INFO @ 20 Dec 2024 05:30:56: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorepT/C0_sorted.tsv -f BED -n C0_pseudoreplicateT -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C0_pseudoreplicateT # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorepT/C0_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 05:30:56: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 05:30:56: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 05:30:58: [99 MB] 1000000 reads parsed INFO @ 20 Dec 2024 05:31:00: [101 MB] 2000000 reads parsed INFO @ 20 Dec 2024 05:31:02: [104 MB] 3000000 reads parsed INFO @ 20 Dec 2024 05:31:04: [108 MB] 4000000 reads parsed INFO @ 20 Dec 2024 05:31:05: [112 MB] 5000000 reads parsed INFO @ 20 Dec 2024 05:31:07: [115 MB] 6000000 reads parsed INFO @ 20 Dec 2024 05:31:09: [119 MB] 7000000 reads parsed INFO @ 20 Dec 2024 05:31:11: [123 MB] 8000000 reads parsed INFO @ 20 Dec 2024 05:31:13: [126 MB] 9000000 reads parsed INFO @ 20 Dec 2024 05:31:15: [129 MB] 10000000 reads parsed INFO @ 20 Dec 2024 05:31:17: [133 MB] 11000000 reads parsed INFO @ 20 Dec 2024 05:31:19: [138 MB] 12000000 reads parsed INFO @ 20 Dec 2024 05:31:21: [142 MB] 13000000 reads parsed INFO @ 20 Dec 2024 05:31:23: [145 MB] 14000000 reads parsed INFO @ 20 Dec 2024 05:31:25: [148 MB] 15000000 reads parsed INFO @ 20 Dec 2024 05:31:26: [152 MB] 16000000 reads parsed INFO @ 20 Dec 2024 05:31:29: [157 MB] 17000000 reads parsed INFO @ 20 Dec 2024 05:31:31: [161 MB] 18000000 reads parsed INFO @ 20 Dec 2024 05:31:33: [164 MB] 19000000 reads parsed INFO @ 20 Dec 2024 05:31:34: [168 MB] 20000000 reads parsed INFO @ 20 Dec 2024 05:31:36: [171 MB] 21000000 reads parsed INFO @ 20 Dec 2024 05:31:38: [176 MB] 22000000 reads parsed INFO @ 20 Dec 2024 05:31:40: [188 MB] 23000000 reads parsed INFO @ 20 Dec 2024 05:31:42: [193 MB] 24000000 reads parsed INFO @ 20 Dec 2024 05:31:44: [198 MB] 25000000 reads parsed INFO @ 20 Dec 2024 05:31:46: [202 MB] 26000000 reads parsed INFO @ 20 Dec 2024 05:31:48: [202 MB] 27000000 reads parsed INFO @ 20 Dec 2024 05:31:50: [202 MB] 28000000 reads parsed INFO @ 20 Dec 2024 05:31:52: [207 MB] 29000000 reads parsed INFO @ 20 Dec 2024 05:31:53: [211 MB] 30000000 reads parsed INFO @ 20 Dec 2024 05:31:55: [213 MB] 31000000 reads parsed INFO @ 20 Dec 2024 05:31:57: [216 MB] 32000000 reads parsed INFO @ 20 Dec 2024 05:31:59: [219 MB] 33000000 reads parsed INFO @ 20 Dec 2024 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05:37:02: [930 MB] 215000000 reads parsed INFO @ 20 Dec 2024 05:37:04: [934 MB] 216000000 reads parsed INFO @ 20 Dec 2024 05:37:06: [937 MB] 217000000 reads parsed INFO @ 20 Dec 2024 05:37:07: [947 MB] 218000000 reads parsed INFO @ 20 Dec 2024 05:37:09: [947 MB] 219000000 reads parsed INFO @ 20 Dec 2024 05:37:10: [950 MB] 220000000 reads parsed INFO @ 20 Dec 2024 05:37:12: [953 MB] 221000000 reads parsed INFO @ 20 Dec 2024 05:37:13: [957 MB] 222000000 reads parsed INFO @ 20 Dec 2024 05:37:16: [960 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 05:37:16: [960 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 05:37:16: [960 MB] #1 total tags in treatment: 222847558 INFO @ 20 Dec 2024 05:37:16: [960 MB] #1 finished! INFO @ 20 Dec 2024 05:37:16: [960 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 05:37:16: [960 MB] #2 Skipped... INFO @ 20 Dec 2024 05:37:16: [960 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 05:37:16: [960 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 05:37:16: [960 MB] #3 Call peaks... INFO @ 20 Dec 2024 05:37:16: [960 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 05:37:16: [960 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 05:37:16: [960 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 05:42:29: [4941 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 05:42:29: [4941 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C0_pseudoreplicateT_treat_pileup.bdg INFO @ 20 Dec 2024 05:42:29: [4941 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C0_pseudoreplicateT_control_lambda.bdg INFO @ 20 Dec 2024 05:42:29: [4941 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 05:42:29: [4941 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 05:46:28: [4941 MB] #4 Write output xls file... 3_peaks/C0_pseudoreplicateT_peaks.xls INFO @ 20 Dec 2024 05:46:29: [4941 MB] #4 Write peak in narrowPeak format file... 3_peaks/C0_pseudoreplicateT_peaks.narrowPeak INFO @ 20 Dec 2024 05:46:30: [4941 MB] #4 Write summits bed file... 3_peaks/C0_pseudoreplicateT_summits.bed INFO @ 20 Dec 2024 05:46:30: [4941 MB] Done!