INFO @ 20 Dec 2024 05:30:56: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorep2/C0_sorted.tsv -f BED -n C0_pseudoreplicate2 -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C0_pseudoreplicate2 # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorep2/C0_sorted.tsv'] # control file = None # effective genome size = 2.91e+09 # band width = 300 # model fold = [5, 50] # pvalue cutoff = 1.00e-02 # qvalue will not be calculated and reported as -1 in the final output. # The maximum gap between significant sites is assigned as the read length/tag size. # The minimum length of peaks is assigned as the predicted fragment length "d". # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off # Searching for subpeak summits is on # MACS will save fragment pileup signal per million reads INFO @ 20 Dec 2024 05:30:56: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 05:30:56: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 05:30:58: [98 MB] 1000000 reads parsed INFO @ 20 Dec 2024 05:31:00: [101 MB] 2000000 reads parsed INFO @ 20 Dec 2024 05:31:02: [104 MB] 3000000 reads parsed INFO @ 20 Dec 2024 05:31:03: [106 MB] 4000000 reads parsed INFO @ 20 Dec 2024 05:31:05: [111 MB] 5000000 reads parsed INFO @ 20 Dec 2024 05:31:07: [113 MB] 6000000 reads parsed INFO @ 20 Dec 2024 05:31:09: [116 MB] 7000000 reads parsed INFO @ 20 Dec 2024 05:31:11: [120 MB] 8000000 reads parsed INFO @ 20 Dec 2024 05:31:12: [125 MB] 9000000 reads parsed INFO @ 20 Dec 2024 05:31:14: [128 MB] 10000000 reads parsed INFO @ 20 Dec 2024 05:31:16: [132 MB] 11000000 reads parsed INFO @ 20 Dec 2024 05:31:18: [142 MB] 12000000 reads parsed INFO @ 20 Dec 2024 05:31:20: [145 MB] 13000000 reads parsed INFO @ 20 Dec 2024 05:31:22: [148 MB] 14000000 reads parsed INFO @ 20 Dec 2024 05:31:24: [151 MB] 15000000 reads parsed INFO @ 20 Dec 2024 05:31:26: [154 MB] 16000000 reads parsed INFO @ 20 Dec 2024 05:31:28: [162 MB] 17000000 reads parsed INFO @ 20 Dec 2024 05:31:30: [170 MB] 18000000 reads parsed INFO @ 20 Dec 2024 05:31:32: [174 MB] 19000000 reads parsed INFO @ 20 Dec 2024 05:31:34: [179 MB] 20000000 reads parsed INFO @ 20 Dec 2024 05:31:35: [179 MB] 21000000 reads parsed INFO @ 20 Dec 2024 05:31:37: [179 MB] 22000000 reads parsed INFO @ 20 Dec 2024 05:31:39: [186 MB] 23000000 reads parsed INFO @ 20 Dec 2024 05:31:42: [191 MB] 24000000 reads parsed INFO @ 20 Dec 2024 05:31:43: [193 MB] 25000000 reads parsed INFO @ 20 Dec 2024 05:31:45: [195 MB] 26000000 reads parsed INFO @ 20 Dec 2024 05:31:47: [198 MB] 27000000 reads parsed INFO @ 20 Dec 2024 05:31:49: [203 MB] 28000000 reads parsed INFO @ 20 Dec 2024 05:31:51: [210 MB] 29000000 reads parsed INFO @ 20 Dec 2024 05:31:53: [214 MB] 30000000 reads parsed INFO @ 20 Dec 2024 05:31:54: [220 MB] 31000000 reads parsed INFO @ 20 Dec 2024 05:31:57: [224 MB] 32000000 reads parsed INFO @ 20 Dec 2024 05:31:58: [225 MB] 33000000 reads parsed INFO @ 20 Dec 2024 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INFO @ 20 Dec 2024 05:32:31: [299 MB] 51000000 reads parsed INFO @ 20 Dec 2024 05:32:33: [303 MB] 52000000 reads parsed INFO @ 20 Dec 2024 05:32:35: [306 MB] 53000000 reads parsed INFO @ 20 Dec 2024 05:32:37: [308 MB] 54000000 reads parsed INFO @ 20 Dec 2024 05:32:38: [313 MB] 55000000 reads parsed INFO @ 20 Dec 2024 05:32:40: [316 MB] 56000000 reads parsed INFO @ 20 Dec 2024 05:32:42: [320 MB] 57000000 reads parsed INFO @ 20 Dec 2024 05:32:44: [323 MB] 58000000 reads parsed INFO @ 20 Dec 2024 05:32:46: [328 MB] 59000000 reads parsed INFO @ 20 Dec 2024 05:32:47: [330 MB] 60000000 reads parsed INFO @ 20 Dec 2024 05:32:49: [333 MB] 61000000 reads parsed INFO @ 20 Dec 2024 05:32:51: [337 MB] 62000000 reads parsed INFO @ 20 Dec 2024 05:32:53: [341 MB] 63000000 reads parsed INFO @ 20 Dec 2024 05:32:54: [345 MB] 64000000 reads parsed INFO @ 20 Dec 2024 05:32:56: [351 MB] 65000000 reads parsed INFO @ 20 Dec 2024 05:32:58: [355 MB] 66000000 reads parsed INFO @ 20 Dec 2024 05:33:00: [358 MB] 67000000 reads parsed INFO @ 20 Dec 2024 05:33:02: [371 MB] 68000000 reads parsed INFO @ 20 Dec 2024 05:33:04: [371 MB] 69000000 reads parsed INFO @ 20 Dec 2024 05:33:05: [378 MB] 70000000 reads parsed INFO @ 20 Dec 2024 05:33:07: [380 MB] 71000000 reads parsed INFO @ 20 Dec 2024 05:33:09: [384 MB] 72000000 reads parsed INFO @ 20 Dec 2024 05:33:11: [389 MB] 73000000 reads parsed INFO @ 20 Dec 2024 05:33:13: [391 MB] 74000000 reads parsed INFO @ 20 Dec 2024 05:33:14: [395 MB] 75000000 reads parsed INFO @ 20 Dec 2024 05:33:16: [399 MB] 76000000 reads parsed INFO @ 20 Dec 2024 05:33:18: [403 MB] 77000000 reads parsed INFO @ 20 Dec 2024 05:33:20: [407 MB] 78000000 reads parsed INFO @ 20 Dec 2024 05:33:22: [412 MB] 79000000 reads parsed INFO @ 20 Dec 2024 05:33:24: [415 MB] 80000000 reads parsed INFO @ 20 Dec 2024 05:33:26: [419 MB] 81000000 reads parsed INFO @ 20 Dec 2024 05:33:28: [423 MB] 82000000 reads parsed INFO @ 20 Dec 2024 05:33:29: [428 MB] 83000000 reads parsed INFO @ 20 Dec 2024 05:33:31: [431 MB] 84000000 reads parsed INFO @ 20 Dec 2024 05:33:33: [435 MB] 85000000 reads parsed INFO @ 20 Dec 2024 05:33:35: [439 MB] 86000000 reads parsed INFO @ 20 Dec 2024 05:33:37: [443 MB] 87000000 reads parsed INFO @ 20 Dec 2024 05:33:39: [446 MB] 88000000 reads parsed INFO @ 20 Dec 2024 05:33:41: [449 MB] 89000000 reads parsed INFO @ 20 Dec 2024 05:33:43: [454 MB] 90000000 reads parsed INFO @ 20 Dec 2024 05:33:45: [458 MB] 91000000 reads parsed INFO @ 20 Dec 2024 05:33:46: [462 MB] 92000000 reads parsed INFO @ 20 Dec 2024 05:33:49: [466 MB] 93000000 reads parsed INFO @ 20 Dec 2024 05:33:50: [469 MB] 94000000 reads parsed INFO @ 20 Dec 2024 05:33:52: [474 MB] 95000000 reads parsed INFO @ 20 Dec 2024 05:33:54: [477 MB] 96000000 reads parsed INFO @ 20 Dec 2024 05:33:56: [481 MB] 97000000 reads parsed INFO @ 20 Dec 2024 05:33:58: [485 MB] 98000000 reads parsed INFO @ 20 Dec 2024 05:33:59: [489 MB] 99000000 reads parsed INFO @ 20 Dec 2024 05:34:01: [493 MB] 100000000 reads parsed INFO @ 20 Dec 2024 05:34:03: [497 MB] 101000000 reads parsed INFO @ 20 Dec 2024 05:34:05: [500 MB] 102000000 reads parsed INFO @ 20 Dec 2024 05:34:07: [504 MB] 103000000 reads parsed INFO @ 20 Dec 2024 05:34:08: [507 MB] 104000000 reads parsed INFO @ 20 Dec 2024 05:34:10: [511 MB] 105000000 reads parsed INFO @ 20 Dec 2024 05:34:12: [518 MB] 106000000 reads parsed INFO @ 20 Dec 2024 05:34:14: [521 MB] 107000000 reads parsed INFO @ 20 Dec 2024 05:34:16: [524 MB] 108000000 reads parsed INFO @ 20 Dec 2024 05:34:18: [528 MB] 109000000 reads parsed INFO @ 20 Dec 2024 05:34:20: [531 MB] 110000000 reads parsed INFO @ 20 Dec 2024 05:34:21: [535 MB] 111000000 reads parsed INFO @ 20 Dec 2024 05:34:22: [536 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 05:34:22: [536 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 05:34:22: [536 MB] #1 total tags in treatment: 111436208 INFO @ 20 Dec 2024 05:34:22: [536 MB] #1 finished! INFO @ 20 Dec 2024 05:34:22: [536 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 05:34:22: [536 MB] #2 Skipped... INFO @ 20 Dec 2024 05:34:22: [536 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 05:34:22: [536 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 05:34:22: [536 MB] #3 Call peaks... INFO @ 20 Dec 2024 05:34:22: [536 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 05:34:22: [536 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 05:34:22: [536 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 05:37:49: [2621 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 05:37:49: [2621 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C0_pseudoreplicate2_treat_pileup.bdg INFO @ 20 Dec 2024 05:37:49: [2621 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C0_pseudoreplicate2_control_lambda.bdg INFO @ 20 Dec 2024 05:37:49: [2621 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 05:37:49: [2621 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 05:40:25: [2621 MB] #4 Write output xls file... 3_peaks/C0_pseudoreplicate2_peaks.xls INFO @ 20 Dec 2024 05:40:27: [2621 MB] #4 Write peak in narrowPeak format file... 3_peaks/C0_pseudoreplicate2_peaks.narrowPeak INFO @ 20 Dec 2024 05:40:28: [2621 MB] #4 Write summits bed file... 3_peaks/C0_pseudoreplicate2_summits.bed INFO @ 20 Dec 2024 05:40:29: [2621 MB] Done!