INFO @ 20 Dec 2024 05:30:56: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorep1/C0_sorted.tsv -f BED -n C0_pseudoreplicate1 -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C0_pseudoreplicate1 # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorep1/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 05:31:01: [104 MB] 3000000 reads parsed INFO @ 20 Dec 2024 05:31:03: [108 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 05:31:13: [124 MB] 9000000 reads parsed INFO @ 20 Dec 2024 05:31:15: [129 MB] 10000000 reads parsed INFO @ 20 Dec 2024 05:31:17: [133 MB] 11000000 reads parsed INFO @ 20 Dec 2024 05:31:19: [141 MB] 12000000 reads parsed INFO @ 20 Dec 2024 05:31:21: [145 MB] 13000000 reads parsed INFO @ 20 Dec 2024 05:31:23: [148 MB] 14000000 reads parsed INFO @ 20 Dec 2024 05:31:25: [151 MB] 15000000 reads parsed INFO @ 20 Dec 2024 05:31:27: [154 MB] 16000000 reads parsed INFO @ 20 Dec 2024 05:31:29: [162 MB] 17000000 reads parsed INFO @ 20 Dec 2024 05:31:31: [176 MB] 18000000 reads parsed INFO @ 20 Dec 2024 05:31:32: [176 MB] 19000000 reads parsed INFO @ 20 Dec 2024 05:31:34: [180 MB] 20000000 reads parsed INFO @ 20 Dec 2024 05:31:36: [180 MB] 21000000 reads parsed INFO @ 20 Dec 2024 05:31:38: [180 MB] 22000000 reads parsed INFO @ 20 Dec 2024 05:31:40: [184 MB] 23000000 reads parsed INFO @ 20 Dec 2024 05:31:43: [193 MB] 24000000 reads parsed INFO @ 20 Dec 2024 05:31:45: [200 MB] 25000000 reads parsed INFO @ 20 Dec 2024 05:31:46: [200 MB] 26000000 reads parsed INFO @ 20 Dec 2024 05:31:48: [200 MB] 27000000 reads parsed INFO @ 20 Dec 2024 05:31:50: [203 MB] 28000000 reads parsed INFO @ 20 Dec 2024 05:31:52: [210 MB] 29000000 reads parsed INFO @ 20 Dec 2024 05:31:54: [213 MB] 30000000 reads parsed INFO @ 20 Dec 2024 05:31:55: [218 MB] 31000000 reads parsed INFO @ 20 Dec 2024 05:31:57: [222 MB] 32000000 reads parsed INFO @ 20 Dec 2024 05:31:59: [225 MB] 33000000 reads parsed INFO @ 20 Dec 2024 05:32:01: [228 MB] 34000000 reads parsed INFO @ 20 Dec 2024 05:32:03: [234 MB] 35000000 reads parsed INFO @ 20 Dec 2024 05:32:05: [237 MB] 36000000 reads parsed INFO @ 20 Dec 2024 05:32:06: [241 MB] 37000000 reads parsed INFO @ 20 Dec 2024 05:32:08: [245 MB] 38000000 reads parsed INFO @ 20 Dec 2024 05:32:10: [249 MB] 39000000 reads parsed INFO @ 20 Dec 2024 05:32:12: [253 MB] 40000000 reads parsed INFO @ 20 Dec 2024 05:32:14: [256 MB] 41000000 reads parsed INFO @ 20 Dec 2024 05:32:15: [258 MB] 42000000 reads parsed INFO @ 20 Dec 2024 05:32:17: [264 MB] 43000000 reads parsed INFO @ 20 Dec 2024 05:32:19: [268 MB] 44000000 reads parsed INFO @ 20 Dec 2024 05:32:21: [272 MB] 45000000 reads parsed INFO @ 20 Dec 2024 05:32:22: [276 MB] 46000000 reads parsed INFO @ 20 Dec 2024 05:32:24: [280 MB] 47000000 reads parsed INFO @ 20 Dec 2024 05:32:26: [283 MB] 48000000 reads parsed INFO @ 20 Dec 2024 05:32:28: [287 MB] 49000000 reads parsed INFO @ 20 Dec 2024 05:32:29: [293 MB] 50000000 reads parsed INFO @ 20 Dec 2024 05:32:31: [299 MB] 51000000 reads parsed INFO @ 20 Dec 2024 05:32:33: [302 MB] 52000000 reads parsed INFO @ 20 Dec 2024 05:32:35: [304 MB] 53000000 reads parsed INFO @ 20 Dec 2024 05:32:37: [309 MB] 54000000 reads parsed INFO @ 20 Dec 2024 05:32:38: [311 MB] 55000000 reads parsed INFO @ 20 Dec 2024 05:32:40: [319 MB] 56000000 reads parsed INFO @ 20 Dec 2024 05:32:41: [322 MB] 57000000 reads parsed INFO @ 20 Dec 2024 05:32:43: [323 MB] 58000000 reads parsed INFO @ 20 Dec 2024 05:32:45: [329 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 05:32:50: [338 MB] 62000000 reads parsed INFO @ 20 Dec 2024 05:32:52: [341 MB] 63000000 reads parsed INFO @ 20 Dec 2024 05:32:54: [345 MB] 64000000 reads parsed INFO @ 20 Dec 2024 05:32:56: [352 MB] 65000000 reads parsed INFO @ 20 Dec 2024 05:32:58: [356 MB] 66000000 reads parsed INFO @ 20 Dec 2024 05:33:00: [358 MB] 67000000 reads parsed INFO @ 20 Dec 2024 05:33:02: [364 MB] 68000000 reads parsed INFO @ 20 Dec 2024 05:33:04: [367 MB] 69000000 reads parsed INFO @ 20 Dec 2024 05:33:05: [371 MB] 70000000 reads parsed INFO @ 20 Dec 2024 05:33:07: [376 MB] 71000000 reads parsed INFO @ 20 Dec 2024 05:33:09: [379 MB] 72000000 reads parsed INFO @ 20 Dec 2024 05:33:11: [383 MB] 73000000 reads parsed INFO @ 20 Dec 2024 05:33:13: [386 MB] 74000000 reads parsed INFO @ 20 Dec 2024 05:33:14: [390 MB] 75000000 reads parsed INFO @ 20 Dec 2024 05:33:17: [394 MB] 76000000 reads parsed INFO @ 20 Dec 2024 05:33:18: [398 MB] 77000000 reads parsed INFO @ 20 Dec 2024 05:33:21: [402 MB] 78000000 reads parsed INFO @ 20 Dec 2024 05:33:23: [406 MB] 79000000 reads parsed INFO @ 20 Dec 2024 05:33:25: [410 MB] 80000000 reads parsed INFO @ 20 Dec 2024 05:33:26: [414 MB] 81000000 reads parsed INFO @ 20 Dec 2024 05:33:28: [418 MB] 82000000 reads parsed INFO @ 20 Dec 2024 05:33:30: [422 MB] 83000000 reads parsed INFO @ 20 Dec 2024 05:33:32: [425 MB] 84000000 reads parsed INFO @ 20 Dec 2024 05:33:34: [429 MB] 85000000 reads parsed INFO @ 20 Dec 2024 05:33:36: [434 MB] 86000000 reads parsed INFO @ 20 Dec 2024 05:33:37: [437 MB] 87000000 reads parsed INFO @ 20 Dec 2024 05:33:39: [440 MB] 88000000 reads parsed INFO @ 20 Dec 2024 05:33:41: [445 MB] 89000000 reads parsed INFO @ 20 Dec 2024 05:33:43: [449 MB] 90000000 reads parsed INFO @ 20 Dec 2024 05:33:45: [453 MB] 91000000 reads parsed INFO @ 20 Dec 2024 05:33:47: [456 MB] 92000000 reads parsed INFO @ 20 Dec 2024 05:33:49: [461 MB] 93000000 reads parsed INFO @ 20 Dec 2024 05:33:51: [464 MB] 94000000 reads parsed INFO @ 20 Dec 2024 05:33:52: [468 MB] 95000000 reads parsed INFO @ 20 Dec 2024 05:33:54: [472 MB] 96000000 reads parsed INFO @ 20 Dec 2024 05:33:56: [475 MB] 97000000 reads parsed INFO @ 20 Dec 2024 05:33:58: [480 MB] 98000000 reads parsed INFO @ 20 Dec 2024 05:34:00: [483 MB] 99000000 reads parsed INFO @ 20 Dec 2024 05:34:01: [488 MB] 100000000 reads parsed INFO @ 20 Dec 2024 05:34:03: [492 MB] 101000000 reads parsed INFO @ 20 Dec 2024 05:34:05: [495 MB] 102000000 reads parsed INFO @ 20 Dec 2024 05:34:06: [499 MB] 103000000 reads parsed INFO @ 20 Dec 2024 05:34:08: [502 MB] 104000000 reads parsed INFO @ 20 Dec 2024 05:34:10: [507 MB] 105000000 reads parsed INFO @ 20 Dec 2024 05:34:12: [517 MB] 106000000 reads parsed INFO @ 20 Dec 2024 05:34:14: [525 MB] 107000000 reads parsed INFO @ 20 Dec 2024 05:34:16: [525 MB] 108000000 reads parsed INFO @ 20 Dec 2024 05:34:18: [525 MB] 109000000 reads parsed INFO @ 20 Dec 2024 05:34:20: [533 MB] 110000000 reads parsed INFO @ 20 Dec 2024 05:34:21: [537 MB] 111000000 reads parsed INFO @ 20 Dec 2024 05:34:23: [537 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 05:34:23: [537 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 05:34:23: [537 MB] #1 total tags in treatment: 111411350 INFO @ 20 Dec 2024 05:34:23: [537 MB] #1 finished! INFO @ 20 Dec 2024 05:34:23: [537 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 05:34:23: [537 MB] #2 Skipped... INFO @ 20 Dec 2024 05:34:23: [537 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 05:34:23: [537 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 05:34:23: [537 MB] #3 Call peaks... INFO @ 20 Dec 2024 05:34:23: [537 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 05:34:23: [537 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 05:34:23: [537 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 05:37:55: [2715 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 05:37:55: [2715 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C0_pseudoreplicate1_treat_pileup.bdg INFO @ 20 Dec 2024 05:37:55: [2715 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C0_pseudoreplicate1_control_lambda.bdg INFO @ 20 Dec 2024 05:37:55: [2715 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 05:37:55: [2715 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 05:40:29: [2715 MB] #4 Write output xls file... 3_peaks/C0_pseudoreplicate1_peaks.xls INFO @ 20 Dec 2024 05:40:30: [2715 MB] #4 Write peak in narrowPeak format file... 3_peaks/C0_pseudoreplicate1_peaks.narrowPeak INFO @ 20 Dec 2024 05:40:30: [2715 MB] #4 Write summits bed file... 3_peaks/C0_pseudoreplicate1_summits.bed INFO @ 20 Dec 2024 05:40:31: [2715 MB] Done!