filtered: 7 Finish binding event prediction: 56.1s Refine read distribution from 260 binding events. Running with 1 threads ... Refine read distribution from 508 binding events. --------------------------- Events discovered Significant: 482 Insignificant: 0 Filtered: 85 Finish binding event prediction: 4.8m Refine read distribution from 322 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 371 Insignificant: 2 Filtered: 80 Finish binding event prediction: 4.8m Refine read distribution from 263 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 349 Insignificant: 2 Filtered: 67 Finish binding event prediction: 4.8m Refine read distribution from 224 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 105 Insignificant: 5 Filtered: 2 Finish binding event prediction: 56.1s Refine read distribution from 84 binding events. --------------------------- Events discovered Significant: 557 Insignificant: 0 Filtered: 71 Finish binding event prediction: 4.9m Refine read distribution from 339 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 650 Insignificant: 1 Filtered: 120 Finish binding event prediction: 4.9m Refine read distribution from 415 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 1131 Insignificant: 267 Filtered: 4 Finish binding event prediction: 1.7m Refine read distribution from 828 binding events. --------------------------- Events discovered Significant: 106 Insignificant: 21 Filtered: 3 Finish binding event prediction: 1.0m Refine read distribution from 56 binding events. --------------------------- Events discovered Significant: 433 Insignificant: 1 Filtered: 88 Finish binding event prediction: 5.1m Refine read distribution from 285 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 954 Insignificant: 143 Filtered: 3 Finish binding event prediction: 2.3m Refine read distribution from 753 binding events. --------------------------- Events discovered Significant: 429 Insignificant: 0 Filtered: 94 Finish binding event prediction: 5.8m Refine read distribution from 315 binding events. Running with 1 threads ... --------------------------- Events discovered Significant: 292 Insignificant: 46 Filtered: 10 Finish binding event prediction: 2.4m Refine read distribution from 238 binding events. --------------------------- Events discovered Significant: 593 Insignificant: 126 Filtered: 13 Finish binding event prediction: 1.3m Refine read distribution from 492 binding events. --------------------------- Events discovered Significant: 997 Insignificant: 249 Filtered: 1 Finish binding event prediction: 2.6m Refine read distribution from 714 binding events. --------------------------- Events discovered Significant: 1141 Insignificant: 260 Filtered: 5 Finish binding event prediction: 2.2m Refine read distribution from 808 binding events. --------------------------- Events discovered Significant: 637 Insignificant: 100 Filtered: 4 Finish binding event prediction: 2.8m Refine read distribution from 492 binding events. --------------------------- Events discovered Significant: 405 Insignificant: 104 Filtered: 11 Finish binding event prediction: 1.8m Refine read distribution from 334 binding events. --------------------------- Events discovered Significant: 849 Insignificant: 165 Filtered: 4 Finish binding event prediction: 2.7m Refine read distribution from 656 binding events. --------------------------- Events discovered Significant: 602 Insignificant: 106 Filtered: 16 Finish binding event prediction: 1.5m Refine read distribution from 530 binding events. --------------------------- Events discovered Significant: 121 Insignificant: 14 Filtered: 3 Finish binding event prediction: 2.4m Refine read distribution from 81 binding events. --------------------------- Events discovered Significant: 1111 Insignificant: 227 Filtered: 9 Finish binding event prediction: 2.6m Refine read distribution from 787 binding events. --------------------------- Events discovered Significant: 595 Insignificant: 141 Filtered: 9 Finish binding event prediction: 1.5m Refine read distribution from 496 binding events. --------------------------- Events discovered Significant: 995 Insignificant: 251 Filtered: 4 Finish binding event prediction: 2.3m Refine read distribution from 715 binding events. --------------------------- Events discovered Significant: 760 Insignificant: 103 Filtered: 3 Finish binding event prediction: 2.0m Refine read distribution from 615 binding events. --------------------------- Events discovered Significant: 680 Insignificant: 114 Filtered: 1 Finish binding event prediction: 2.5m Refine read distribution from 528 binding events. --------------------------- Events discovered Significant: 1100 Insignificant: 239 Filtered: 3 Finish binding event prediction: 3.0m Refine read distribution from 778 binding events. --------------------------- Events discovered Significant: 984 Insignificant: 251 Filtered: 7 Finish binding event prediction: 2.6m Refine read distribution from 697 binding events. --------------------------- Events discovered Significant: 980 Insignificant: 256 Filtered: 5 Finish binding event prediction: 3.2m Refine read distribution from 694 binding events. --------------------------- Events discovered Significant: 873 Insignificant: 173 Filtered: 3 Finish binding event prediction: 3.0m Refine read distribution from 671 binding events. --------------------------- Events discovered Significant: 979 Insignificant: 139 Filtered: 1 Finish binding event prediction: 2.6m Refine read distribution from 753 binding events. --------------------------- Events discovered Significant: 79 Insignificant: 12 Filtered: 13 Finish binding event prediction: 6.4m Refine read distribution from 53 binding events.