INFO @ 20 Dec 2024 06:46:39: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorep2/C6_sorted.tsv -f BED -n C6_pseudoreplicate2 -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C6_pseudoreplicate2 # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorep2/C6_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 06:46:39: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 06:46:39: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 06:46:41: [98 MB] 1000000 reads parsed INFO @ 20 Dec 2024 06:46:43: [100 MB] 2000000 reads parsed INFO @ 20 Dec 2024 06:46:45: [102 MB] 3000000 reads parsed INFO @ 20 Dec 2024 06:46:47: [109 MB] 4000000 reads parsed INFO @ 20 Dec 2024 06:46:49: [114 MB] 5000000 reads parsed INFO @ 20 Dec 2024 06:46:51: [117 MB] 6000000 reads parsed INFO @ 20 Dec 2024 06:46:53: [121 MB] 7000000 reads parsed INFO @ 20 Dec 2024 06:46:54: [124 MB] 8000000 reads parsed INFO @ 20 Dec 2024 06:46:56: [128 MB] 9000000 reads parsed INFO @ 20 Dec 2024 06:46:58: [133 MB] 10000000 reads parsed INFO @ 20 Dec 2024 06:47:00: [137 MB] 11000000 reads parsed INFO @ 20 Dec 2024 06:47:02: [142 MB] 12000000 reads parsed INFO @ 20 Dec 2024 06:47:03: [147 MB] 13000000 reads parsed INFO @ 20 Dec 2024 06:47:05: [151 MB] 14000000 reads parsed INFO @ 20 Dec 2024 06:47:07: [155 MB] 15000000 reads parsed INFO @ 20 Dec 2024 06:47:09: [160 MB] 16000000 reads parsed INFO @ 20 Dec 2024 06:47:11: [164 MB] 17000000 reads parsed INFO @ 20 Dec 2024 06:47:13: [168 MB] 18000000 reads parsed INFO @ 20 Dec 2024 06:47:14: [172 MB] 19000000 reads parsed INFO @ 20 Dec 2024 06:47:16: [176 MB] 20000000 reads parsed INFO @ 20 Dec 2024 06:47:18: [181 MB] 21000000 reads parsed INFO @ 20 Dec 2024 06:47:19: [184 MB] 22000000 reads parsed INFO @ 20 Dec 2024 06:47:21: [188 MB] 23000000 reads parsed INFO @ 20 Dec 2024 06:47:23: [193 MB] 24000000 reads parsed INFO @ 20 Dec 2024 06:47:25: [199 MB] 25000000 reads parsed INFO @ 20 Dec 2024 06:47:26: [204 MB] 26000000 reads parsed INFO @ 20 Dec 2024 06:47:28: [208 MB] 27000000 reads parsed INFO @ 20 Dec 2024 06:47:30: [212 MB] 28000000 reads parsed INFO @ 20 Dec 2024 06:47:32: [216 MB] 29000000 reads parsed INFO @ 20 Dec 2024 06:47:33: [219 MB] 30000000 reads parsed INFO @ 20 Dec 2024 06:47:35: [223 MB] 31000000 reads parsed INFO @ 20 Dec 2024 06:47:37: [228 MB] 32000000 reads parsed INFO @ 20 Dec 2024 06:47:38: [232 MB] 33000000 reads parsed INFO @ 20 Dec 2024 06:47:40: [235 MB] 34000000 reads parsed INFO @ 20 Dec 2024 06:47:42: [240 MB] 35000000 reads parsed INFO @ 20 Dec 2024 06:47:44: [244 MB] 36000000 reads parsed INFO @ 20 Dec 2024 06:47:44: [244 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 06:47:44: [244 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 06:47:44: [244 MB] #1 total tags in treatment: 36283869 INFO @ 20 Dec 2024 06:47:44: [244 MB] #1 finished! INFO @ 20 Dec 2024 06:47:44: [244 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 06:47:44: [244 MB] #2 Skipped... INFO @ 20 Dec 2024 06:47:44: [244 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 06:47:44: [244 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 06:47:44: [244 MB] #3 Call peaks... INFO @ 20 Dec 2024 06:47:44: [244 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 06:47:44: [244 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 06:47:44: [244 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 06:48:54: [939 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 06:48:54: [939 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C6_pseudoreplicate2_treat_pileup.bdg INFO @ 20 Dec 2024 06:48:54: [939 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C6_pseudoreplicate2_control_lambda.bdg INFO @ 20 Dec 2024 06:48:54: [939 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 06:48:54: [939 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 06:50:21: [939 MB] #4 Write output xls file... 3_peaks/C6_pseudoreplicate2_peaks.xls INFO @ 20 Dec 2024 06:50:21: [939 MB] #4 Write peak in narrowPeak format file... 3_peaks/C6_pseudoreplicate2_peaks.narrowPeak INFO @ 20 Dec 2024 06:50:22: [939 MB] #4 Write summits bed file... 3_peaks/C6_pseudoreplicate2_summits.bed INFO @ 20 Dec 2024 06:50:23: [939 MB] Done!