INFO @ 04 Jul 2024 22:38:29: [36 MB] # Command line: callpeak -t /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/splitfrags_out/OPC.bed -f BED -n OPC -g hs --nomodel --shift -100 --extsize 200 --call-summits --outdir /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/ # ARGUMENTS LIST: # name = OPC # format = BED # ChIP-seq file = ['/tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/splitfrags_out/OPC.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: [102 MB] 1000000 reads parsed INFO @ 04 Jul 2024 22:38:43: [111 MB] 2000000 reads parsed INFO @ 04 Jul 2024 22:38:50: [121 MB] 3000000 reads parsed INFO @ 04 Jul 2024 22:38:56: [130 MB] 4000000 reads parsed INFO @ 04 Jul 2024 22:39:03: [137 MB] 5000000 reads parsed INFO @ 04 Jul 2024 22:39:09: [141 MB] 6000000 reads parsed INFO @ 04 Jul 2024 22:39:16: [146 MB] 7000000 reads parsed INFO @ 04 Jul 2024 22:39:22: [147 MB] 8000000 reads parsed INFO @ 04 Jul 2024 22:39:29: [151 MB] 9000000 reads parsed INFO @ 04 Jul 2024 22:39:35: [158 MB] 10000000 reads parsed INFO @ 04 Jul 2024 22:39:42: [163 MB] 11000000 reads parsed INFO @ 04 Jul 2024 22:39:48: [163 MB] 12000000 reads parsed INFO @ 04 Jul 2024 22:39:55: [170 MB] 13000000 reads parsed INFO @ 04 Jul 2024 22:40:01: [173 MB] 14000000 reads parsed INFO @ 04 Jul 2024 22:40:08: [185 MB] 15000000 reads parsed INFO @ 04 Jul 2024 22:40:14: [185 MB] 16000000 reads parsed INFO @ 04 Jul 2024 22:40:21: [194 MB] 17000000 reads parsed INFO @ 04 Jul 2024 22:40:27: [199 MB] 18000000 reads parsed INFO @ 04 Jul 2024 22:40:33: [201 MB] 19000000 reads parsed INFO @ 04 Jul 2024 22:40:40: [208 MB] 20000000 reads parsed INFO @ 04 Jul 2024 22:40:46: [212 MB] 21000000 reads parsed INFO @ 04 Jul 2024 22:40:53: [212 MB] 22000000 reads parsed INFO @ 04 Jul 2024 22:40:59: [214 MB] 23000000 reads parsed INFO @ 04 Jul 2024 22:41:05: [221 MB] 24000000 reads parsed INFO @ 04 Jul 2024 22:41:12: [226 MB] 25000000 reads parsed INFO @ 04 Jul 2024 22:41:18: [230 MB] 26000000 reads parsed INFO @ 04 Jul 2024 22:41:25: [236 MB] 27000000 reads parsed INFO @ 04 Jul 2024 22:41:31: [236 MB] 28000000 reads parsed INFO @ 04 Jul 2024 22:41:37: [243 MB] 29000000 reads parsed INFO @ 04 Jul 2024 22:41:44: [253 MB] 30000000 reads parsed INFO @ 04 Jul 2024 22:41:50: [254 MB] 31000000 reads parsed INFO @ 04 Jul 2024 22:41:56: [254 MB] 32000000 reads parsed INFO @ 04 Jul 2024 22:42:03: [271 MB] 33000000 reads parsed INFO @ 04 Jul 2024 22:42:09: [271 MB] 34000000 reads parsed INFO @ 04 Jul 2024 22:42:15: [273 MB] 35000000 reads parsed INFO @ 04 Jul 2024 22:42:22: [282 MB] 36000000 reads parsed INFO @ 04 Jul 2024 22:42:28: [291 MB] 37000000 reads parsed INFO @ 04 Jul 2024 22:42:34: [291 MB] 38000000 reads parsed INFO @ 04 Jul 2024 22:42:41: [301 MB] 39000000 reads parsed INFO @ 04 Jul 2024 22:42:47: [311 MB] 40000000 reads parsed INFO @ 04 Jul 2024 22:42:53: [314 MB] 41000000 reads parsed INFO @ 04 Jul 2024 22:42:59: [314 MB] 42000000 reads parsed INFO @ 04 Jul 2024 22:43:06: [315 MB] 43000000 reads parsed INFO @ 04 Jul 2024 22:43:12: [316 MB] 44000000 reads parsed INFO @ 04 Jul 2024 22:43:18: [316 MB] 45000000 reads parsed INFO @ 04 Jul 2024 22:43:24: [328 MB] 46000000 reads parsed INFO @ 04 Jul 2024 22:43:31: [329 MB] 47000000 reads parsed INFO @ 04 Jul 2024 22:43:37: [332 MB] 48000000 reads parsed INFO @ 04 Jul 2024 22:43:43: [333 MB] 49000000 reads parsed INFO @ 04 Jul 2024 22:43:49: [347 MB] 50000000 reads parsed INFO @ 04 Jul 2024 22:43:56: [348 MB] 51000000 reads parsed INFO @ 04 Jul 2024 22:44:02: [350 MB] 52000000 reads parsed INFO @ 04 Jul 2024 22:44:08: [350 MB] 53000000 reads parsed INFO @ 04 Jul 2024 22:44:14: [353 MB] 54000000 reads parsed INFO @ 04 Jul 2024 22:44:21: [368 MB] 55000000 reads parsed INFO @ 04 Jul 2024 22:44:28: [368 MB] #1 tag size is determined as 241 bps INFO @ 04 Jul 2024 22:44:28: [368 MB] #1 tag size = 241.0 INFO @ 04 Jul 2024 22:44:28: [368 MB] #1 total tags in treatment: 55705208 INFO @ 04 Jul 2024 22:44:28: [368 MB] #1 user defined the maximum tags... INFO @ 04 Jul 2024 22:44:28: [368 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 22:44:29: [368 MB] #1 tags after filtering in treatment: 42377530 INFO @ 04 Jul 2024 22:44:29: [368 MB] #1 Redundant rate of treatment: 0.24 INFO @ 04 Jul 2024 22:44:29: [368 MB] #1 finished! INFO @ 04 Jul 2024 22:44:29: [368 MB] #2 Build Peak Model... INFO @ 04 Jul 2024 22:44:29: [368 MB] #2 Skipped... INFO @ 04 Jul 2024 22:44:29: [368 MB] #2 Use 200 as fragment length INFO @ 04 Jul 2024 22:44:29: [368 MB] #2 Sequencing ends will be shifted towards 5' by 100 bp(s) INFO @ 04 Jul 2024 22:44:29: [368 MB] #3 Call peaks... INFO @ 04 Jul 2024 22:44:29: [368 MB] #3 Going to call summits inside each peak ... INFO @ 04 Jul 2024 22:44:29: [368 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 04 Jul 2024 22:53:09: [1084 MB] #3 Call peaks for each chromosome... INFO @ 04 Jul 2024 22:59:15: [1084 MB] #4 Write output xls file... /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/OPC_peaks.xls INFO @ 04 Jul 2024 22:59:17: [1084 MB] #4 Write peak in narrowPeak format file... /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/OPC_peaks.narrowPeak INFO @ 04 Jul 2024 22:59:18: [1084 MB] #4 Write summits bed file... /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/OPC_summits.bed INFO @ 04 Jul 2024 22:59:18: [1084 MB] Done!