INFO @ 20 Dec 2024 06:12:56: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorepT/C14_0_sorted.tsv -f BED -n C14_0_pseudoreplicateT -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C14_0_pseudoreplicateT # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorepT/C14_0_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 06:12:56: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 06:12:56: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 06:12:58: [97 MB] 1000000 reads parsed INFO @ 20 Dec 2024 06:13:00: [100 MB] 2000000 reads parsed INFO @ 20 Dec 2024 06:13:02: [111 MB] 3000000 reads parsed INFO @ 20 Dec 2024 06:13:04: [114 MB] 4000000 reads parsed INFO @ 20 Dec 2024 06:13:05: [117 MB] 5000000 reads parsed INFO @ 20 Dec 2024 06:13:07: [121 MB] 6000000 reads parsed INFO @ 20 Dec 2024 06:13:09: [125 MB] 7000000 reads parsed INFO @ 20 Dec 2024 06:13:11: [132 MB] 8000000 reads parsed INFO @ 20 Dec 2024 06:13:13: [136 MB] 9000000 reads parsed INFO @ 20 Dec 2024 06:13:15: [139 MB] 10000000 reads parsed INFO @ 20 Dec 2024 06:13:17: [147 MB] 11000000 reads parsed INFO @ 20 Dec 2024 06:13:19: [149 MB] 12000000 reads parsed INFO @ 20 Dec 2024 06:13:20: [155 MB] 13000000 reads parsed INFO @ 20 Dec 2024 06:13:22: [157 MB] 14000000 reads parsed INFO @ 20 Dec 2024 06:13:23: [162 MB] 15000000 reads parsed INFO @ 20 Dec 2024 06:13:25: [171 MB] 16000000 reads parsed INFO @ 20 Dec 2024 06:13:26: [177 MB] 17000000 reads parsed INFO @ 20 Dec 2024 06:13:28: [177 MB] 18000000 reads parsed INFO @ 20 Dec 2024 06:13:30: [184 MB] 19000000 reads parsed INFO @ 20 Dec 2024 06:13:31: [190 MB] 20000000 reads parsed INFO @ 20 Dec 2024 06:13:33: [195 MB] 21000000 reads parsed INFO @ 20 Dec 2024 06:13:35: [195 MB] 22000000 reads parsed INFO @ 20 Dec 2024 06:13:36: [204 MB] 23000000 reads parsed INFO @ 20 Dec 2024 06:13:37: [204 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 06:13:37: [204 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 06:13:37: [204 MB] #1 total tags in treatment: 23489386 INFO @ 20 Dec 2024 06:13:37: [204 MB] #1 finished! INFO @ 20 Dec 2024 06:13:37: [204 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 06:13:37: [204 MB] #2 Skipped... INFO @ 20 Dec 2024 06:13:37: [204 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 06:13:37: [204 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 06:13:37: [204 MB] #3 Call peaks... INFO @ 20 Dec 2024 06:13:37: [204 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 06:13:37: [204 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 06:13:37: [204 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 06:14:17: [642 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 06:14:17: [642 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C14_0_pseudoreplicateT_treat_pileup.bdg INFO @ 20 Dec 2024 06:14:17: [642 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C14_0_pseudoreplicateT_control_lambda.bdg INFO @ 20 Dec 2024 06:14:17: [642 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 06:14:17: [642 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 06:15:06: [642 MB] #4 Write output xls file... 3_peaks/C14_0_pseudoreplicateT_peaks.xls INFO @ 20 Dec 2024 06:15:07: [642 MB] #4 Write peak in narrowPeak format file... 3_peaks/C14_0_pseudoreplicateT_peaks.narrowPeak INFO @ 20 Dec 2024 06:15:08: [642 MB] #4 Write summits bed file... 3_peaks/C14_0_pseudoreplicateT_summits.bed INFO @ 20 Dec 2024 06:15:08: [642 MB] Done!