INFO @ 20 Dec 2024 05:57:26: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorepT/C11_sorted.tsv -f BED -n C11_pseudoreplicateT -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C11_pseudoreplicateT # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorepT/C11_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 05:57:26: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 05:57:26: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 05:57:29: [98 MB] 1000000 reads parsed INFO @ 20 Dec 2024 05:57:31: [101 MB] 2000000 reads parsed INFO @ 20 Dec 2024 05:57:32: [103 MB] 3000000 reads parsed INFO @ 20 Dec 2024 05:57:34: [105 MB] 4000000 reads parsed INFO @ 20 Dec 2024 05:57:36: [114 MB] 5000000 reads parsed INFO @ 20 Dec 2024 05:57:38: [117 MB] 6000000 reads parsed INFO @ 20 Dec 2024 05:57:40: [122 MB] 7000000 reads parsed INFO @ 20 Dec 2024 05:57:42: [129 MB] 8000000 reads parsed INFO @ 20 Dec 2024 05:57:43: [133 MB] 9000000 reads parsed INFO @ 20 Dec 2024 05:57:45: [138 MB] 10000000 reads parsed INFO @ 20 Dec 2024 05:57:47: [142 MB] 11000000 reads parsed INFO @ 20 Dec 2024 05:57:49: [146 MB] 12000000 reads parsed INFO @ 20 Dec 2024 05:57:52: [150 MB] 13000000 reads parsed INFO @ 20 Dec 2024 05:57:53: [154 MB] 14000000 reads parsed INFO @ 20 Dec 2024 05:57:55: [158 MB] 15000000 reads parsed INFO @ 20 Dec 2024 05:57:57: [162 MB] 16000000 reads parsed INFO @ 20 Dec 2024 05:57:59: [168 MB] 17000000 reads parsed INFO @ 20 Dec 2024 05:58:01: [172 MB] 18000000 reads parsed INFO @ 20 Dec 2024 05:58:02: [176 MB] 19000000 reads parsed INFO @ 20 Dec 2024 05:58:04: [181 MB] 20000000 reads parsed INFO @ 20 Dec 2024 05:58:06: [182 MB] 21000000 reads parsed INFO @ 20 Dec 2024 05:58:08: [186 MB] 22000000 reads parsed INFO @ 20 Dec 2024 05:58:10: [188 MB] 23000000 reads parsed INFO @ 20 Dec 2024 05:58:11: [193 MB] 24000000 reads parsed INFO @ 20 Dec 2024 05:58:13: [197 MB] 25000000 reads parsed INFO @ 20 Dec 2024 05:58:15: [201 MB] 26000000 reads parsed INFO @ 20 Dec 2024 05:58:16: [206 MB] 27000000 reads parsed INFO @ 20 Dec 2024 05:58:18: [208 MB] 28000000 reads parsed INFO @ 20 Dec 2024 05:58:20: [213 MB] 29000000 reads parsed INFO @ 20 Dec 2024 05:58:21: [217 MB] 30000000 reads parsed INFO @ 20 Dec 2024 05:58:23: [221 MB] 31000000 reads parsed INFO @ 20 Dec 2024 05:58:24: [225 MB] 32000000 reads parsed INFO @ 20 Dec 2024 05:58:26: [229 MB] 33000000 reads parsed INFO @ 20 Dec 2024 05:58:27: [232 MB] 34000000 reads parsed INFO @ 20 Dec 2024 05:58:29: [237 MB] 35000000 reads parsed INFO @ 20 Dec 2024 05:58:31: [241 MB] 36000000 reads parsed INFO @ 20 Dec 2024 05:58:32: [244 MB] 37000000 reads parsed INFO @ 20 Dec 2024 05:58:34: [248 MB] 38000000 reads parsed INFO @ 20 Dec 2024 05:58:36: [253 MB] 39000000 reads parsed INFO @ 20 Dec 2024 05:58:37: [257 MB] 40000000 reads parsed INFO @ 20 Dec 2024 05:58:39: [261 MB] 41000000 reads parsed INFO @ 20 Dec 2024 05:58:41: [266 MB] 42000000 reads parsed INFO @ 20 Dec 2024 05:58:42: [269 MB] 43000000 reads parsed INFO @ 20 Dec 2024 05:58:44: [273 MB] 44000000 reads parsed INFO @ 20 Dec 2024 05:58:46: [277 MB] 45000000 reads parsed INFO @ 20 Dec 2024 05:58:48: [282 MB] 46000000 reads parsed INFO @ 20 Dec 2024 05:58:49: [284 MB] 47000000 reads parsed INFO @ 20 Dec 2024 05:58:49: [284 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 05:58:49: [284 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 05:58:49: [284 MB] #1 total tags in treatment: 47068842 INFO @ 20 Dec 2024 05:58:49: [284 MB] #1 finished! INFO @ 20 Dec 2024 05:58:49: [284 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 05:58:49: [284 MB] #2 Skipped... INFO @ 20 Dec 2024 05:58:49: [284 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 05:58:49: [284 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 05:58:49: [284 MB] #3 Call peaks... INFO @ 20 Dec 2024 05:58:49: [284 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 05:58:49: [284 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 05:58:49: [284 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 05:59:55: [1275 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 05:59:55: [1275 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C11_pseudoreplicateT_treat_pileup.bdg INFO @ 20 Dec 2024 05:59:55: [1275 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C11_pseudoreplicateT_control_lambda.bdg INFO @ 20 Dec 2024 05:59:55: [1275 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 05:59:55: [1275 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 06:01:13: [1275 MB] #4 Write output xls file... 3_peaks/C11_pseudoreplicateT_peaks.xls INFO @ 20 Dec 2024 06:01:14: [1275 MB] #4 Write peak in narrowPeak format file... 3_peaks/C11_pseudoreplicateT_peaks.narrowPeak INFO @ 20 Dec 2024 06:01:15: [1275 MB] #4 Write summits bed file... 3_peaks/C11_pseudoreplicateT_summits.bed INFO @ 20 Dec 2024 06:01:15: [1275 MB] Done!