INFO @ 20 Dec 2024 07:04:32: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorepT/C9_sorted.tsv -f BED -n C9_pseudoreplicateT -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C9_pseudoreplicateT # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorepT/C9_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 07:04:32: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 07:04:32: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 07:04:35: [98 MB] 1000000 reads parsed INFO @ 20 Dec 2024 07:04:36: [102 MB] 2000000 reads parsed INFO @ 20 Dec 2024 07:04:38: [103 MB] 3000000 reads parsed INFO @ 20 Dec 2024 07:04:40: [105 MB] 4000000 reads parsed INFO @ 20 Dec 2024 07:04:42: [113 MB] 5000000 reads parsed INFO @ 20 Dec 2024 07:04:44: [117 MB] 6000000 reads parsed INFO @ 20 Dec 2024 07:04:46: [119 MB] 7000000 reads parsed INFO @ 20 Dec 2024 07:04:48: [125 MB] 8000000 reads parsed INFO @ 20 Dec 2024 07:04:49: [128 MB] 9000000 reads parsed INFO @ 20 Dec 2024 07:04:51: [133 MB] 10000000 reads parsed INFO @ 20 Dec 2024 07:04:54: [143 MB] 11000000 reads parsed INFO @ 20 Dec 2024 07:04:55: [146 MB] 12000000 reads parsed INFO @ 20 Dec 2024 07:04:58: [150 MB] 13000000 reads parsed INFO @ 20 Dec 2024 07:05:00: [155 MB] 14000000 reads parsed INFO @ 20 Dec 2024 07:05:01: [160 MB] 15000000 reads parsed INFO @ 20 Dec 2024 07:05:03: [164 MB] 16000000 reads parsed INFO @ 20 Dec 2024 07:05:05: [168 MB] 17000000 reads parsed INFO @ 20 Dec 2024 07:05:07: [169 MB] 18000000 reads parsed INFO @ 20 Dec 2024 07:05:09: [175 MB] 19000000 reads parsed INFO @ 20 Dec 2024 07:05:11: [177 MB] 20000000 reads parsed INFO @ 20 Dec 2024 07:05:13: [184 MB] 21000000 reads parsed INFO @ 20 Dec 2024 07:05:14: [187 MB] 22000000 reads parsed INFO @ 20 Dec 2024 07:05:16: [190 MB] 23000000 reads parsed INFO @ 20 Dec 2024 07:05:18: [195 MB] 24000000 reads parsed INFO @ 20 Dec 2024 07:05:20: [199 MB] 25000000 reads parsed INFO @ 20 Dec 2024 07:05:21: [203 MB] 26000000 reads parsed INFO @ 20 Dec 2024 07:05:23: [207 MB] 27000000 reads parsed INFO @ 20 Dec 2024 07:05:25: [219 MB] 28000000 reads parsed INFO @ 20 Dec 2024 07:05:26: [219 MB] 29000000 reads parsed INFO @ 20 Dec 2024 07:05:28: [219 MB] 30000000 reads parsed INFO @ 20 Dec 2024 07:05:30: [228 MB] 31000000 reads parsed INFO @ 20 Dec 2024 07:05:31: [230 MB] 32000000 reads parsed INFO @ 20 Dec 2024 07:05:33: [233 MB] 33000000 reads parsed INFO @ 20 Dec 2024 07:05:34: [239 MB] 34000000 reads parsed INFO @ 20 Dec 2024 07:05:36: [245 MB] 35000000 reads parsed INFO @ 20 Dec 2024 07:05:38: [248 MB] 36000000 reads parsed INFO @ 20 Dec 2024 07:05:40: [249 MB] 37000000 reads parsed INFO @ 20 Dec 2024 07:05:41: [258 MB] 38000000 reads parsed INFO @ 20 Dec 2024 07:05:43: [262 MB] 39000000 reads parsed INFO @ 20 Dec 2024 07:05:44: [262 MB] 40000000 reads parsed INFO @ 20 Dec 2024 07:05:46: [269 MB] 41000000 reads parsed INFO @ 20 Dec 2024 07:05:48: [272 MB] 42000000 reads parsed INFO @ 20 Dec 2024 07:05:49: [278 MB] 43000000 reads parsed INFO @ 20 Dec 2024 07:05:51: [281 MB] 44000000 reads parsed INFO @ 20 Dec 2024 07:05:53: [285 MB] 45000000 reads parsed INFO @ 20 Dec 2024 07:05:54: [289 MB] 46000000 reads parsed INFO @ 20 Dec 2024 07:05:56: [295 MB] 47000000 reads parsed INFO @ 20 Dec 2024 07:05:57: [297 MB] 48000000 reads parsed INFO @ 20 Dec 2024 07:05:59: [301 MB] 49000000 reads parsed INFO @ 20 Dec 2024 07:06:01: [306 MB] 50000000 reads parsed INFO @ 20 Dec 2024 07:06:02: [306 MB] 51000000 reads parsed INFO @ 20 Dec 2024 07:06:04: [314 MB] 52000000 reads parsed INFO @ 20 Dec 2024 07:06:05: [314 MB] 53000000 reads parsed INFO @ 20 Dec 2024 07:06:06: [320 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 07:06:06: [320 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 07:06:06: [320 MB] #1 total tags in treatment: 53557716 INFO @ 20 Dec 2024 07:06:06: [320 MB] #1 finished! INFO @ 20 Dec 2024 07:06:06: [320 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 07:06:06: [320 MB] #2 Skipped... INFO @ 20 Dec 2024 07:06:06: [320 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 07:06:06: [320 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 07:06:06: [320 MB] #3 Call peaks... INFO @ 20 Dec 2024 07:06:06: [320 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 07:06:06: [320 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 07:06:06: [320 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 07:07:32: [1350 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 07:07:32: [1350 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C9_pseudoreplicateT_treat_pileup.bdg INFO @ 20 Dec 2024 07:07:32: [1350 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C9_pseudoreplicateT_control_lambda.bdg INFO @ 20 Dec 2024 07:07:32: [1350 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 07:07:32: [1350 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 07:08:56: [1350 MB] #4 Write output xls file... 3_peaks/C9_pseudoreplicateT_peaks.xls INFO @ 20 Dec 2024 07:08:56: [1350 MB] #4 Write peak in narrowPeak format file... 3_peaks/C9_pseudoreplicateT_peaks.narrowPeak INFO @ 20 Dec 2024 07:08:57: [1350 MB] #4 Write summits bed file... 3_peaks/C9_pseudoreplicateT_summits.bed INFO @ 20 Dec 2024 07:08:57: [1350 MB] Done!