============================================== 2018-06-06 13:35:56 Options: --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_static_aerobic_growth_rep1_run_299-GSM2251957/alignments.36mers.unique.bam --out Sig70_static_aerobic_growth_rep1_run_299-GSM2251957/alignments.36mers.unique.GPS Original read count stats: _IP Bases: 328674 HitCounts: 1.7509608E7 ============================================== 2018-06-06 13:35:58 Options: --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_static_aerobic_growth_rep1_run_299-GSM2251957/alignments.36mers.unique.bam --out Sig70_static_aerobic_growth_rep1_run_299-GSM2251957/alignments.36mers.unique.GPS ============================================== 2018-06-06 13:35:59 Options: --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_exponential_aerobic_growth_rep2_run_299-GSM2251956/alignments.36mers.unique.bam --out Sig70_exponential_aerobic_growth_rep2_run_299-GSM2251956/alignments.36mers.unique.GPS Original read count stats: _IP Bases: 328674 HitCounts: 1.7509608E7 Original read count stats: _IP Bases: 177241 HitCounts: 1.6325999E7 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 4 threads ... 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 4 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 4 threads ... --------------------------- Events discovered Significant: 1169 Insignificant: 0 Filtered: 126 Finish binding event prediction: 1.2m Refine read distribution from 457 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 1378 Insignificant: 0 Filtered: 72 Finish binding event prediction: 1.3m Refine read distribution from 554 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 693 Insignificant: 154 Filtered: 49 Finish binding event prediction: 5.1s Refine read distribution from 473 binding events. --------------------------- Events discovered Significant: 822 Insignificant: 189 Filtered: 22 Finish binding event prediction: 7.1s Refine read distribution from 572 binding events. --------------------------- Events discovered Significant: 1378 Insignificant: 0 Filtered: 72 Finish binding event prediction: 1.5m Refine read distribution from 554 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 822 Insignificant: 189 Filtered: 22 Finish binding event prediction: 5.1s Refine read distribution from 572 binding events. ============================================== 2018-06-06 13:40:37 Options: --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_exponential_aerobic_growth_rep2_run_423-GSM2251961/alignments.36mers.unique.bam --out Sig70_exponential_aerobic_growth_rep2_run_423-GSM2251961/alignments.36mers.unique.GPS Original read count stats: _IP Bases: 91635 HitCounts: 2183353.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 40 reads. The genome is segmented into 2102 regions for analysis. Running with 4 threads ... ============================================== 2018-06-06 13:40:43 Options: --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_exponential_aerobic_growth_rep1_run_423-GSM2251959/alignments.36mers.unique.bam --out Sig70_exponential_aerobic_growth_rep1_run_423-GSM2251959/alignments.36mers.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. The genome is segmented into 2050 regions for analysis. Running with 4 threads ... ============================================== 2018-06-06 13:40:46 Options: --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1_run_423-GSM2251960/alignments.36mers.unique.bam --out Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1_run_423-GSM2251960/alignments.36mers.unique.GPS Original read count stats: _IP Bases: 231019 HitCounts: 1963578.0 At Poisson p-value 1.0e-03, in a 301bp window, expect 78 reads. The genome is segmented into 4737 regions for analysis. Running with 4 threads ... ============================================== 2018-06-06 13:40:54 Options: --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2_run_423-GSM2251962/alignments.36mers.unique.bam --out Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2_run_423-GSM2251962/alignments.36mers.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 4 threads ... --------------------------- Events discovered Significant: 1260 Insignificant: 0 Filtered: 214 Finish binding event prediction: 1.3m Refine read distribution from 625 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 937 Insignificant: 0 Filtered: 77 Finish binding event prediction: 1.6m Refine read distribution from 369 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 661 Insignificant: 113 Filtered: 13 Finish binding event prediction: 3.1s Refine read distribution from 415 binding events. --------------------------- Events discovered Significant: 854 Insignificant: 1 Filtered: 77 Finish binding event prediction: 1.6m Refine read distribution from 344 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 674 Insignificant: 82 Filtered: 8 Finish binding event prediction: 6.1s Refine read distribution from 469 binding events. --------------------------- Events discovered Significant: 1390 Insignificant: 0 Filtered: 286 Finish binding event prediction: 1.8m Refine read distribution from 668 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 1137 Insignificant: 237 Filtered: 19 Finish binding event prediction: 37.3s Refine read distribution from 739 binding events. --------------------------- Events discovered Significant: 1077 Insignificant: 243 Filtered: 65 Finish binding event prediction: 47.1s Refine read distribution from 690 binding events. ============================================== 2018-06-06 18:56:55 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_exponential_aerobic_growth_rep1_run_423-GSM2251959/alignments.36mers.unique.bam --out Sig70_exponential_aerobic_growth_rep1_run_423-GSM2251959/alignments.36mers.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. The genome is segmented into 2050 regions for analysis. Running with 4 threads ... ============================================== 2018-06-06 18:56:57 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1_run_423-GSM2251960/alignments.36mers.unique.bam --out Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1_run_423-GSM2251960/alignments.36mers.unique.GPS Original read count stats: _IP Bases: 231019 HitCounts: 1963578.0 ============================================== 2018-06-06 18:56:58 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_exponential_aerobic_growth_rep2_run_423-GSM2251961/alignments.36mers.unique.bam --out Sig70_exponential_aerobic_growth_rep2_run_423-GSM2251961/alignments.36mers.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. The genome is segmented into 4737 regions for analysis. Running with 4 threads ... At Poisson p-value 1.0e-03, in a 301bp window, expect 40 reads. The genome is segmented into 2102 regions for analysis. Running with 4 threads ... ============================================== 2018-06-06 18:57:31 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2_run_423-GSM2251962/alignments.36mers.unique.bam --out Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2_run_423-GSM2251962/alignments.36mers.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 4 threads ... ============================================== 2018-06-06 18:57:34 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_exponential_aerobic_growth_rep2_run_299-GSM2251956/alignments.36mers.unique.bam --out Sig70_exponential_aerobic_growth_rep2_run_299-GSM2251956/alignments.36mers.unique.GPS Original read count stats: _IP Bases: 177241 HitCounts: 1.6325999E7 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 4 threads ... ============================================== 2018-06-06 18:57:38 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_static_aerobic_growth_rep1_run_299-GSM2251957/alignments.36mers.unique.bam --out Sig70_static_aerobic_growth_rep1_run_299-GSM2251957/alignments.36mers.unique.GPS ============================================== 2018-06-06 18:57:38 Original read count stats: _IP Bases: 328674 HitCounts: 1.7509608E7 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_static_aerobic_growth_rep1_run_299-GSM2251957/alignments.36mers.unique.bam --out Sig70_static_aerobic_growth_rep1_run_299-GSM2251957/alignments.36mers.unique.GPS Original read count stats: _IP Bases: 328674 HitCounts: 1.7509608E7 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 4 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 4 threads ... --------------------------- Events discovered Significant: 854 Insignificant: 1 Filtered: 77 Finish binding event prediction: 1.0m Refine read distribution from 344 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 674 Insignificant: 82 Filtered: 8 Finish binding event prediction: 13.0s Refine read distribution from 469 binding events. --------------------------- Events discovered Significant: 937 Insignificant: 0 Filtered: 77 Finish binding event prediction: 1.2m Refine read distribution from 369 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 1260 Insignificant: 0 Filtered: 214 Finish binding event prediction: 1.2m Refine read distribution from 625 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 661 Insignificant: 113 Filtered: 13 Finish binding event prediction: 4.0s Refine read distribution from 415 binding events. --------------------------- Events discovered Significant: 1378 Insignificant: 0 Filtered: 72 Finish binding event prediction: 1.1m Refine read distribution from 554 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 1137 Insignificant: 237 Filtered: 19 Finish binding event prediction: 40.1s Refine read distribution from 739 binding events. --------------------------- Events discovered Significant: 822 Insignificant: 189 Filtered: 22 Finish binding event prediction: 7.1s Refine read distribution from 572 binding events. --------------------------- Events discovered Significant: 1390 Insignificant: 0 Filtered: 286 Finish binding event prediction: 1.6m Refine read distribution from 668 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 1169 Insignificant: 0 Filtered: 126 Finish binding event prediction: 1.7m Refine read distribution from 457 binding events. Running with 4 threads ... --------------------------- Events discovered Significant: 693 Insignificant: 154 Filtered: 49 Finish binding event prediction: 5.0s Refine read distribution from 473 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 4 threads ... --------------------------- Events discovered Significant: 1077 Insignificant: 243 Filtered: 65 Finish binding event prediction: 25.1s Refine read distribution from 690 binding events. --------------------------- Events discovered Significant: 822 Insignificant: 189 Filtered: 22 Finish binding event prediction: 6.1s Refine read distribution from 572 binding events. ============================================== 2018-06-07 06:07:21 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_exponential_aerobic_growth_rep1_run_299-GSM2251955/alignments.36mers.unique.bam --out Sig70_exponential_aerobic_growth_rep1_run_299-GSM2251955/alignments.36mers.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 16 threads ... --------------------------- Events discovered Significant: 1324 Insignificant: 0 Filtered: 81 Finish binding event prediction: 2.3m Refine read distribution from 509 binding events. Running with 16 threads ... --------------------------- Events discovered Significant: 789 Insignificant: 174 Filtered: 26 Finish binding event prediction: 9.2s Refine read distribution from 529 binding events. ============================================== 2018-06-07 07:55:41 Options: --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt Sig70_static_aerobic_growth_rep2_run_299-GSM2251958/alignments.36mers.unique.bam --out Sig70_static_aerobic_growth_rep2_run_299-GSM2251958/alignments.36mers.unique.GPS Original read count stats: _IP Bases: 202055 HitCounts: 1.5130991E7 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 16 threads ... --------------------------- Events discovered Significant: 1086 Insignificant: 0 Filtered: 107 Finish binding event prediction: 3.1m Refine read distribution from 470 binding events. Running with 16 threads ... --------------------------- Events discovered Significant: 677 Insignificant: 148 Filtered: 51 Finish binding event prediction: 16.1s Refine read distribution from 475 binding events.