INFO @ 20 Dec 2024 06:09:11: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorep1/C13_sorted.tsv -f BED -n C13_pseudoreplicate1 -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C13_pseudoreplicate1 # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorep1/C13_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 06:09:11: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 06:09:11: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 06:09:13: [97 MB] 1000000 reads parsed INFO @ 20 Dec 2024 06:09:15: [100 MB] 2000000 reads parsed INFO @ 20 Dec 2024 06:09:17: [105 MB] 3000000 reads parsed INFO @ 20 Dec 2024 06:09:19: [110 MB] 4000000 reads parsed INFO @ 20 Dec 2024 06:09:21: [113 MB] 5000000 reads parsed INFO @ 20 Dec 2024 06:09:22: [118 MB] 6000000 reads parsed INFO @ 20 Dec 2024 06:09:25: [125 MB] 7000000 reads parsed INFO @ 20 Dec 2024 06:09:26: [126 MB] 8000000 reads parsed INFO @ 20 Dec 2024 06:09:28: [133 MB] 9000000 reads parsed INFO @ 20 Dec 2024 06:09:30: [143 MB] 10000000 reads parsed INFO @ 20 Dec 2024 06:09:33: [148 MB] 11000000 reads parsed INFO @ 20 Dec 2024 06:09:35: [148 MB] 12000000 reads parsed INFO @ 20 Dec 2024 06:09:37: [154 MB] 13000000 reads parsed INFO @ 20 Dec 2024 06:09:39: [159 MB] 14000000 reads parsed INFO @ 20 Dec 2024 06:09:41: [162 MB] 15000000 reads parsed INFO @ 20 Dec 2024 06:09:43: [166 MB] 16000000 reads parsed INFO @ 20 Dec 2024 06:09:45: [170 MB] 17000000 reads parsed INFO @ 20 Dec 2024 06:09:47: [175 MB] 18000000 reads parsed INFO @ 20 Dec 2024 06:09:49: [179 MB] 19000000 reads parsed INFO @ 20 Dec 2024 06:09:50: [183 MB] 20000000 reads parsed INFO @ 20 Dec 2024 06:09:51: [184 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 06:09:51: [184 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 06:09:51: [184 MB] #1 total tags in treatment: 20524329 INFO @ 20 Dec 2024 06:09:51: [184 MB] #1 finished! INFO @ 20 Dec 2024 06:09:51: [184 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 06:09:51: [184 MB] #2 Skipped... INFO @ 20 Dec 2024 06:09:51: [184 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 06:09:51: [184 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 06:09:51: [184 MB] #3 Call peaks... INFO @ 20 Dec 2024 06:09:51: [184 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 06:09:51: [184 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 06:09:51: [184 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 06:10:27: [580 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 06:10:27: [580 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C13_pseudoreplicate1_treat_pileup.bdg INFO @ 20 Dec 2024 06:10:27: [580 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C13_pseudoreplicate1_control_lambda.bdg INFO @ 20 Dec 2024 06:10:27: [580 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 06:10:27: [580 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 06:11:30: [580 MB] #4 Write output xls file... 3_peaks/C13_pseudoreplicate1_peaks.xls INFO @ 20 Dec 2024 06:11:30: [580 MB] #4 Write peak in narrowPeak format file... 3_peaks/C13_pseudoreplicate1_peaks.narrowPeak INFO @ 20 Dec 2024 06:11:31: [580 MB] #4 Write summits bed file... 3_peaks/C13_pseudoreplicate1_summits.bed INFO @ 20 Dec 2024 06:11:31: [580 MB] Done!