INFO @ 20 Dec 2024 06:34:25: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorepT/C4_0_sorted.tsv -f BED -n C4_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 = C4_0_pseudoreplicateT # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorepT/C4_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 06:34:25: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 06:34:25: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 06:34:27: [100 MB] 1000000 reads parsed INFO @ 20 Dec 2024 06:34:29: [104 MB] 2000000 reads parsed INFO @ 20 Dec 2024 06:34:30: [105 MB] 3000000 reads parsed INFO @ 20 Dec 2024 06:34:32: [106 MB] 4000000 reads parsed INFO @ 20 Dec 2024 06:34:34: [113 MB] 5000000 reads parsed INFO @ 20 Dec 2024 06:34:36: [118 MB] 6000000 reads parsed INFO @ 20 Dec 2024 06:34:38: [121 MB] 7000000 reads parsed INFO @ 20 Dec 2024 06:34:40: [127 MB] 8000000 reads parsed INFO @ 20 Dec 2024 06:34:42: [130 MB] 9000000 reads parsed INFO @ 20 Dec 2024 06:34:44: [134 MB] 10000000 reads parsed INFO @ 20 Dec 2024 06:34:45: [140 MB] 11000000 reads parsed INFO @ 20 Dec 2024 06:34:47: [143 MB] 12000000 reads parsed INFO @ 20 Dec 2024 06:34:49: [148 MB] 13000000 reads parsed INFO @ 20 Dec 2024 06:34:51: [154 MB] 14000000 reads parsed INFO @ 20 Dec 2024 06:34:53: [159 MB] 15000000 reads parsed INFO @ 20 Dec 2024 06:34:55: [162 MB] 16000000 reads parsed INFO @ 20 Dec 2024 06:34:57: [167 MB] 17000000 reads parsed INFO @ 20 Dec 2024 06:34:58: [169 MB] 18000000 reads parsed INFO @ 20 Dec 2024 06:35:00: [174 MB] 19000000 reads parsed INFO @ 20 Dec 2024 06:35:02: [179 MB] 20000000 reads parsed INFO @ 20 Dec 2024 06:35:04: [183 MB] 21000000 reads parsed INFO @ 20 Dec 2024 06:35:06: [186 MB] 22000000 reads parsed INFO @ 20 Dec 2024 06:35:08: [190 MB] 23000000 reads parsed INFO @ 20 Dec 2024 06:35:10: [197 MB] 24000000 reads parsed INFO @ 20 Dec 2024 06:35:12: [200 MB] 25000000 reads parsed INFO @ 20 Dec 2024 06:35:13: [205 MB] 26000000 reads parsed INFO @ 20 Dec 2024 06:35:15: [208 MB] 27000000 reads parsed INFO @ 20 Dec 2024 06:35:17: [213 MB] 28000000 reads parsed INFO @ 20 Dec 2024 06:35:18: [216 MB] 29000000 reads parsed INFO @ 20 Dec 2024 06:35:20: [220 MB] 30000000 reads parsed INFO @ 20 Dec 2024 06:35:22: [223 MB] 31000000 reads parsed INFO @ 20 Dec 2024 06:35:24: [228 MB] 32000000 reads parsed INFO @ 20 Dec 2024 06:35:25: [231 MB] 33000000 reads parsed INFO @ 20 Dec 2024 06:35:27: [238 MB] 34000000 reads parsed INFO @ 20 Dec 2024 06:35:29: [242 MB] 35000000 reads parsed INFO @ 20 Dec 2024 06:35:30: [243 MB] 36000000 reads parsed INFO @ 20 Dec 2024 06:35:32: [250 MB] 37000000 reads parsed INFO @ 20 Dec 2024 06:35:34: [254 MB] 38000000 reads parsed INFO @ 20 Dec 2024 06:35:35: [258 MB] 39000000 reads parsed INFO @ 20 Dec 2024 06:35:37: [261 MB] 40000000 reads parsed INFO @ 20 Dec 2024 06:35:39: [266 MB] 41000000 reads parsed INFO @ 20 Dec 2024 06:35:40: [270 MB] 42000000 reads parsed INFO @ 20 Dec 2024 06:35:42: [273 MB] 43000000 reads parsed INFO @ 20 Dec 2024 06:35:44: [276 MB] 44000000 reads parsed INFO @ 20 Dec 2024 06:35:45: [283 MB] 45000000 reads parsed INFO @ 20 Dec 2024 06:35:47: [287 MB] 46000000 reads parsed INFO @ 20 Dec 2024 06:35:48: [289 MB] 47000000 reads parsed INFO @ 20 Dec 2024 06:35:50: [294 MB] 48000000 reads parsed INFO @ 20 Dec 2024 06:35:52: [298 MB] 49000000 reads parsed INFO @ 20 Dec 2024 06:35:53: [302 MB] 50000000 reads parsed INFO @ 20 Dec 2024 06:35:55: [306 MB] 51000000 reads parsed INFO @ 20 Dec 2024 06:35:56: [309 MB] 52000000 reads parsed INFO @ 20 Dec 2024 06:35:58: [311 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 06:35:58: [311 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 06:35:58: [311 MB] #1 total tags in treatment: 52678858 INFO @ 20 Dec 2024 06:35:58: [311 MB] #1 finished! INFO @ 20 Dec 2024 06:35:58: [311 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 06:35:58: [311 MB] #2 Skipped... INFO @ 20 Dec 2024 06:35:58: [311 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 06:35:58: [311 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 06:35:58: [311 MB] #3 Call peaks... INFO @ 20 Dec 2024 06:35:58: [311 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 06:35:58: [311 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 06:35:58: [311 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 06:37:22: [1433 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 06:37:22: [1433 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C4_0_pseudoreplicateT_treat_pileup.bdg INFO @ 20 Dec 2024 06:37:22: [1433 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C4_0_pseudoreplicateT_control_lambda.bdg INFO @ 20 Dec 2024 06:37:22: [1433 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 06:37:22: [1433 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 06:38:45: [1433 MB] #4 Write output xls file... 3_peaks/C4_0_pseudoreplicateT_peaks.xls INFO @ 20 Dec 2024 06:38:46: [1433 MB] #4 Write peak in narrowPeak format file... 3_peaks/C4_0_pseudoreplicateT_peaks.narrowPeak INFO @ 20 Dec 2024 06:38:47: [1433 MB] #4 Write summits bed file... 3_peaks/C4_0_pseudoreplicateT_summits.bed INFO @ 20 Dec 2024 06:38:47: [1433 MB] Done!