INFO @ 04 Jul 2024 22:38:29: [36 MB] # Command line: callpeak -t /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/splitfrags_out/Doublet.bed -f BED -n Doublet -g hs --nomodel --shift -100 --extsize 200 --call-summits --outdir /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/ # ARGUMENTS LIST: # name = Doublet # format = BED # ChIP-seq file = ['/tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/splitfrags_out/Doublet.bed'] # control file = None # effective genome size = 2.91e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 5.00e-02 # 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 INFO @ 04 Jul 2024 22:38:29: [36 MB] #1 read tag files... INFO @ 04 Jul 2024 22:38:29: [36 MB] #1 read treatment tags... INFO @ 04 Jul 2024 22:38:37: [101 MB] 1000000 reads parsed INFO @ 04 Jul 2024 22:38:43: [110 MB] 2000000 reads parsed INFO @ 04 Jul 2024 22:38:50: [117 MB] 3000000 reads parsed INFO @ 04 Jul 2024 22:38:56: [129 MB] 4000000 reads parsed INFO @ 04 Jul 2024 22:39:03: [138 MB] 5000000 reads parsed INFO @ 04 Jul 2024 22:39:09: [143 MB] 6000000 reads parsed INFO @ 04 Jul 2024 22:39:16: [152 MB] 7000000 reads parsed INFO @ 04 Jul 2024 22:39:22: [158 MB] 8000000 reads parsed INFO @ 04 Jul 2024 22:39:29: [165 MB] 9000000 reads parsed INFO @ 04 Jul 2024 22:39:35: [168 MB] 10000000 reads parsed INFO @ 04 Jul 2024 22:39:42: [173 MB] 11000000 reads parsed INFO @ 04 Jul 2024 22:39:48: [179 MB] 12000000 reads parsed INFO @ 04 Jul 2024 22:39:55: [185 MB] 13000000 reads parsed INFO @ 04 Jul 2024 22:40:01: [191 MB] 14000000 reads parsed INFO @ 04 Jul 2024 22:40:08: [195 MB] 15000000 reads parsed INFO @ 04 Jul 2024 22:40:14: [200 MB] 16000000 reads parsed INFO @ 04 Jul 2024 22:40:21: [209 MB] 17000000 reads parsed INFO @ 04 Jul 2024 22:40:27: [209 MB] 18000000 reads parsed INFO @ 04 Jul 2024 22:40:34: [215 MB] 19000000 reads parsed INFO @ 04 Jul 2024 22:40:40: [220 MB] 20000000 reads parsed INFO @ 04 Jul 2024 22:40:47: [228 MB] 21000000 reads parsed INFO @ 04 Jul 2024 22:40:53: [235 MB] 22000000 reads parsed INFO @ 04 Jul 2024 22:41:00: [242 MB] 23000000 reads parsed INFO @ 04 Jul 2024 22:41:06: [242 MB] 24000000 reads parsed INFO @ 04 Jul 2024 22:41:13: [249 MB] 25000000 reads parsed INFO @ 04 Jul 2024 22:41:19: [249 MB] 26000000 reads parsed INFO @ 04 Jul 2024 22:41:25: [254 MB] 27000000 reads parsed INFO @ 04 Jul 2024 22:41:32: [260 MB] 28000000 reads parsed INFO @ 04 Jul 2024 22:41:38: [268 MB] 29000000 reads parsed INFO @ 04 Jul 2024 22:41:44: [277 MB] 30000000 reads parsed INFO @ 04 Jul 2024 22:41:51: [277 MB] 31000000 reads parsed INFO @ 04 Jul 2024 22:41:56: [277 MB] #1 tag size is determined as 162 bps INFO @ 04 Jul 2024 22:41:56: [277 MB] #1 tag size = 162.0 INFO @ 04 Jul 2024 22:41:56: [277 MB] #1 total tags in treatment: 31576599 INFO @ 04 Jul 2024 22:41:56: [277 MB] #1 user defined the maximum tags... INFO @ 04 Jul 2024 22:41:56: [277 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ 04 Jul 2024 22:41:56: [277 MB] #1 tags after filtering in treatment: 25109018 INFO @ 04 Jul 2024 22:41:56: [277 MB] #1 Redundant rate of treatment: 0.20 INFO @ 04 Jul 2024 22:41:56: [277 MB] #1 finished! INFO @ 04 Jul 2024 22:41:56: [277 MB] #2 Build Peak Model... INFO @ 04 Jul 2024 22:41:56: [277 MB] #2 Skipped... INFO @ 04 Jul 2024 22:41:56: [277 MB] #2 Use 200 as fragment length INFO @ 04 Jul 2024 22:41:56: [277 MB] #2 Sequencing ends will be shifted towards 5' by 100 bp(s) INFO @ 04 Jul 2024 22:41:56: [277 MB] #3 Call peaks... INFO @ 04 Jul 2024 22:41:56: [277 MB] #3 Going to call summits inside each peak ... INFO @ 04 Jul 2024 22:41:56: [277 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 04 Jul 2024 22:47:19: [696 MB] #3 Call peaks for each chromosome... INFO @ 04 Jul 2024 22:52:46: [696 MB] #4 Write output xls file... /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/Doublet_peaks.xls INFO @ 04 Jul 2024 22:52:48: [696 MB] #4 Write peak in narrowPeak format file... /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/Doublet_peaks.narrowPeak INFO @ 04 Jul 2024 22:52:49: [696 MB] #4 Write summits bed file... /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/Doublet_summits.bed INFO @ 04 Jul 2024 22:52:50: [696 MB] Done!