INFO @ 20 Dec 2024 06:03:50: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorep2/C12_sorted.tsv -f BED -n C12_pseudoreplicate2 -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C12_pseudoreplicate2 # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorep2/C12_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 06:03:50: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 06:03:50: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 06:03:52: [97 MB] 1000000 reads parsed INFO @ 20 Dec 2024 06:03:53: [99 MB] 2000000 reads parsed INFO @ 20 Dec 2024 06:03:55: [108 MB] 3000000 reads parsed INFO @ 20 Dec 2024 06:03:58: [117 MB] 4000000 reads parsed INFO @ 20 Dec 2024 06:03:59: [120 MB] 5000000 reads parsed INFO @ 20 Dec 2024 06:04:01: [122 MB] 6000000 reads parsed INFO @ 20 Dec 2024 06:04:04: [128 MB] 7000000 reads parsed INFO @ 20 Dec 2024 06:04:06: [132 MB] 8000000 reads parsed INFO @ 20 Dec 2024 06:04:07: [134 MB] 9000000 reads parsed INFO @ 20 Dec 2024 06:04:09: [140 MB] 10000000 reads parsed INFO @ 20 Dec 2024 06:04:12: [144 MB] 11000000 reads parsed INFO @ 20 Dec 2024 06:04:13: [148 MB] 12000000 reads parsed INFO @ 20 Dec 2024 06:04:15: [158 MB] 13000000 reads parsed INFO @ 20 Dec 2024 06:04:17: [160 MB] 14000000 reads parsed INFO @ 20 Dec 2024 06:04:19: [164 MB] 15000000 reads parsed INFO @ 20 Dec 2024 06:04:21: [170 MB] 16000000 reads parsed INFO @ 20 Dec 2024 06:04:23: [173 MB] 17000000 reads parsed INFO @ 20 Dec 2024 06:04:25: [177 MB] 18000000 reads parsed INFO @ 20 Dec 2024 06:04:27: [181 MB] 19000000 reads parsed INFO @ 20 Dec 2024 06:04:29: [186 MB] 20000000 reads parsed INFO @ 20 Dec 2024 06:04:30: [186 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 06:04:30: [186 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 06:04:30: [186 MB] #1 total tags in treatment: 20252845 INFO @ 20 Dec 2024 06:04:30: [186 MB] #1 finished! INFO @ 20 Dec 2024 06:04:30: [186 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 06:04:30: [186 MB] #2 Skipped... INFO @ 20 Dec 2024 06:04:30: [186 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 06:04:30: [186 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 06:04:30: [186 MB] #3 Call peaks... INFO @ 20 Dec 2024 06:04:30: [186 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 06:04:30: [186 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 06:04:30: [186 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 06:05:04: [524 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 06:05:04: [524 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C12_pseudoreplicate2_treat_pileup.bdg INFO @ 20 Dec 2024 06:05:04: [524 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C12_pseudoreplicate2_control_lambda.bdg INFO @ 20 Dec 2024 06:05:04: [524 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 06:05:04: [524 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 06:06:01: [524 MB] #4 Write output xls file... 3_peaks/C12_pseudoreplicate2_peaks.xls INFO @ 20 Dec 2024 06:06:02: [524 MB] #4 Write peak in narrowPeak format file... 3_peaks/C12_pseudoreplicate2_peaks.narrowPeak INFO @ 20 Dec 2024 06:06:03: [524 MB] #4 Write summits bed file... 3_peaks/C12_pseudoreplicate2_summits.bed INFO @ 20 Dec 2024 06:06:03: [524 MB] Done!