INFO @ 20 Dec 2024 06:26:58: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorepT/C3_0_sorted.tsv -f BED -n C3_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 = C3_0_pseudoreplicateT # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorepT/C3_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 06:26:58: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 06:26:58: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 06:27:00: [98 MB] 1000000 reads parsed INFO @ 20 Dec 2024 06:27:02: [102 MB] 2000000 reads parsed INFO @ 20 Dec 2024 06:27:04: [103 MB] 3000000 reads parsed INFO @ 20 Dec 2024 06:27:06: [105 MB] 4000000 reads parsed INFO @ 20 Dec 2024 06:27:07: [109 MB] 5000000 reads parsed INFO @ 20 Dec 2024 06:27:09: [118 MB] 6000000 reads parsed INFO @ 20 Dec 2024 06:27:11: [121 MB] 7000000 reads parsed INFO @ 20 Dec 2024 06:27:13: [126 MB] 8000000 reads parsed INFO @ 20 Dec 2024 06:27:15: [133 MB] 9000000 reads parsed INFO @ 20 Dec 2024 06:27:17: [137 MB] 10000000 reads parsed INFO @ 20 Dec 2024 06:27:19: [140 MB] 11000000 reads parsed INFO @ 20 Dec 2024 06:27:21: [144 MB] 12000000 reads parsed INFO @ 20 Dec 2024 06:27:23: [147 MB] 13000000 reads parsed INFO @ 20 Dec 2024 06:27:25: [152 MB] 14000000 reads parsed INFO @ 20 Dec 2024 06:27:27: [157 MB] 15000000 reads parsed INFO @ 20 Dec 2024 06:27:29: [163 MB] 16000000 reads parsed INFO @ 20 Dec 2024 06:27:30: [167 MB] 17000000 reads parsed INFO @ 20 Dec 2024 06:27:32: [172 MB] 18000000 reads parsed INFO @ 20 Dec 2024 06:27:34: [172 MB] 19000000 reads parsed INFO @ 20 Dec 2024 06:27:36: [180 MB] 20000000 reads parsed INFO @ 20 Dec 2024 06:27:38: [185 MB] 21000000 reads parsed INFO @ 20 Dec 2024 06:27:40: [189 MB] 22000000 reads parsed INFO @ 20 Dec 2024 06:27:42: [190 MB] 23000000 reads parsed INFO @ 20 Dec 2024 06:27:44: [195 MB] 24000000 reads parsed INFO @ 20 Dec 2024 06:27:45: [199 MB] 25000000 reads parsed INFO @ 20 Dec 2024 06:27:47: [202 MB] 26000000 reads parsed INFO @ 20 Dec 2024 06:27:49: [205 MB] 27000000 reads parsed INFO @ 20 Dec 2024 06:27:50: [211 MB] 28000000 reads parsed INFO @ 20 Dec 2024 06:27:52: [214 MB] 29000000 reads parsed INFO @ 20 Dec 2024 06:27:54: [217 MB] 30000000 reads parsed INFO @ 20 Dec 2024 06:27:56: [222 MB] 31000000 reads parsed INFO @ 20 Dec 2024 06:27:57: [226 MB] 32000000 reads parsed INFO @ 20 Dec 2024 06:27:59: [230 MB] 33000000 reads parsed INFO @ 20 Dec 2024 06:28:00: [235 MB] 34000000 reads parsed INFO @ 20 Dec 2024 06:28:02: [238 MB] 35000000 reads parsed INFO @ 20 Dec 2024 06:28:04: [242 MB] 36000000 reads parsed INFO @ 20 Dec 2024 06:28:05: [245 MB] 37000000 reads parsed INFO @ 20 Dec 2024 06:28:07: [250 MB] 38000000 reads parsed INFO @ 20 Dec 2024 06:28:08: [254 MB] 39000000 reads parsed INFO @ 20 Dec 2024 06:28:10: [257 MB] 40000000 reads parsed INFO @ 20 Dec 2024 06:28:12: [262 MB] 41000000 reads parsed INFO @ 20 Dec 2024 06:28:13: [265 MB] 42000000 reads parsed INFO @ 20 Dec 2024 06:28:15: [269 MB] 43000000 reads parsed INFO @ 20 Dec 2024 06:28:16: [273 MB] 44000000 reads parsed INFO @ 20 Dec 2024 06:28:18: [277 MB] 45000000 reads parsed INFO @ 20 Dec 2024 06:28:20: [281 MB] 46000000 reads parsed INFO @ 20 Dec 2024 06:28:21: [284 MB] 47000000 reads parsed INFO @ 20 Dec 2024 06:28:23: [288 MB] 48000000 reads parsed INFO @ 20 Dec 2024 06:28:24: [292 MB] 49000000 reads parsed INFO @ 20 Dec 2024 06:28:26: [297 MB] 50000000 reads parsed INFO @ 20 Dec 2024 06:28:28: [300 MB] 51000000 reads parsed INFO @ 20 Dec 2024 06:28:29: [304 MB] 52000000 reads parsed INFO @ 20 Dec 2024 06:28:31: [309 MB] 53000000 reads parsed INFO @ 20 Dec 2024 06:28:32: [309 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 06:28:32: [309 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 06:28:32: [309 MB] #1 total tags in treatment: 53408782 INFO @ 20 Dec 2024 06:28:32: [309 MB] #1 finished! INFO @ 20 Dec 2024 06:28:32: [309 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 06:28:32: [309 MB] #2 Skipped... INFO @ 20 Dec 2024 06:28:32: [309 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 06:28:32: [309 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 06:28:32: [309 MB] #3 Call peaks... INFO @ 20 Dec 2024 06:28:32: [309 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 06:28:32: [309 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 06:28:32: [309 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 06:30:01: [1371 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 06:30:01: [1371 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C3_0_pseudoreplicateT_treat_pileup.bdg INFO @ 20 Dec 2024 06:30:01: [1371 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C3_0_pseudoreplicateT_control_lambda.bdg INFO @ 20 Dec 2024 06:30:01: [1371 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 06:30:01: [1371 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 06:31:24: [1371 MB] #4 Write output xls file... 3_peaks/C3_0_pseudoreplicateT_peaks.xls INFO @ 20 Dec 2024 06:31:25: [1371 MB] #4 Write peak in narrowPeak format file... 3_peaks/C3_0_pseudoreplicateT_peaks.narrowPeak INFO @ 20 Dec 2024 06:31:25: [1371 MB] #4 Write summits bed file... 3_peaks/C3_0_pseudoreplicateT_summits.bed INFO @ 20 Dec 2024 06:31:26: [1371 MB] Done!