INFO @ 20 Dec 2024 06:40:42: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorepT/C5_sorted.tsv -f BED -n C5_pseudoreplicateT -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C5_pseudoreplicateT # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorepT/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: [98 MB] 1000000 reads parsed INFO @ 20 Dec 2024 06:40:46: [102 MB] 2000000 reads parsed INFO @ 20 Dec 2024 06:40:48: [103 MB] 3000000 reads parsed INFO @ 20 Dec 2024 06:40:50: [104 MB] 4000000 reads parsed INFO @ 20 Dec 2024 06:40:52: [109 MB] 5000000 reads parsed INFO @ 20 Dec 2024 06:40:54: [112 MB] 6000000 reads parsed INFO @ 20 Dec 2024 06:40:55: [127 MB] 7000000 reads parsed INFO @ 20 Dec 2024 06:40:57: [127 MB] 8000000 reads parsed INFO @ 20 Dec 2024 06:40:59: [129 MB] 9000000 reads parsed INFO @ 20 Dec 2024 06:41:01: [130 MB] 10000000 reads parsed INFO @ 20 Dec 2024 06:41:03: [138 MB] 11000000 reads parsed INFO @ 20 Dec 2024 06:41:04: [142 MB] 12000000 reads parsed INFO @ 20 Dec 2024 06:41:06: [144 MB] 13000000 reads parsed INFO @ 20 Dec 2024 06:41:08: [150 MB] 14000000 reads parsed INFO @ 20 Dec 2024 06:41:10: [157 MB] 15000000 reads parsed INFO @ 20 Dec 2024 06:41:12: [161 MB] 16000000 reads parsed INFO @ 20 Dec 2024 06:41:14: [163 MB] 17000000 reads parsed INFO @ 20 Dec 2024 06:41:15: [166 MB] 18000000 reads parsed INFO @ 20 Dec 2024 06:41:17: [173 MB] 19000000 reads parsed INFO @ 20 Dec 2024 06:41:19: [180 MB] 20000000 reads parsed INFO @ 20 Dec 2024 06:41:21: [180 MB] 21000000 reads parsed INFO @ 20 Dec 2024 06:41:23: [187 MB] 22000000 reads parsed INFO @ 20 Dec 2024 06:41:25: [187 MB] 23000000 reads parsed INFO @ 20 Dec 2024 06:41:27: [193 MB] 24000000 reads parsed INFO @ 20 Dec 2024 06:41:29: [195 MB] 25000000 reads parsed INFO @ 20 Dec 2024 06:41:31: [201 MB] 26000000 reads parsed INFO @ 20 Dec 2024 06:41:33: [204 MB] 27000000 reads parsed INFO @ 20 Dec 2024 06:41:35: [208 MB] 28000000 reads parsed INFO @ 20 Dec 2024 06:41:37: [212 MB] 29000000 reads parsed INFO @ 20 Dec 2024 06:41:39: [215 MB] 30000000 reads parsed INFO @ 20 Dec 2024 06:41:41: [220 MB] 31000000 reads parsed INFO @ 20 Dec 2024 06:41:42: [224 MB] 32000000 reads parsed INFO @ 20 Dec 2024 06:41:44: [227 MB] 33000000 reads parsed INFO @ 20 Dec 2024 06:41:46: [232 MB] 34000000 reads parsed INFO @ 20 Dec 2024 06:41:48: [235 MB] 35000000 reads parsed INFO @ 20 Dec 2024 06:41:50: [239 MB] 36000000 reads parsed INFO @ 20 Dec 2024 06:41:51: [243 MB] 37000000 reads parsed INFO @ 20 Dec 2024 06:41:53: [247 MB] 38000000 reads parsed INFO @ 20 Dec 2024 06:41:54: [250 MB] 39000000 reads parsed INFO @ 20 Dec 2024 06:41:56: [254 MB] 40000000 reads parsed INFO @ 20 Dec 2024 06:41:58: [259 MB] 41000000 reads parsed INFO @ 20 Dec 2024 06:41:59: [262 MB] 42000000 reads parsed INFO @ 20 Dec 2024 06:42:01: [266 MB] 43000000 reads parsed INFO @ 20 Dec 2024 06:42:02: [270 MB] 44000000 reads parsed INFO @ 20 Dec 2024 06:42:04: [275 MB] 45000000 reads parsed INFO @ 20 Dec 2024 06:42:06: [278 MB] 46000000 reads parsed INFO @ 20 Dec 2024 06:42:07: [291 MB] 47000000 reads parsed INFO @ 20 Dec 2024 06:42:09: [294 MB] 48000000 reads parsed INFO @ 20 Dec 2024 06:42:10: [294 MB] 49000000 reads parsed INFO @ 20 Dec 2024 06:42:12: [304 MB] 50000000 reads parsed INFO @ 20 Dec 2024 06:42:14: [304 MB] 51000000 reads parsed INFO @ 20 Dec 2024 06:42:15: [304 MB] 52000000 reads parsed INFO @ 20 Dec 2024 06:42:17: [308 MB] 53000000 reads parsed INFO @ 20 Dec 2024 06:42:19: [319 MB] 54000000 reads parsed INFO @ 20 Dec 2024 06:42:20: [319 MB] 55000000 reads parsed INFO @ 20 Dec 2024 06:42:22: [329 MB] 56000000 reads parsed INFO @ 20 Dec 2024 06:42:23: [330 MB] 57000000 reads parsed INFO @ 20 Dec 2024 06:42:25: [330 MB] 58000000 reads parsed INFO @ 20 Dec 2024 06:42:27: [337 MB] 59000000 reads parsed INFO @ 20 Dec 2024 06:42:28: [337 MB] 60000000 reads parsed INFO @ 20 Dec 2024 06:42:30: [340 MB] 61000000 reads parsed INFO @ 20 Dec 2024 06:42:31: [349 MB] 62000000 reads parsed INFO @ 20 Dec 2024 06:42:33: [357 MB] 63000000 reads parsed INFO @ 20 Dec 2024 06:42:35: [357 MB] 64000000 reads parsed INFO @ 20 Dec 2024 06:42:36: [362 MB] 65000000 reads parsed INFO @ 20 Dec 2024 06:42:38: [367 MB] 66000000 reads parsed INFO @ 20 Dec 2024 06:42:39: [372 MB] 67000000 reads parsed INFO @ 20 Dec 2024 06:42:41: [372 MB] 68000000 reads parsed INFO @ 20 Dec 2024 06:42:42: [379 MB] 69000000 reads parsed INFO @ 20 Dec 2024 06:42:43: [380 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 06:42:43: [380 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 06:42:43: [380 MB] #1 total tags in treatment: 69438592 INFO @ 20 Dec 2024 06:42:43: [380 MB] #1 finished! INFO @ 20 Dec 2024 06:42:43: [380 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 06:42:43: [380 MB] #2 Skipped... INFO @ 20 Dec 2024 06:42:43: [380 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 06:42:43: [380 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 06:42:43: [380 MB] #3 Call peaks... INFO @ 20 Dec 2024 06:42:43: [380 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 06:42:43: [380 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 06:42:43: [380 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 06:44:47: [1634 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 06:44:47: [1634 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C5_pseudoreplicateT_treat_pileup.bdg INFO @ 20 Dec 2024 06:44:47: [1634 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C5_pseudoreplicateT_control_lambda.bdg INFO @ 20 Dec 2024 06:44:47: [1634 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 06:44:47: [1634 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 06:46:32: [1634 MB] #4 Write output xls file... 3_peaks/C5_pseudoreplicateT_peaks.xls INFO @ 20 Dec 2024 06:46:32: [1634 MB] #4 Write peak in narrowPeak format file... 3_peaks/C5_pseudoreplicateT_peaks.narrowPeak INFO @ 20 Dec 2024 06:46:33: [1634 MB] #4 Write summits bed file... 3_peaks/C5_pseudoreplicateT_summits.bed INFO @ 20 Dec 2024 06:46:33: [1634 MB] Done!