INFO @ 20 Dec 2024 06:52:56: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorepT/C7_sorted.tsv -f BED -n C7_pseudoreplicateT -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C7_pseudoreplicateT # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorepT/C7_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 06:52:56: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 06:52:56: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 06:52:58: [98 MB] 1000000 reads parsed INFO @ 20 Dec 2024 06:53:00: [102 MB] 2000000 reads parsed INFO @ 20 Dec 2024 06:53:02: [104 MB] 3000000 reads parsed INFO @ 20 Dec 2024 06:53:03: [106 MB] 4000000 reads parsed INFO @ 20 Dec 2024 06:53:05: [109 MB] 5000000 reads parsed INFO @ 20 Dec 2024 06:53:07: [113 MB] 6000000 reads parsed INFO @ 20 Dec 2024 06:53:09: [116 MB] 7000000 reads parsed INFO @ 20 Dec 2024 06:53:11: [121 MB] 8000000 reads parsed INFO @ 20 Dec 2024 06:53:13: [128 MB] 9000000 reads parsed INFO @ 20 Dec 2024 06:53:15: [135 MB] 10000000 reads parsed INFO @ 20 Dec 2024 06:53:16: [139 MB] 11000000 reads parsed INFO @ 20 Dec 2024 06:53:18: [139 MB] 12000000 reads parsed INFO @ 20 Dec 2024 06:53:20: [146 MB] 13000000 reads parsed INFO @ 20 Dec 2024 06:53:22: [150 MB] 14000000 reads parsed INFO @ 20 Dec 2024 06:53:24: [153 MB] 15000000 reads parsed INFO @ 20 Dec 2024 06:53:26: [155 MB] 16000000 reads parsed INFO @ 20 Dec 2024 06:53:28: [162 MB] 17000000 reads parsed INFO @ 20 Dec 2024 06:53:29: [167 MB] 18000000 reads parsed INFO @ 20 Dec 2024 06:53:31: [171 MB] 19000000 reads parsed INFO @ 20 Dec 2024 06:53:33: [172 MB] 20000000 reads parsed INFO @ 20 Dec 2024 06:53:35: [178 MB] 21000000 reads parsed INFO @ 20 Dec 2024 06:53:37: [186 MB] 22000000 reads parsed INFO @ 20 Dec 2024 06:53:39: [188 MB] 23000000 reads parsed INFO @ 20 Dec 2024 06:53:41: [195 MB] 24000000 reads parsed INFO @ 20 Dec 2024 06:53:43: [200 MB] 25000000 reads parsed INFO @ 20 Dec 2024 06:53:45: [201 MB] 26000000 reads parsed INFO @ 20 Dec 2024 06:53:46: [209 MB] 27000000 reads parsed INFO @ 20 Dec 2024 06:53:48: [213 MB] 28000000 reads parsed INFO @ 20 Dec 2024 06:53:50: [213 MB] 29000000 reads parsed INFO @ 20 Dec 2024 06:53:52: [221 MB] 30000000 reads parsed INFO @ 20 Dec 2024 06:53:54: [224 MB] 31000000 reads parsed INFO @ 20 Dec 2024 06:53:55: [224 MB] 32000000 reads parsed INFO @ 20 Dec 2024 06:53:57: [233 MB] 33000000 reads parsed INFO @ 20 Dec 2024 06:53:59: [236 MB] 34000000 reads parsed INFO @ 20 Dec 2024 06:54:01: [238 MB] 35000000 reads parsed INFO @ 20 Dec 2024 06:54:03: [244 MB] 36000000 reads parsed INFO @ 20 Dec 2024 06:54:05: [248 MB] 37000000 reads parsed INFO @ 20 Dec 2024 06:54:07: [254 MB] 38000000 reads parsed INFO @ 20 Dec 2024 06:54:08: [257 MB] 39000000 reads parsed INFO @ 20 Dec 2024 06:54:10: [258 MB] 40000000 reads parsed INFO @ 20 Dec 2024 06:54:12: [266 MB] 41000000 reads parsed INFO @ 20 Dec 2024 06:54:14: [269 MB] 42000000 reads parsed INFO @ 20 Dec 2024 06:54:16: [271 MB] 43000000 reads parsed INFO @ 20 Dec 2024 06:54:17: [275 MB] 44000000 reads parsed INFO @ 20 Dec 2024 06:54:19: [279 MB] 45000000 reads parsed INFO @ 20 Dec 2024 06:54:21: [282 MB] 46000000 reads parsed INFO @ 20 Dec 2024 06:54:22: [286 MB] 47000000 reads parsed INFO @ 20 Dec 2024 06:54:24: [290 MB] 48000000 reads parsed INFO @ 20 Dec 2024 06:54:26: [294 MB] 49000000 reads parsed INFO @ 20 Dec 2024 06:54:27: [295 MB] 50000000 reads parsed INFO @ 20 Dec 2024 06:54:29: [301 MB] 51000000 reads parsed INFO @ 20 Dec 2024 06:54:31: [308 MB] 52000000 reads parsed INFO @ 20 Dec 2024 06:54:32: [311 MB] 53000000 reads parsed INFO @ 20 Dec 2024 06:54:34: [320 MB] 54000000 reads parsed INFO @ 20 Dec 2024 06:54:36: [320 MB] 55000000 reads parsed INFO @ 20 Dec 2024 06:54:37: [320 MB] 56000000 reads parsed INFO @ 20 Dec 2024 06:54:39: [324 MB] 57000000 reads parsed INFO @ 20 Dec 2024 06:54:41: [335 MB] 58000000 reads parsed INFO @ 20 Dec 2024 06:54:42: [335 MB] 59000000 reads parsed INFO @ 20 Dec 2024 06:54:44: [336 MB] 60000000 reads parsed INFO @ 20 Dec 2024 06:54:46: [340 MB] 61000000 reads parsed INFO @ 20 Dec 2024 06:54:47: [350 MB] 62000000 reads parsed INFO @ 20 Dec 2024 06:54:49: [350 MB] 63000000 reads parsed INFO @ 20 Dec 2024 06:54:51: [352 MB] 64000000 reads parsed INFO @ 20 Dec 2024 06:54:52: [356 MB] 65000000 reads parsed INFO @ 20 Dec 2024 06:54:54: [367 MB] 66000000 reads parsed INFO @ 20 Dec 2024 06:54:56: [367 MB] 67000000 reads parsed INFO @ 20 Dec 2024 06:54:57: [375 MB] 68000000 reads parsed INFO @ 20 Dec 2024 06:54:59: [379 MB] 69000000 reads parsed INFO @ 20 Dec 2024 06:55:01: [379 MB] 70000000 reads parsed INFO @ 20 Dec 2024 06:55:02: [386 MB] 71000000 reads parsed INFO @ 20 Dec 2024 06:55:04: [392 MB] 72000000 reads parsed INFO @ 20 Dec 2024 06:55:06: [393 MB] 73000000 reads parsed INFO @ 20 Dec 2024 06:55:07: [393 MB] 74000000 reads parsed INFO @ 20 Dec 2024 06:55:09: [403 MB] 75000000 reads parsed INFO @ 20 Dec 2024 06:55:11: [403 MB] 76000000 reads parsed INFO @ 20 Dec 2024 06:55:12: [411 MB] 77000000 reads parsed INFO @ 20 Dec 2024 06:55:14: [411 MB] 78000000 reads parsed INFO @ 20 Dec 2024 06:55:15: [417 MB] 79000000 reads parsed INFO @ 20 Dec 2024 06:55:17: [421 MB] 80000000 reads parsed INFO @ 20 Dec 2024 06:55:19: [427 MB] 81000000 reads parsed INFO @ 20 Dec 2024 06:55:21: [429 MB] 82000000 reads parsed INFO @ 20 Dec 2024 06:55:22: [433 MB] 83000000 reads parsed INFO @ 20 Dec 2024 06:55:24: [439 MB] 84000000 reads parsed INFO @ 20 Dec 2024 06:55:25: [439 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 06:55:25: [439 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 06:55:25: [439 MB] #1 total tags in treatment: 84271230 INFO @ 20 Dec 2024 06:55:25: [439 MB] #1 finished! INFO @ 20 Dec 2024 06:55:25: [439 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 06:55:25: [439 MB] #2 Skipped... INFO @ 20 Dec 2024 06:55:25: [439 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 06:55:25: [439 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 06:55:25: [439 MB] #3 Call peaks... INFO @ 20 Dec 2024 06:55:25: [439 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 06:55:25: [439 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 06:55:25: [439 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 06:57:35: [2168 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 06:57:35: [2168 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C7_pseudoreplicateT_treat_pileup.bdg INFO @ 20 Dec 2024 06:57:35: [2168 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C7_pseudoreplicateT_control_lambda.bdg INFO @ 20 Dec 2024 06:57:35: [2168 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 06:57:35: [2168 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 06:59:40: [2168 MB] #4 Write output xls file... 3_peaks/C7_pseudoreplicateT_peaks.xls INFO @ 20 Dec 2024 06:59:41: [2168 MB] #4 Write peak in narrowPeak format file... 3_peaks/C7_pseudoreplicateT_peaks.narrowPeak INFO @ 20 Dec 2024 06:59:42: [2168 MB] #4 Write summits bed file... 3_peaks/C7_pseudoreplicateT_summits.bed INFO @ 20 Dec 2024 06:59:43: [2168 MB] Done!