INFO @ 20 Dec 2024 06:40:42: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorep1/C5_sorted.tsv -f BED -n C5_pseudoreplicate1 -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C5_pseudoreplicate1 # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorep1/C5_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 06:40:42: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 06:40:42: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 06:40:44: [104 MB] 1000000 reads parsed INFO @ 20 Dec 2024 06:40:46: [104 MB] 2000000 reads parsed INFO @ 20 Dec 2024 06:40:48: [104 MB] 3000000 reads parsed INFO @ 20 Dec 2024 06:40:50: [111 MB] 4000000 reads parsed INFO @ 20 Dec 2024 06:40:52: [113 MB] 5000000 reads parsed INFO @ 20 Dec 2024 06:40:53: [122 MB] 6000000 reads parsed INFO @ 20 Dec 2024 06:40:55: [126 MB] 7000000 reads parsed INFO @ 20 Dec 2024 06:40:57: [130 MB] 8000000 reads parsed INFO @ 20 Dec 2024 06:40:59: [135 MB] 9000000 reads parsed INFO @ 20 Dec 2024 06:41:01: [139 MB] 10000000 reads parsed INFO @ 20 Dec 2024 06:41:03: [141 MB] 11000000 reads parsed INFO @ 20 Dec 2024 06:41:05: [147 MB] 12000000 reads parsed INFO @ 20 Dec 2024 06:41:06: [154 MB] 13000000 reads parsed INFO @ 20 Dec 2024 06:41:08: [156 MB] 14000000 reads parsed INFO @ 20 Dec 2024 06:41:10: [161 MB] 15000000 reads parsed INFO @ 20 Dec 2024 06:41:11: [165 MB] 16000000 reads parsed INFO @ 20 Dec 2024 06:41:13: [169 MB] 17000000 reads parsed INFO @ 20 Dec 2024 06:41:15: [176 MB] 18000000 reads parsed INFO @ 20 Dec 2024 06:41:17: [179 MB] 19000000 reads parsed INFO @ 20 Dec 2024 06:41:19: [179 MB] 20000000 reads parsed INFO @ 20 Dec 2024 06:41:21: [189 MB] 21000000 reads parsed INFO @ 20 Dec 2024 06:41:23: [195 MB] 22000000 reads parsed INFO @ 20 Dec 2024 06:41:25: [196 MB] 23000000 reads parsed INFO @ 20 Dec 2024 06:41:27: [203 MB] 24000000 reads parsed INFO @ 20 Dec 2024 06:41:29: [204 MB] 25000000 reads parsed INFO @ 20 Dec 2024 06:41:31: [209 MB] 26000000 reads parsed INFO @ 20 Dec 2024 06:41:32: [212 MB] 27000000 reads parsed INFO @ 20 Dec 2024 06:41:34: [217 MB] 28000000 reads parsed INFO @ 20 Dec 2024 06:41:36: [221 MB] 29000000 reads parsed INFO @ 20 Dec 2024 06:41:38: [225 MB] 30000000 reads parsed INFO @ 20 Dec 2024 06:41:40: [227 MB] 31000000 reads parsed INFO @ 20 Dec 2024 06:41:42: [233 MB] 32000000 reads parsed INFO @ 20 Dec 2024 06:41:44: [237 MB] 33000000 reads parsed INFO @ 20 Dec 2024 06:41:46: [239 MB] 34000000 reads parsed INFO @ 20 Dec 2024 06:41:47: [242 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 06:41:47: [242 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 06:41:47: [242 MB] #1 total tags in treatment: 34724060 INFO @ 20 Dec 2024 06:41:47: [242 MB] #1 finished! INFO @ 20 Dec 2024 06:41:47: [242 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 06:41:47: [242 MB] #2 Skipped... INFO @ 20 Dec 2024 06:41:47: [242 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 06:41:47: [242 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 06:41:47: [242 MB] #3 Call peaks... INFO @ 20 Dec 2024 06:41:47: [242 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 06:41:47: [242 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 06:41:47: [242 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 06:42:48: [878 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 06:42:48: [878 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C5_pseudoreplicate1_treat_pileup.bdg INFO @ 20 Dec 2024 06:42:48: [878 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C5_pseudoreplicate1_control_lambda.bdg INFO @ 20 Dec 2024 06:42:48: [878 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 06:42:48: [878 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 06:44:06: [878 MB] #4 Write output xls file... 3_peaks/C5_pseudoreplicate1_peaks.xls INFO @ 20 Dec 2024 06:44:07: [878 MB] #4 Write peak in narrowPeak format file... 3_peaks/C5_pseudoreplicate1_peaks.narrowPeak INFO @ 20 Dec 2024 06:44:07: [878 MB] #4 Write summits bed file... 3_peaks/C5_pseudoreplicate1_summits.bed INFO @ 20 Dec 2024 06:44:08: [878 MB] Done!