INFO @ 20 Dec 2024 05:50:36: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorep2/C10_sorted.tsv -f BED -n C10_pseudoreplicate2 -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C10_pseudoreplicate2 # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorep2/C10_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 05:50:36: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 05:50:36: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 05:50:38: [97 MB] 1000000 reads parsed INFO @ 20 Dec 2024 05:50:39: [100 MB] 2000000 reads parsed INFO @ 20 Dec 2024 05:50:41: [110 MB] 3000000 reads parsed INFO @ 20 Dec 2024 05:50:43: [114 MB] 4000000 reads parsed INFO @ 20 Dec 2024 05:50:45: [118 MB] 5000000 reads parsed INFO @ 20 Dec 2024 05:50:47: [120 MB] 6000000 reads parsed INFO @ 20 Dec 2024 05:50:49: [128 MB] 7000000 reads parsed INFO @ 20 Dec 2024 05:50:51: [133 MB] 8000000 reads parsed INFO @ 20 Dec 2024 05:50:53: [136 MB] 9000000 reads parsed INFO @ 20 Dec 2024 05:50:55: [139 MB] 10000000 reads parsed INFO @ 20 Dec 2024 05:50:57: [145 MB] 11000000 reads parsed INFO @ 20 Dec 2024 05:50:59: [149 MB] 12000000 reads parsed INFO @ 20 Dec 2024 05:51:00: [151 MB] 13000000 reads parsed INFO @ 20 Dec 2024 05:51:02: [156 MB] 14000000 reads parsed INFO @ 20 Dec 2024 05:51:04: [160 MB] 15000000 reads parsed INFO @ 20 Dec 2024 05:51:06: [165 MB] 16000000 reads parsed INFO @ 20 Dec 2024 05:51:07: [169 MB] 17000000 reads parsed INFO @ 20 Dec 2024 05:51:10: [174 MB] 18000000 reads parsed INFO @ 20 Dec 2024 05:51:12: [178 MB] 19000000 reads parsed INFO @ 20 Dec 2024 05:51:13: [182 MB] 20000000 reads parsed INFO @ 20 Dec 2024 05:51:15: [187 MB] 21000000 reads parsed INFO @ 20 Dec 2024 05:51:17: [190 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 05:51:17: [190 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 05:51:17: [190 MB] #1 total tags in treatment: 21927664 INFO @ 20 Dec 2024 05:51:17: [190 MB] #1 finished! INFO @ 20 Dec 2024 05:51:17: [190 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 05:51:17: [190 MB] #2 Skipped... INFO @ 20 Dec 2024 05:51:17: [190 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 05:51:17: [190 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 05:51:17: [190 MB] #3 Call peaks... INFO @ 20 Dec 2024 05:51:17: [190 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 05:51:17: [190 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 05:51:17: [190 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 05:51:54: [615 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 05:51:54: [615 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C10_pseudoreplicate2_treat_pileup.bdg INFO @ 20 Dec 2024 05:51:54: [615 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C10_pseudoreplicate2_control_lambda.bdg INFO @ 20 Dec 2024 05:51:54: [615 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 05:51:54: [615 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 05:52:52: [615 MB] #4 Write output xls file... 3_peaks/C10_pseudoreplicate2_peaks.xls INFO @ 20 Dec 2024 05:52:52: [615 MB] #4 Write peak in narrowPeak format file... 3_peaks/C10_pseudoreplicate2_peaks.narrowPeak INFO @ 20 Dec 2024 05:52:53: [615 MB] #4 Write summits bed file... 3_peaks/C10_pseudoreplicate2_summits.bed INFO @ 20 Dec 2024 05:52:53: [615 MB] Done!