INFO @ 10 Jun 2025 23:28:13: [32 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorepT/1_sorted.tsv -f BED -n 1_pseudoreplicateT -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = 1_pseudoreplicateT # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorepT/1_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 @ 10 Jun 2025 23:28:13: [32 MB] #1 read tag files... INFO @ 10 Jun 2025 23:28:13: [32 MB] #1 read treatment tags... INFO @ 10 Jun 2025 23:28:15: [98 MB] 1000000 reads parsed INFO @ 10 Jun 2025 23:28:16: [101 MB] 2000000 reads parsed INFO @ 10 Jun 2025 23:28:18: [103 MB] 3000000 reads parsed INFO @ 10 Jun 2025 23:28:19: [106 MB] 4000000 reads parsed INFO @ 10 Jun 2025 23:28:21: [109 MB] 5000000 reads parsed INFO @ 10 Jun 2025 23:28:22: [113 MB] 6000000 reads parsed INFO @ 10 Jun 2025 23:28:24: [119 MB] 7000000 reads parsed INFO @ 10 Jun 2025 23:28:25: [123 MB] 8000000 reads parsed INFO @ 10 Jun 2025 23:28:27: [124 MB] 9000000 reads parsed INFO @ 10 Jun 2025 23:28:28: [130 MB] 10000000 reads parsed INFO @ 10 Jun 2025 23:28:30: [133 MB] 11000000 reads parsed INFO @ 10 Jun 2025 23:28:31: [137 MB] 12000000 reads parsed INFO @ 10 Jun 2025 23:28:33: [140 MB] 13000000 reads parsed INFO @ 10 Jun 2025 23:28:34: [146 MB] 14000000 reads parsed INFO @ 10 Jun 2025 23:28:36: [149 MB] 15000000 reads parsed INFO @ 10 Jun 2025 23:28:37: [152 MB] 16000000 reads parsed INFO @ 10 Jun 2025 23:28:39: [156 MB] 17000000 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INFO @ 10 Jun 2025 23:32:37: [873 MB] 199000000 reads parsed INFO @ 10 Jun 2025 23:32:38: [873 MB] 200000000 reads parsed INFO @ 10 Jun 2025 23:32:39: [875 MB] 201000000 reads parsed INFO @ 10 Jun 2025 23:32:41: [876 MB] #1 tag size is determined as 1 bps INFO @ 10 Jun 2025 23:32:41: [876 MB] #1 tag size = 1.0 INFO @ 10 Jun 2025 23:32:41: [876 MB] #1 total tags in treatment: 201432522 INFO @ 10 Jun 2025 23:32:41: [876 MB] #1 finished! INFO @ 10 Jun 2025 23:32:41: [876 MB] #2 Build Peak Model... INFO @ 10 Jun 2025 23:32:41: [876 MB] #2 Skipped... INFO @ 10 Jun 2025 23:32:41: [876 MB] #2 Use 150 as fragment length INFO @ 10 Jun 2025 23:32:41: [876 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 10 Jun 2025 23:32:41: [876 MB] #3 Call peaks... INFO @ 10 Jun 2025 23:32:41: [876 MB] #3 Going to call summits inside each peak ... INFO @ 10 Jun 2025 23:32:41: [876 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 10 Jun 2025 23:32:41: [876 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 10 Jun 2025 23:46:58: [4369 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 10 Jun 2025 23:46:58: [4369 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... 1_pseudoreplicateT_treat_pileup.bdg INFO @ 10 Jun 2025 23:46:58: [4369 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... 1_pseudoreplicateT_control_lambda.bdg INFO @ 10 Jun 2025 23:46:58: [4369 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 10 Jun 2025 23:46:58: [4369 MB] #3 Call peaks for each chromosome... INFO @ 11 Jun 2025 00:02:18: [4369 MB] #4 Write output xls file... 3_peaks/1_pseudoreplicateT_peaks.xls INFO @ 11 Jun 2025 00:02:19: [4369 MB] #4 Write peak in narrowPeak format file... 3_peaks/1_pseudoreplicateT_peaks.narrowPeak INFO @ 11 Jun 2025 00:02:20: [4369 MB] #4 Write summits bed file... 3_peaks/1_pseudoreplicateT_summits.bed INFO @ 11 Jun 2025 00:02:20: [4369 MB] Done!