INFO @ 04 Jul 2024 22:38:29: [36 MB] # Command line: callpeak -t /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/splitfrags_out/Microglia.bed -f BED -n Microglia -g hs --nomodel --shift -100 --extsize 200 --call-summits --outdir /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/ # ARGUMENTS LIST: # name = Microglia # format = BED # ChIP-seq file = ['/tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/splitfrags_out/Microglia.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: [99 MB] 1000000 reads parsed INFO @ 04 Jul 2024 22:38:43: [109 MB] 2000000 reads parsed INFO @ 04 Jul 2024 22:38:50: [115 MB] 3000000 reads parsed INFO @ 04 Jul 2024 22:38:57: [121 MB] 4000000 reads parsed INFO @ 04 Jul 2024 22:39:03: [138 MB] 5000000 reads parsed INFO @ 04 Jul 2024 22:39:10: [143 MB] 6000000 reads parsed INFO @ 04 Jul 2024 22:39:16: [152 MB] 7000000 reads parsed INFO @ 04 Jul 2024 22:39:23: [161 MB] 8000000 reads parsed INFO @ 04 Jul 2024 22:39:29: [169 MB] 9000000 reads parsed INFO @ 04 Jul 2024 22:39:36: [177 MB] 10000000 reads parsed INFO @ 04 Jul 2024 22:39:42: [179 MB] 11000000 reads parsed INFO @ 04 Jul 2024 22:39:49: [189 MB] 12000000 reads parsed INFO @ 04 Jul 2024 22:39:56: [194 MB] 13000000 reads parsed INFO @ 04 Jul 2024 22:40:02: [201 MB] 14000000 reads parsed INFO @ 04 Jul 2024 22:40:09: [202 MB] 15000000 reads parsed INFO @ 04 Jul 2024 22:40:15: [208 MB] 16000000 reads parsed INFO @ 04 Jul 2024 22:40:22: [208 MB] 17000000 reads parsed INFO @ 04 Jul 2024 22:40:28: [216 MB] 18000000 reads parsed INFO @ 04 Jul 2024 22:40:34: [217 MB] 19000000 reads parsed INFO @ 04 Jul 2024 22:40:41: [223 MB] 20000000 reads parsed INFO @ 04 Jul 2024 22:40:47: [225 MB] 21000000 reads parsed INFO @ 04 Jul 2024 22:40:54: [233 MB] 22000000 reads parsed INFO @ 04 Jul 2024 22:41:00: [235 MB] 23000000 reads parsed INFO @ 04 Jul 2024 22:41:07: [243 MB] 24000000 reads parsed INFO @ 04 Jul 2024 22:41:13: [250 MB] 25000000 reads parsed INFO @ 04 Jul 2024 22:41:19: [251 MB] 26000000 reads parsed INFO @ 04 Jul 2024 22:41:26: [251 MB] 27000000 reads parsed INFO @ 04 Jul 2024 22:41:32: [257 MB] 28000000 reads parsed INFO @ 04 Jul 2024 22:41:39: [257 MB] 29000000 reads parsed INFO @ 04 Jul 2024 22:41:45: [267 MB] 30000000 reads parsed INFO @ 04 Jul 2024 22:41:52: [267 MB] 31000000 reads parsed INFO @ 04 Jul 2024 22:41:58: [275 MB] 32000000 reads parsed INFO @ 04 Jul 2024 22:42:04: [284 MB] 33000000 reads parsed INFO @ 04 Jul 2024 22:42:11: [295 MB] 34000000 reads parsed INFO @ 04 Jul 2024 22:42:17: [295 MB] 35000000 reads parsed INFO @ 04 Jul 2024 22:42:23: [304 MB] 36000000 reads parsed INFO @ 04 Jul 2024 22:42:30: [304 MB] 37000000 reads parsed INFO @ 04 Jul 2024 22:42:36: [308 MB] 38000000 reads parsed INFO @ 04 Jul 2024 22:42:43: [308 MB] 39000000 reads parsed INFO @ 04 Jul 2024 22:42:49: [312 MB] 40000000 reads parsed INFO @ 04 Jul 2024 22:42:55: [312 MB] 41000000 reads parsed INFO @ 04 Jul 2024 22:43:01: [321 MB] 42000000 reads parsed INFO @ 04 Jul 2024 22:43:08: [329 MB] 43000000 reads parsed INFO @ 04 Jul 2024 22:43:14: [332 MB] 44000000 reads parsed INFO @ 04 Jul 2024 22:43:21: [342 MB] 45000000 reads parsed INFO @ 04 Jul 2024 22:43:24: [347 MB] #1 tag size is determined as 140 bps INFO @ 04 Jul 2024 22:43:24: [347 MB] #1 tag size = 140.0 INFO @ 04 Jul 2024 22:43:24: [347 MB] #1 total tags in treatment: 45208111 INFO @ 04 Jul 2024 22:43:24: [347 MB] #1 user defined the maximum tags... INFO @ 04 Jul 2024 22:43:24: [347 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 22:43:25: [347 MB] #1 tags after filtering in treatment: 29128778 INFO @ 04 Jul 2024 22:43:25: [347 MB] #1 Redundant rate of treatment: 0.36 INFO @ 04 Jul 2024 22:43:25: [347 MB] #1 finished! INFO @ 04 Jul 2024 22:43:25: [347 MB] #2 Build Peak Model... INFO @ 04 Jul 2024 22:43:25: [347 MB] #2 Skipped... INFO @ 04 Jul 2024 22:43:25: [347 MB] #2 Use 200 as fragment length INFO @ 04 Jul 2024 22:43:25: [347 MB] #2 Sequencing ends will be shifted towards 5' by 100 bp(s) INFO @ 04 Jul 2024 22:43:25: [347 MB] #3 Call peaks... INFO @ 04 Jul 2024 22:43:25: [347 MB] #3 Going to call summits inside each peak ... INFO @ 04 Jul 2024 22:43:25: [347 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 04 Jul 2024 22:50:26: [851 MB] #3 Call peaks for each chromosome... INFO @ 04 Jul 2024 22:56:03: [851 MB] #4 Write output xls file... /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/Microglia_peaks.xls INFO @ 04 Jul 2024 22:56:05: [851 MB] #4 Write peak in narrowPeak format file... /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/Microglia_peaks.narrowPeak INFO @ 04 Jul 2024 22:56:06: [851 MB] #4 Write summits bed file... /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/Microglia_summits.bed INFO @ 04 Jul 2024 22:56:06: [851 MB] Done!