Job ID = 2640615 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,755,847 reads read : 33,511,694 reads written : 16,755,847 reads 0-length : 16,755,847 rm: cannot remove ‘[DSE]RR*’: 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: 00:14:18 16755847 reads; of these: 16755847 (100.00%) were unpaired; of these: 764455 (4.56%) aligned 0 times 11999797 (71.62%) aligned exactly 1 time 3991595 (23.82%) aligned >1 times 95.44% overall alignment rate Time searching: 00:14:21 Overall time: 00:14:21 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 8 files... [bam_rmdupse_core] 1057438 / 15991392 = 0.0661 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:28:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.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 @ Sat, 24 Aug 2019 18:28:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:28:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:28:48: 1000000 INFO @ Sat, 24 Aug 2019 18:28:57: 2000000 INFO @ Sat, 24 Aug 2019 18:29:07: 3000000 INFO @ Sat, 24 Aug 2019 18:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.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 @ Sat, 24 Aug 2019 18:29:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:29:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:29:16: 4000000 INFO @ Sat, 24 Aug 2019 18:29:16: 1000000 INFO @ Sat, 24 Aug 2019 18:29:24: 2000000 INFO @ Sat, 24 Aug 2019 18:29:25: 5000000 INFO @ Sat, 24 Aug 2019 18:29:32: 3000000 INFO @ Sat, 24 Aug 2019 18:29:34: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:29:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.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 @ Sat, 24 Aug 2019 18:29:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:29:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:29:39: 4000000 INFO @ Sat, 24 Aug 2019 18:29:43: 7000000 INFO @ Sat, 24 Aug 2019 18:29:46: 1000000 INFO @ Sat, 24 Aug 2019 18:29:48: 5000000 INFO @ Sat, 24 Aug 2019 18:29:53: 8000000 INFO @ Sat, 24 Aug 2019 18:29:55: 2000000 INFO @ Sat, 24 Aug 2019 18:29:56: 6000000 INFO @ Sat, 24 Aug 2019 18:30:02: 9000000 INFO @ Sat, 24 Aug 2019 18:30:04: 3000000 INFO @ Sat, 24 Aug 2019 18:30:05: 7000000 INFO @ Sat, 24 Aug 2019 18:30:12: 10000000 INFO @ Sat, 24 Aug 2019 18:30:12: 4000000 INFO @ Sat, 24 Aug 2019 18:30:13: 8000000 INFO @ Sat, 24 Aug 2019 18:30:21: 5000000 INFO @ Sat, 24 Aug 2019 18:30:21: 11000000 INFO @ Sat, 24 Aug 2019 18:30:22: 9000000 INFO @ Sat, 24 Aug 2019 18:30:29: 6000000 INFO @ Sat, 24 Aug 2019 18:30:30: 12000000 INFO @ Sat, 24 Aug 2019 18:30:30: 10000000 INFO @ Sat, 24 Aug 2019 18:30:38: 7000000 INFO @ Sat, 24 Aug 2019 18:30:39: 11000000 INFO @ Sat, 24 Aug 2019 18:30:40: 13000000 INFO @ Sat, 24 Aug 2019 18:30:47: 8000000 INFO @ Sat, 24 Aug 2019 18:30:48: 12000000 INFO @ Sat, 24 Aug 2019 18:30:49: 14000000 INFO @ Sat, 24 Aug 2019 18:30:55: 9000000 INFO @ Sat, 24 Aug 2019 18:30:56: 13000000 INFO @ Sat, 24 Aug 2019 18:30:58: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:30:58: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:30:58: #1 total tags in treatment: 14933954 INFO @ Sat, 24 Aug 2019 18:30:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:30:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:30:58: #1 tags after filtering in treatment: 14933770 INFO @ Sat, 24 Aug 2019 18:30:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:30:58: #1 finished! INFO @ Sat, 24 Aug 2019 18:30:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:31:00: #2 number of paired peaks: 10503 INFO @ Sat, 24 Aug 2019 18:31:00: start model_add_line... INFO @ Sat, 24 Aug 2019 18:31:00: start X-correlation... INFO @ Sat, 24 Aug 2019 18:31:00: end of X-cor INFO @ Sat, 24 Aug 2019 18:31:00: #2 finished! INFO @ Sat, 24 Aug 2019 18:31:00: #2 predicted fragment length is 117 bps INFO @ Sat, 24 Aug 2019 18:31:00: #2 alternative fragment length(s) may be 117 bps INFO @ Sat, 24 Aug 2019 18:31:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.05_model.r INFO @ Sat, 24 Aug 2019 18:31:00: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:31:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:31:04: 10000000 INFO @ Sat, 24 Aug 2019 18:31:05: 14000000 INFO @ Sat, 24 Aug 2019 18:31:12: 11000000 INFO @ Sat, 24 Aug 2019 18:31:13: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:31:13: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:31:13: #1 total tags in treatment: 14933954 INFO @ Sat, 24 Aug 2019 18:31:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:31:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:31:13: #1 tags after filtering in treatment: 14933770 INFO @ Sat, 24 Aug 2019 18:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:31:13: #1 finished! INFO @ Sat, 24 Aug 2019 18:31:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:31:16: #2 number of paired peaks: 10503 INFO @ Sat, 24 Aug 2019 18:31:16: start model_add_line... INFO @ Sat, 24 Aug 2019 18:31:16: start X-correlation... INFO @ Sat, 24 Aug 2019 18:31:16: end of X-cor INFO @ Sat, 24 Aug 2019 18:31:16: #2 finished! INFO @ Sat, 24 Aug 2019 18:31:16: #2 predicted fragment length is 117 bps INFO @ Sat, 24 Aug 2019 18:31:16: #2 alternative fragment length(s) may be 117 bps INFO @ Sat, 24 Aug 2019 18:31:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.10_model.r INFO @ Sat, 24 Aug 2019 18:31:16: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:31:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:31:20: 12000000 INFO @ Sat, 24 Aug 2019 18:31:28: 13000000 INFO @ Sat, 24 Aug 2019 18:31:36: 14000000 INFO @ Sat, 24 Aug 2019 18:31:43: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:31:43: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:31:43: #1 total tags in treatment: 14933954 INFO @ Sat, 24 Aug 2019 18:31:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:31:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:31:43: #1 tags after filtering in treatment: 14933770 INFO @ Sat, 24 Aug 2019 18:31:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:31:43: #1 finished! INFO @ Sat, 24 Aug 2019 18:31:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:31:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:31:46: #2 number of paired peaks: 10503 INFO @ Sat, 24 Aug 2019 18:31:46: start model_add_line... INFO @ Sat, 24 Aug 2019 18:31:46: start X-correlation... INFO @ Sat, 24 Aug 2019 18:31:46: end of X-cor INFO @ Sat, 24 Aug 2019 18:31:46: #2 finished! INFO @ Sat, 24 Aug 2019 18:31:46: #2 predicted fragment length is 117 bps INFO @ Sat, 24 Aug 2019 18:31:46: #2 alternative fragment length(s) may be 117 bps INFO @ Sat, 24 Aug 2019 18:31:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.20_model.r INFO @ Sat, 24 Aug 2019 18:31:46: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:31:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:31:48: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:32:04: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:32:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.05_summits.bed INFO @ Sat, 24 Aug 2019 18:32:12: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (2665 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:32:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:32:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:32:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.10_summits.bed INFO @ Sat, 24 Aug 2019 18:32:27: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (1145 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:32:34: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:32:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:32:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:32:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375038/SRX5375038.20_summits.bed INFO @ Sat, 24 Aug 2019 18:32:57: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (386 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。