Job ID = 2002532 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,232,414 reads read : 24,232,414 reads written : 24,232,414 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR572251.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:54:19 24232414 reads; of these: 24232414 (100.00%) were unpaired; of these: 661392 (2.73%) aligned 0 times 20482236 (84.52%) aligned exactly 1 time 3088786 (12.75%) aligned >1 times 97.27% overall alignment rate Time searching: 00:54:22 Overall time: 00:54:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 1072253 / 23571022 = 0.0455 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 13:06:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # 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 INFO @ Fri, 05 Jul 2019 13:06:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:06:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:06:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # 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 INFO @ Fri, 05 Jul 2019 13:06:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:06:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:06:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # 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 INFO @ Fri, 05 Jul 2019 13:06:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:06:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:06:54: 1000000 INFO @ Fri, 05 Jul 2019 13:06:58: 1000000 INFO @ Fri, 05 Jul 2019 13:06:58: 1000000 INFO @ Fri, 05 Jul 2019 13:07:03: 2000000 INFO @ Fri, 05 Jul 2019 13:07:11: 2000000 INFO @ Fri, 05 Jul 2019 13:07:11: 2000000 INFO @ Fri, 05 Jul 2019 13:07:12: 3000000 INFO @ Fri, 05 Jul 2019 13:07:21: 4000000 INFO @ Fri, 05 Jul 2019 13:07:23: 3000000 INFO @ Fri, 05 Jul 2019 13:07:24: 3000000 INFO @ Fri, 05 Jul 2019 13:07:31: 5000000 INFO @ Fri, 05 Jul 2019 13:07:36: 4000000 INFO @ Fri, 05 Jul 2019 13:07:37: 4000000 INFO @ Fri, 05 Jul 2019 13:07:40: 6000000 INFO @ Fri, 05 Jul 2019 13:07:49: 5000000 INFO @ Fri, 05 Jul 2019 13:07:49: 7000000 INFO @ Fri, 05 Jul 2019 13:07:49: 5000000 INFO @ Fri, 05 Jul 2019 13:07:58: 8000000 INFO @ Fri, 05 Jul 2019 13:08:02: 6000000 INFO @ Fri, 05 Jul 2019 13:08:02: 6000000 INFO @ Fri, 05 Jul 2019 13:08:08: 9000000 INFO @ Fri, 05 Jul 2019 13:08:15: 7000000 INFO @ Fri, 05 Jul 2019 13:08:15: 7000000 INFO @ Fri, 05 Jul 2019 13:08:17: 10000000 INFO @ Fri, 05 Jul 2019 13:08:26: 11000000 INFO @ Fri, 05 Jul 2019 13:08:28: 8000000 INFO @ Fri, 05 Jul 2019 13:08:28: 8000000 INFO @ Fri, 05 Jul 2019 13:08:36: 12000000 INFO @ Fri, 05 Jul 2019 13:08:41: 9000000 INFO @ Fri, 05 Jul 2019 13:08:41: 9000000 INFO @ Fri, 05 Jul 2019 13:08:45: 13000000 INFO @ Fri, 05 Jul 2019 13:08:53: 10000000 INFO @ Fri, 05 Jul 2019 13:08:54: 10000000 INFO @ Fri, 05 Jul 2019 13:08:55: 14000000 INFO @ Fri, 05 Jul 2019 13:09:04: 15000000 INFO @ Fri, 05 Jul 2019 13:09:07: 11000000 INFO @ Fri, 05 Jul 2019 13:09:08: 11000000 INFO @ Fri, 05 Jul 2019 13:09:14: 16000000 INFO @ Fri, 05 Jul 2019 13:09:21: 12000000 INFO @ Fri, 05 Jul 2019 13:09:22: 12000000 INFO @ Fri, 05 Jul 2019 13:09:23: 17000000 INFO @ Fri, 05 Jul 2019 13:09:32: 18000000 INFO @ Fri, 05 Jul 2019 13:09:34: 13000000 INFO @ Fri, 05 Jul 2019 13:09:35: 13000000 INFO @ Fri, 05 Jul 2019 13:09:41: 19000000 INFO @ Fri, 05 Jul 2019 13:09:47: 14000000 INFO @ Fri, 05 Jul 2019 13:09:48: 14000000 INFO @ Fri, 05 Jul 2019 13:09:51: 20000000 INFO @ Fri, 05 Jul 2019 13:10:00: 15000000 INFO @ Fri, 05 Jul 2019 13:10:00: 21000000 INFO @ Fri, 05 Jul 2019 13:10:01: 15000000 INFO @ Fri, 05 Jul 2019 13:10:09: 22000000 INFO @ Fri, 05 Jul 2019 13:10:14: 16000000 INFO @ Fri, 05 Jul 2019 13:10:14: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 13:10:14: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 13:10:14: #1 total tags in treatment: 22498769 INFO @ Fri, 05 Jul 2019 13:10:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:10:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:10:15: #1 tags after filtering in treatment: 22498550 INFO @ Fri, 05 Jul 2019 13:10:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:10:15: #1 finished! INFO @ Fri, 05 Jul 2019 13:10:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:10:15: 16000000 INFO @ Fri, 05 Jul 2019 13:10:22: #2 number of paired peaks: 119548 INFO @ Fri, 05 Jul 2019 13:10:23: start model_add_line... INFO @ Fri, 05 Jul 2019 13:10:23: start X-correlation... INFO @ Fri, 05 Jul 2019 13:10:24: end of X-cor INFO @ Fri, 05 Jul 2019 13:10:24: #2 finished! INFO @ Fri, 05 Jul 2019 13:10:24: #2 predicted fragment length is 236 bps INFO @ Fri, 05 Jul 2019 13:10:24: #2 alternative fragment length(s) may be 236 bps INFO @ Fri, 05 Jul 2019 13:10:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.20_model.r INFO @ Fri, 05 Jul 2019 13:10:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:10:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:10:27: 17000000 INFO @ Fri, 05 Jul 2019 13:10:29: 17000000 INFO @ Fri, 05 Jul 2019 13:10:40: 18000000 INFO @ Fri, 05 Jul 2019 13:10:42: 18000000 INFO @ Fri, 05 Jul 2019 13:10:53: 19000000 INFO @ Fri, 05 Jul 2019 13:10:55: 19000000 INFO @ Fri, 05 Jul 2019 13:11:08: 20000000 INFO @ Fri, 05 Jul 2019 13:11:08: 20000000 INFO @ Fri, 05 Jul 2019 13:11:21: 21000000 INFO @ Fri, 05 Jul 2019 13:11:21: 21000000 INFO @ Fri, 05 Jul 2019 13:11:34: 22000000 INFO @ Fri, 05 Jul 2019 13:11:34: 22000000 INFO @ Fri, 05 Jul 2019 13:11:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:11:40: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 13:11:40: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 13:11:40: #1 total tags in treatment: 22498769 INFO @ Fri, 05 Jul 2019 13:11:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:11:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:11:41: #1 tags after filtering in treatment: 22498550 INFO @ Fri, 05 Jul 2019 13:11:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:11:41: #1 finished! INFO @ Fri, 05 Jul 2019 13:11:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:11:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:11:41: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 13:11:41: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 13:11:41: #1 total tags in treatment: 22498769 INFO @ Fri, 05 Jul 2019 13:11:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:11:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:11:42: #1 tags after filtering in treatment: 22498550 INFO @ Fri, 05 Jul 2019 13:11:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:11:42: #1 finished! INFO @ Fri, 05 Jul 2019 13:11:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:11:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:11:48: #2 number of paired peaks: 119548 INFO @ Fri, 05 Jul 2019 13:11:48: start model_add_line... INFO @ Fri, 05 Jul 2019 13:11:49: start X-correlation... INFO @ Fri, 05 Jul 2019 13:11:49: end of X-cor INFO @ Fri, 05 Jul 2019 13:11:49: #2 finished! INFO @ Fri, 05 Jul 2019 13:11:49: #2 predicted fragment length is 236 bps INFO @ Fri, 05 Jul 2019 13:11:49: #2 alternative fragment length(s) may be 236 bps INFO @ Fri, 05 Jul 2019 13:11:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.05_model.r INFO @ Fri, 05 Jul 2019 13:11:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:11:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:11:49: #2 number of paired peaks: 119548 INFO @ Fri, 05 Jul 2019 13:11:49: start model_add_line... INFO @ Fri, 05 Jul 2019 13:11:50: start X-correlation... INFO @ Fri, 05 Jul 2019 13:11:50: end of X-cor INFO @ Fri, 05 Jul 2019 13:11:50: #2 finished! INFO @ Fri, 05 Jul 2019 13:11:50: #2 predicted fragment length is 236 bps INFO @ Fri, 05 Jul 2019 13:11:50: #2 alternative fragment length(s) may be 236 bps INFO @ Fri, 05 Jul 2019 13:11:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.10_model.r INFO @ Fri, 05 Jul 2019 13:11:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:12:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.20_peaks.xls INFO @ Fri, 05 Jul 2019 13:12:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:12:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.20_summits.bed INFO @ Fri, 05 Jul 2019 13:12:17: Done! pass1 - making usageList (56 chroms): 5 millis pass2 - checking and writing primary data (10156 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:13:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:13:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:13:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.05_peaks.xls INFO @ Fri, 05 Jul 2019 13:13:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:13:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.10_peaks.xls INFO @ Fri, 05 Jul 2019 13:13:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.05_summits.bed INFO @ Fri, 05 Jul 2019 13:13:44: Done! INFO @ Fri, 05 Jul 2019 13:13:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:13:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530985/ERX530985.10_summits.bed INFO @ Fri, 05 Jul 2019 13:13:45: Done! pass1 - making usageList (122 chroms): 7 millis pass2 - checking and writing primary data (35591 records, 4 fields): 49 millis pass1 - making usageList (96 chroms): 8 millis pass2 - checking and writing primary data (21950 records, 4 fields): 33 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。