INFO @ 04 Jul 2024 22:38:29: [36 MB] # Command line: callpeak -t /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/splitfrags_out/Astrocyte.bed -f BED -n Astrocyte -g hs --nomodel --shift -100 --extsize 200 --call-summits --outdir /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/ # ARGUMENTS LIST: # name = Astrocyte # format = BED # ChIP-seq file = ['/tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/splitfrags_out/Astrocyte.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: [128 MB] 3000000 reads parsed INFO @ 04 Jul 2024 22:38:56: [136 MB] 4000000 reads parsed INFO @ 04 Jul 2024 22:39:03: [142 MB] 5000000 reads parsed INFO @ 04 Jul 2024 22:39:09: [150 MB] 6000000 reads parsed INFO @ 04 Jul 2024 22:39:16: [157 MB] 7000000 reads parsed INFO @ 04 Jul 2024 22:39:23: [158 MB] 8000000 reads parsed INFO @ 04 Jul 2024 22:39:29: [160 MB] 9000000 reads parsed INFO @ 04 Jul 2024 22:39:36: [168 MB] 10000000 reads parsed INFO @ 04 Jul 2024 22:39:42: [171 MB] 11000000 reads parsed INFO @ 04 Jul 2024 22:39:49: [178 MB] 12000000 reads parsed INFO @ 04 Jul 2024 22:39:55: [181 MB] 13000000 reads parsed INFO @ 04 Jul 2024 22:40:02: [185 MB] 14000000 reads parsed INFO @ 04 Jul 2024 22:40:08: [186 MB] 15000000 reads parsed INFO @ 04 Jul 2024 22:40:15: [196 MB] 16000000 reads parsed INFO @ 04 Jul 2024 22:40:21: [196 MB] 17000000 reads parsed INFO @ 04 Jul 2024 22:40:28: [205 MB] 18000000 reads parsed INFO @ 04 Jul 2024 22:40:34: [211 MB] 19000000 reads parsed INFO @ 04 Jul 2024 22:40:41: [216 MB] 20000000 reads parsed INFO @ 04 Jul 2024 22:40:47: [218 MB] 21000000 reads parsed INFO @ 04 Jul 2024 22:40:54: [224 MB] 22000000 reads parsed INFO @ 04 Jul 2024 22:41:00: [227 MB] 23000000 reads parsed INFO @ 04 Jul 2024 22:41:07: [235 MB] 24000000 reads parsed INFO @ 04 Jul 2024 22:41:13: [237 MB] 25000000 reads parsed INFO @ 04 Jul 2024 22:41:20: [237 MB] 26000000 reads parsed INFO @ 04 Jul 2024 22:41:26: [249 MB] 27000000 reads parsed INFO @ 04 Jul 2024 22:41:32: [249 MB] 28000000 reads parsed INFO @ 04 Jul 2024 22:41:39: [250 MB] 29000000 reads parsed INFO @ 04 Jul 2024 22:41:45: [251 MB] 30000000 reads parsed INFO @ 04 Jul 2024 22:41:52: [262 MB] 31000000 reads parsed INFO @ 04 Jul 2024 22:41:58: [270 MB] 32000000 reads parsed INFO @ 04 Jul 2024 22:42:04: [271 MB] 33000000 reads parsed INFO @ 04 Jul 2024 22:42:11: [271 MB] 34000000 reads parsed INFO @ 04 Jul 2024 22:42:17: [281 MB] 35000000 reads parsed INFO @ 04 Jul 2024 22:42:24: [281 MB] 36000000 reads parsed INFO @ 04 Jul 2024 22:42:30: [289 MB] 37000000 reads parsed INFO @ 04 Jul 2024 22:42:36: [301 MB] 38000000 reads parsed INFO @ 04 Jul 2024 22:42:43: [309 MB] 39000000 reads parsed INFO @ 04 Jul 2024 22:42:49: [311 MB] 40000000 reads parsed INFO @ 04 Jul 2024 22:42:56: [313 MB] 41000000 reads parsed INFO @ 04 Jul 2024 22:43:02: [323 MB] 42000000 reads parsed INFO @ 04 Jul 2024 22:43:08: [323 MB] 43000000 reads parsed INFO @ 04 Jul 2024 22:43:14: [324 MB] 44000000 reads parsed INFO @ 04 Jul 2024 22:43:21: [327 MB] 45000000 reads parsed INFO @ 04 Jul 2024 22:43:27: [338 MB] 46000000 reads parsed INFO @ 04 Jul 2024 22:43:33: [338 MB] 47000000 reads parsed INFO @ 04 Jul 2024 22:43:40: [340 MB] 48000000 reads parsed INFO @ 04 Jul 2024 22:43:46: [346 MB] 49000000 reads parsed INFO @ 04 Jul 2024 22:43:52: [353 MB] 50000000 reads parsed INFO @ 04 Jul 2024 22:43:59: [354 MB] 51000000 reads parsed INFO @ 04 Jul 2024 22:44:05: [355 MB] 52000000 reads parsed INFO @ 04 Jul 2024 22:44:11: [358 MB] 53000000 reads parsed INFO @ 04 Jul 2024 22:44:18: [372 MB] 54000000 reads parsed INFO @ 04 Jul 2024 22:44:24: [374 MB] 55000000 reads parsed INFO @ 04 Jul 2024 22:44:30: [376 MB] 56000000 reads parsed INFO @ 04 Jul 2024 22:44:37: [376 MB] 57000000 reads parsed INFO @ 04 Jul 2024 22:44:43: [376 MB] 58000000 reads parsed INFO @ 04 Jul 2024 22:44:49: [379 MB] 59000000 reads parsed INFO @ 04 Jul 2024 22:44:55: [379 MB] 60000000 reads parsed INFO @ 04 Jul 2024 22:45:02: [391 MB] 61000000 reads parsed INFO @ 04 Jul 2024 22:45:08: [393 MB] 62000000 reads parsed INFO @ 04 Jul 2024 22:45:14: [396 MB] 63000000 reads parsed INFO @ 04 Jul 2024 22:45:21: [400 MB] 64000000 reads parsed INFO @ 04 Jul 2024 22:45:27: [415 MB] 65000000 reads parsed INFO @ 04 Jul 2024 22:45:33: [429 MB] 66000000 reads parsed INFO @ 04 Jul 2024 22:45:40: [429 MB] 67000000 reads parsed INFO @ 04 Jul 2024 22:45:46: [430 MB] 68000000 reads parsed INFO @ 04 Jul 2024 22:45:52: [433 MB] 69000000 reads parsed INFO @ 04 Jul 2024 22:45:59: [433 MB] 70000000 reads parsed INFO @ 04 Jul 2024 22:46:05: [435 MB] 71000000 reads parsed INFO @ 04 Jul 2024 22:46:11: [438 MB] 72000000 reads parsed INFO @ 04 Jul 2024 22:46:17: [440 MB] 73000000 reads parsed INFO @ 04 Jul 2024 22:46:24: [443 MB] 74000000 reads parsed INFO @ 04 Jul 2024 22:46:30: [446 MB] 75000000 reads parsed INFO @ 04 Jul 2024 22:46:36: [449 MB] 76000000 reads parsed INFO @ 04 Jul 2024 22:46:43: [453 MB] 77000000 reads parsed INFO @ 04 Jul 2024 22:46:49: [457 MB] 78000000 reads parsed INFO @ 04 Jul 2024 22:46:55: [475 MB] 79000000 reads parsed INFO @ 04 Jul 2024 22:47:02: [497 MB] 80000000 reads parsed INFO @ 04 Jul 2024 22:47:08: [499 MB] 81000000 reads parsed INFO @ 04 Jul 2024 22:47:14: [500 MB] 82000000 reads parsed INFO @ 04 Jul 2024 22:47:21: [502 MB] 83000000 reads parsed INFO @ 04 Jul 2024 22:47:27: [504 MB] 84000000 reads parsed INFO @ 04 Jul 2024 22:47:33: [506 MB] 85000000 reads parsed INFO @ 04 Jul 2024 22:47:39: [525 MB] 86000000 reads parsed INFO @ 04 Jul 2024 22:47:46: [529 MB] 87000000 reads parsed INFO @ 04 Jul 2024 22:47:52: [532 MB] 88000000 reads parsed INFO @ 04 Jul 2024 22:47:58: [536 MB] 89000000 reads parsed INFO @ 04 Jul 2024 22:48:05: [538 MB] 90000000 reads parsed INFO @ 04 Jul 2024 22:48:11: [540 MB] 91000000 reads parsed INFO @ 04 Jul 2024 22:48:17: [541 MB] 92000000 reads parsed INFO @ 04 Jul 2024 22:48:24: [544 MB] 93000000 reads parsed INFO @ 04 Jul 2024 22:48:30: [548 MB] 94000000 reads parsed INFO @ 04 Jul 2024 22:48:36: [552 MB] 95000000 reads parsed INFO @ 04 Jul 2024 22:48:43: [555 MB] 96000000 reads parsed INFO @ 04 Jul 2024 22:48:49: [557 MB] 97000000 reads parsed INFO @ 04 Jul 2024 22:48:55: [559 MB] 98000000 reads parsed INFO @ 04 Jul 2024 22:49:00: [559 MB] 99000000 reads parsed INFO @ 04 Jul 2024 22:49:06: [561 MB] 100000000 reads parsed INFO @ 04 Jul 2024 22:49:11: [563 MB] 101000000 reads parsed INFO @ 04 Jul 2024 22:49:17: [564 MB] 102000000 reads parsed INFO @ 04 Jul 2024 22:49:22: [567 MB] 103000000 reads parsed INFO @ 04 Jul 2024 22:49:28: [570 MB] 104000000 reads parsed INFO @ 04 Jul 2024 22:49:33: [574 MB] 105000000 reads parsed INFO @ 04 Jul 2024 22:49:39: [578 MB] 106000000 reads parsed INFO @ 04 Jul 2024 22:49:44: [582 MB] 107000000 reads parsed INFO @ 04 Jul 2024 22:49:50: [586 MB] 108000000 reads parsed INFO @ 04 Jul 2024 22:49:56: [590 MB] 109000000 reads parsed INFO @ 04 Jul 2024 22:50:05: [592 MB] #1 tag size is determined as 175 bps INFO @ 04 Jul 2024 22:50:05: [592 MB] #1 tag size = 175.0 INFO @ 04 Jul 2024 22:50:05: [592 MB] #1 total tags in treatment: 109902574 INFO @ 04 Jul 2024 22:50:05: [592 MB] #1 user defined the maximum tags... INFO @ 04 Jul 2024 22:50:05: [592 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 22:50:07: [592 MB] #1 tags after filtering in treatment: 70672347 INFO @ 04 Jul 2024 22:50:07: [592 MB] #1 Redundant rate of treatment: 0.36 INFO @ 04 Jul 2024 22:50:07: [592 MB] #1 finished! INFO @ 04 Jul 2024 22:50:07: [592 MB] #2 Build Peak Model... INFO @ 04 Jul 2024 22:50:07: [592 MB] #2 Skipped... INFO @ 04 Jul 2024 22:50:07: [592 MB] #2 Use 200 as fragment length INFO @ 04 Jul 2024 22:50:07: [592 MB] #2 Sequencing ends will be shifted towards 5' by 100 bp(s) INFO @ 04 Jul 2024 22:50:07: [592 MB] #3 Call peaks... INFO @ 04 Jul 2024 22:50:07: [592 MB] #3 Going to call summits inside each peak ... INFO @ 04 Jul 2024 22:50:07: [592 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 04 Jul 2024 23:00:58: [1587 MB] #3 Call peaks for each chromosome... INFO @ 04 Jul 2024 23:06:16: [1587 MB] #4 Write output xls file... /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/Astrocyte_peaks.xls INFO @ 04 Jul 2024 23:06:18: [1587 MB] #4 Write peak in narrowPeak format file... /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/Astrocyte_peaks.narrowPeak INFO @ 04 Jul 2024 23:06:18: [1587 MB] #4 Write summits bed file... /tscc/projects/ps-epigen/users/kdang/ASAP/DASeq_broadCT/callpeak_out/Astrocyte_summits.bed INFO @ 04 Jul 2024 23:06:19: [1587 MB] Done!