INFO @ 20 Dec 2024 06:21:29: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorepT/C2_sorted.tsv -f BED -n C2_pseudoreplicateT -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C2_pseudoreplicateT # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorepT/C2_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 06:21:29: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 06:21:29: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 06:21:31: [98 MB] 1000000 reads parsed INFO @ 20 Dec 2024 06:21:33: [102 MB] 2000000 reads parsed INFO @ 20 Dec 2024 06:21:35: [104 MB] 3000000 reads parsed INFO @ 20 Dec 2024 06:21:37: [105 MB] 4000000 reads parsed INFO @ 20 Dec 2024 06:21:39: [109 MB] 5000000 reads parsed INFO @ 20 Dec 2024 06:21:41: [113 MB] 6000000 reads parsed INFO @ 20 Dec 2024 06:21:43: [121 MB] 7000000 reads parsed INFO @ 20 Dec 2024 06:21:45: [126 MB] 8000000 reads parsed INFO @ 20 Dec 2024 06:21:47: [129 MB] 9000000 reads parsed INFO @ 20 Dec 2024 06:21:49: [139 MB] 10000000 reads parsed INFO @ 20 Dec 2024 06:21:52: [146 MB] 11000000 reads parsed INFO @ 20 Dec 2024 06:21:54: [146 MB] 12000000 reads parsed INFO @ 20 Dec 2024 06:21:55: [153 MB] 13000000 reads parsed INFO @ 20 Dec 2024 06:21:57: [153 MB] 14000000 reads parsed INFO @ 20 Dec 2024 06:21:59: [162 MB] 15000000 reads parsed INFO @ 20 Dec 2024 06:22:01: [166 MB] 16000000 reads parsed INFO @ 20 Dec 2024 06:22:03: [166 MB] 17000000 reads parsed INFO @ 20 Dec 2024 06:22:05: [168 MB] 18000000 reads parsed INFO @ 20 Dec 2024 06:22:07: [172 MB] 19000000 reads parsed INFO @ 20 Dec 2024 06:22:09: [177 MB] 20000000 reads parsed INFO @ 20 Dec 2024 06:22:11: [180 MB] 21000000 reads parsed INFO @ 20 Dec 2024 06:22:13: [184 MB] 22000000 reads parsed INFO @ 20 Dec 2024 06:22:15: [188 MB] 23000000 reads parsed INFO @ 20 Dec 2024 06:22:17: [191 MB] 24000000 reads parsed INFO @ 20 Dec 2024 06:22:18: [195 MB] 25000000 reads parsed INFO @ 20 Dec 2024 06:22:20: [199 MB] 26000000 reads parsed INFO @ 20 Dec 2024 06:22:22: [203 MB] 27000000 reads parsed INFO @ 20 Dec 2024 06:22:24: [208 MB] 28000000 reads parsed INFO @ 20 Dec 2024 06:22:26: [212 MB] 29000000 reads parsed INFO @ 20 Dec 2024 06:22:28: [215 MB] 30000000 reads parsed INFO @ 20 Dec 2024 06:22:30: [220 MB] 31000000 reads parsed INFO @ 20 Dec 2024 06:22:31: [224 MB] 32000000 reads parsed INFO @ 20 Dec 2024 06:22:33: [227 MB] 33000000 reads parsed INFO @ 20 Dec 2024 06:22:35: [231 MB] 34000000 reads parsed INFO @ 20 Dec 2024 06:22:37: [235 MB] 35000000 reads parsed INFO @ 20 Dec 2024 06:22:39: [238 MB] 36000000 reads parsed INFO @ 20 Dec 2024 06:22:40: [243 MB] 37000000 reads parsed INFO @ 20 Dec 2024 06:22:42: [247 MB] 38000000 reads parsed INFO @ 20 Dec 2024 06:22:44: [251 MB] 39000000 reads parsed INFO @ 20 Dec 2024 06:22:46: [255 MB] 40000000 reads parsed INFO @ 20 Dec 2024 06:22:47: [260 MB] 41000000 reads parsed INFO @ 20 Dec 2024 06:22:49: [263 MB] 42000000 reads parsed INFO @ 20 Dec 2024 06:22:51: [267 MB] 43000000 reads parsed INFO @ 20 Dec 2024 06:22:53: [271 MB] 44000000 reads parsed INFO @ 20 Dec 2024 06:22:54: [277 MB] 45000000 reads parsed INFO @ 20 Dec 2024 06:22:56: [281 MB] 46000000 reads parsed INFO @ 20 Dec 2024 06:22:58: [284 MB] 47000000 reads parsed INFO @ 20 Dec 2024 06:22:59: [290 MB] 48000000 reads parsed INFO @ 20 Dec 2024 06:23:01: [302 MB] 49000000 reads parsed INFO @ 20 Dec 2024 06:23:03: [304 MB] 50000000 reads parsed INFO @ 20 Dec 2024 06:23:04: [304 MB] 51000000 reads parsed INFO @ 20 Dec 2024 06:23:07: [310 MB] 52000000 reads parsed INFO @ 20 Dec 2024 06:23:08: [310 MB] 53000000 reads parsed INFO @ 20 Dec 2024 06:23:10: [313 MB] 54000000 reads parsed INFO @ 20 Dec 2024 06:23:11: [325 MB] 55000000 reads parsed INFO @ 20 Dec 2024 06:23:13: [330 MB] 56000000 reads parsed INFO @ 20 Dec 2024 06:23:15: [332 MB] 57000000 reads parsed INFO @ 20 Dec 2024 06:23:16: [332 MB] 58000000 reads parsed INFO @ 20 Dec 2024 06:23:18: [338 MB] 59000000 reads parsed INFO @ 20 Dec 2024 06:23:20: [338 MB] 60000000 reads parsed INFO @ 20 Dec 2024 06:23:22: [348 MB] 61000000 reads parsed INFO @ 20 Dec 2024 06:23:23: [354 MB] 62000000 reads parsed INFO @ 20 Dec 2024 06:23:25: [354 MB] 63000000 reads parsed INFO @ 20 Dec 2024 06:23:27: [359 MB] 64000000 reads parsed INFO @ 20 Dec 2024 06:23:29: [366 MB] 65000000 reads parsed INFO @ 20 Dec 2024 06:23:29: [366 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 06:23:29: [366 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 06:23:29: [366 MB] #1 total tags in treatment: 65096974 INFO @ 20 Dec 2024 06:23:29: [366 MB] #1 finished! INFO @ 20 Dec 2024 06:23:29: [366 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 06:23:29: [366 MB] #2 Skipped... INFO @ 20 Dec 2024 06:23:29: [366 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 06:23:29: [366 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 06:23:29: [366 MB] #3 Call peaks... INFO @ 20 Dec 2024 06:23:29: [366 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 06:23:29: [366 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 06:23:29: [366 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 06:25:24: [1851 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 06:25:24: [1851 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C2_pseudoreplicateT_treat_pileup.bdg INFO @ 20 Dec 2024 06:25:24: [1851 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C2_pseudoreplicateT_control_lambda.bdg INFO @ 20 Dec 2024 06:25:24: [1851 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 06:25:24: [1851 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 06:26:52: [1851 MB] #4 Write output xls file... 3_peaks/C2_pseudoreplicateT_peaks.xls INFO @ 20 Dec 2024 06:26:52: [1851 MB] #4 Write peak in narrowPeak format file... 3_peaks/C2_pseudoreplicateT_peaks.narrowPeak INFO @ 20 Dec 2024 06:26:53: [1851 MB] #4 Write summits bed file... 3_peaks/C2_pseudoreplicateT_summits.bed INFO @ 20 Dec 2024 06:26:53: [1851 MB] Done!