INFO @ 20 Dec 2024 06:03:50: [31 MB] # Command line: callpeak -t 2_celltype_fragments/pseudorepT/C12_sorted.tsv -f BED -n C12_pseudoreplicateT -g hs --outdir 3_peaks -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = C12_pseudoreplicateT # format = BED # ChIP-seq file = ['2_celltype_fragments/pseudorepT/C12_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 06:03:50: [31 MB] #1 read tag files... INFO @ 20 Dec 2024 06:03:50: [31 MB] #1 read treatment tags... INFO @ 20 Dec 2024 06:03:52: [98 MB] 1000000 reads parsed INFO @ 20 Dec 2024 06:03:54: [100 MB] 2000000 reads parsed INFO @ 20 Dec 2024 06:03:55: [102 MB] 3000000 reads parsed INFO @ 20 Dec 2024 06:03:57: [111 MB] 4000000 reads parsed INFO @ 20 Dec 2024 06:03:59: [116 MB] 5000000 reads parsed INFO @ 20 Dec 2024 06:04:01: [120 MB] 6000000 reads parsed INFO @ 20 Dec 2024 06:04:03: [124 MB] 7000000 reads parsed INFO @ 20 Dec 2024 06:04:05: [127 MB] 8000000 reads parsed INFO @ 20 Dec 2024 06:04:07: [131 MB] 9000000 reads parsed INFO @ 20 Dec 2024 06:04:09: [136 MB] 10000000 reads parsed INFO @ 20 Dec 2024 06:04:11: [139 MB] 11000000 reads parsed INFO @ 20 Dec 2024 06:04:12: [143 MB] 12000000 reads parsed INFO @ 20 Dec 2024 06:04:15: [150 MB] 13000000 reads parsed INFO @ 20 Dec 2024 06:04:16: [158 MB] 14000000 reads parsed INFO @ 20 Dec 2024 06:04:18: [160 MB] 15000000 reads parsed INFO @ 20 Dec 2024 06:04:20: [166 MB] 16000000 reads parsed INFO @ 20 Dec 2024 06:04:22: [170 MB] 17000000 reads parsed INFO @ 20 Dec 2024 06:04:24: [172 MB] 18000000 reads parsed INFO @ 20 Dec 2024 06:04:26: [178 MB] 19000000 reads parsed INFO @ 20 Dec 2024 06:04:28: [183 MB] 20000000 reads parsed INFO @ 20 Dec 2024 06:04:29: [187 MB] 21000000 reads parsed INFO @ 20 Dec 2024 06:04:31: [190 MB] 22000000 reads parsed INFO @ 20 Dec 2024 06:04:33: [194 MB] 23000000 reads parsed INFO @ 20 Dec 2024 06:04:34: [196 MB] 24000000 reads parsed INFO @ 20 Dec 2024 06:04:36: [201 MB] 25000000 reads parsed INFO @ 20 Dec 2024 06:04:38: [205 MB] 26000000 reads parsed INFO @ 20 Dec 2024 06:04:39: [208 MB] 27000000 reads parsed INFO @ 20 Dec 2024 06:04:41: [215 MB] 28000000 reads parsed INFO @ 20 Dec 2024 06:04:43: [218 MB] 29000000 reads parsed INFO @ 20 Dec 2024 06:04:44: [224 MB] 30000000 reads parsed INFO @ 20 Dec 2024 06:04:46: [227 MB] 31000000 reads parsed INFO @ 20 Dec 2024 06:04:47: [232 MB] 32000000 reads parsed INFO @ 20 Dec 2024 06:04:49: [236 MB] 33000000 reads parsed INFO @ 20 Dec 2024 06:04:51: [238 MB] 34000000 reads parsed INFO @ 20 Dec 2024 06:04:52: [244 MB] 35000000 reads parsed INFO @ 20 Dec 2024 06:04:54: [248 MB] 36000000 reads parsed INFO @ 20 Dec 2024 06:04:55: [251 MB] 37000000 reads parsed INFO @ 20 Dec 2024 06:04:57: [253 MB] 38000000 reads parsed INFO @ 20 Dec 2024 06:04:59: [259 MB] 39000000 reads parsed INFO @ 20 Dec 2024 06:05:00: [266 MB] 40000000 reads parsed INFO @ 20 Dec 2024 06:05:01: [266 MB] #1 tag size is determined as 1 bps INFO @ 20 Dec 2024 06:05:01: [266 MB] #1 tag size = 1.0 INFO @ 20 Dec 2024 06:05:01: [266 MB] #1 total tags in treatment: 40518400 INFO @ 20 Dec 2024 06:05:01: [266 MB] #1 finished! INFO @ 20 Dec 2024 06:05:01: [266 MB] #2 Build Peak Model... INFO @ 20 Dec 2024 06:05:01: [266 MB] #2 Skipped... INFO @ 20 Dec 2024 06:05:01: [266 MB] #2 Use 150 as fragment length INFO @ 20 Dec 2024 06:05:01: [266 MB] #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ 20 Dec 2024 06:05:01: [266 MB] #3 Call peaks... INFO @ 20 Dec 2024 06:05:01: [266 MB] #3 Going to call summits inside each peak ... INFO @ 20 Dec 2024 06:05:01: [266 MB] #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ 20 Dec 2024 06:05:01: [266 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 20 Dec 2024 06:06:12: [1090 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 20 Dec 2024 06:06:12: [1090 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... C12_pseudoreplicateT_treat_pileup.bdg INFO @ 20 Dec 2024 06:06:12: [1090 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... C12_pseudoreplicateT_control_lambda.bdg INFO @ 20 Dec 2024 06:06:12: [1090 MB] #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ 20 Dec 2024 06:06:12: [1090 MB] #3 Call peaks for each chromosome... INFO @ 20 Dec 2024 06:07:26: [1090 MB] #4 Write output xls file... 3_peaks/C12_pseudoreplicateT_peaks.xls INFO @ 20 Dec 2024 06:07:27: [1090 MB] #4 Write peak in narrowPeak format file... 3_peaks/C12_pseudoreplicateT_peaks.narrowPeak INFO @ 20 Dec 2024 06:07:28: [1090 MB] #4 Write summits bed file... 3_peaks/C12_pseudoreplicateT_summits.bed INFO @ 20 Dec 2024 06:07:28: [1090 MB] Done!