Job ID = 5790661 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 39,979,304 reads read : 39,979,304 reads written : 39,979,304 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8982399.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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:50 39979304 reads; of these: 39979304 (100.00%) were unpaired; of these: 4953012 (12.39%) aligned 0 times 27369664 (68.46%) aligned exactly 1 time 7656628 (19.15%) aligned >1 times 87.61% overall alignment rate Time searching: 00:09:52 Overall time: 00:09:52 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] 11483838 / 35026292 = 0.3279 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 05:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.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 @ Wed, 22 Apr 2020 05:29:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:29:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:29:59: 1000000 INFO @ Wed, 22 Apr 2020 05:30:04: 2000000 INFO @ Wed, 22 Apr 2020 05:30:08: 3000000 INFO @ Wed, 22 Apr 2020 05:30:13: 4000000 INFO @ Wed, 22 Apr 2020 05:30:18: 5000000 INFO @ Wed, 22 Apr 2020 05:30:22: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 05:30:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.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 @ Wed, 22 Apr 2020 05:30:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:30:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:30:27: 7000000 INFO @ Wed, 22 Apr 2020 05:30:30: 1000000 INFO @ Wed, 22 Apr 2020 05:30:31: 8000000 INFO @ Wed, 22 Apr 2020 05:30:34: 2000000 INFO @ Wed, 22 Apr 2020 05:30:36: 9000000 INFO @ Wed, 22 Apr 2020 05:30:39: 3000000 INFO @ Wed, 22 Apr 2020 05:30:40: 10000000 INFO @ Wed, 22 Apr 2020 05:30:44: 4000000 INFO @ Wed, 22 Apr 2020 05:30:45: 11000000 INFO @ Wed, 22 Apr 2020 05:30:48: 5000000 INFO @ Wed, 22 Apr 2020 05:30:50: 12000000 INFO @ Wed, 22 Apr 2020 05:30:53: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 05:30:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.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 @ Wed, 22 Apr 2020 05:30:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:30:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:30:55: 13000000 INFO @ Wed, 22 Apr 2020 05:30:58: 7000000 INFO @ Wed, 22 Apr 2020 05:31:00: 1000000 INFO @ Wed, 22 Apr 2020 05:31:00: 14000000 INFO @ Wed, 22 Apr 2020 05:31:02: 8000000 INFO @ Wed, 22 Apr 2020 05:31:04: 2000000 INFO @ Wed, 22 Apr 2020 05:31:04: 15000000 INFO @ Wed, 22 Apr 2020 05:31:07: 9000000 INFO @ Wed, 22 Apr 2020 05:31:09: 16000000 INFO @ Wed, 22 Apr 2020 05:31:09: 3000000 INFO @ Wed, 22 Apr 2020 05:31:12: 10000000 INFO @ Wed, 22 Apr 2020 05:31:13: 4000000 INFO @ Wed, 22 Apr 2020 05:31:13: 17000000 INFO @ Wed, 22 Apr 2020 05:31:16: 11000000 INFO @ Wed, 22 Apr 2020 05:31:18: 18000000 INFO @ Wed, 22 Apr 2020 05:31:18: 5000000 INFO @ Wed, 22 Apr 2020 05:31:21: 12000000 INFO @ Wed, 22 Apr 2020 05:31:23: 19000000 INFO @ Wed, 22 Apr 2020 05:31:23: 6000000 INFO @ Wed, 22 Apr 2020 05:31:26: 13000000 INFO @ Wed, 22 Apr 2020 05:31:27: 7000000 INFO @ Wed, 22 Apr 2020 05:31:28: 20000000 INFO @ Wed, 22 Apr 2020 05:31:31: 14000000 INFO @ Wed, 22 Apr 2020 05:31:32: 8000000 INFO @ Wed, 22 Apr 2020 05:31:32: 21000000 INFO @ Wed, 22 Apr 2020 05:31:35: 15000000 INFO @ Wed, 22 Apr 2020 05:31:37: 9000000 INFO @ Wed, 22 Apr 2020 05:31:37: 22000000 INFO @ Wed, 22 Apr 2020 05:31:40: 16000000 INFO @ Wed, 22 Apr 2020 05:31:41: 10000000 INFO @ Wed, 22 Apr 2020 05:31:42: 23000000 INFO @ Wed, 22 Apr 2020 05:31:44: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:31:44: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:31:44: #1 total tags in treatment: 23542454 INFO @ Wed, 22 Apr 2020 05:31:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:31:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:31:44: 17000000 INFO @ Wed, 22 Apr 2020 05:31:45: #1 tags after filtering in treatment: 23542325 INFO @ Wed, 22 Apr 2020 05:31:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:31:45: #1 finished! INFO @ Wed, 22 Apr 2020 05:31:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:31:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:31:46: 11000000 INFO @ Wed, 22 Apr 2020 05:31:48: #2 number of paired peaks: 23375 INFO @ Wed, 22 Apr 2020 05:31:48: start model_add_line... INFO @ Wed, 22 Apr 2020 05:31:48: start X-correlation... INFO @ Wed, 22 Apr 2020 05:31:48: end of X-cor INFO @ Wed, 22 Apr 2020 05:31:48: #2 finished! INFO @ Wed, 22 Apr 2020 05:31:48: #2 predicted fragment length is 174 bps INFO @ Wed, 22 Apr 2020 05:31:48: #2 alternative fragment length(s) may be 174 bps INFO @ Wed, 22 Apr 2020 05:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.05_model.r INFO @ Wed, 22 Apr 2020 05:31:48: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:31:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:31:49: 18000000 INFO @ Wed, 22 Apr 2020 05:31:50: 12000000 INFO @ Wed, 22 Apr 2020 05:31:54: 19000000 INFO @ Wed, 22 Apr 2020 05:31:55: 13000000 INFO @ Wed, 22 Apr 2020 05:31:58: 20000000 INFO @ Wed, 22 Apr 2020 05:32:00: 14000000 INFO @ Wed, 22 Apr 2020 05:32:03: 21000000 INFO @ Wed, 22 Apr 2020 05:32:05: 15000000 INFO @ Wed, 22 Apr 2020 05:32:08: 22000000 INFO @ Wed, 22 Apr 2020 05:32:09: 16000000 INFO @ Wed, 22 Apr 2020 05:32:12: 23000000 INFO @ Wed, 22 Apr 2020 05:32:14: 17000000 INFO @ Wed, 22 Apr 2020 05:32:15: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:32:15: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:32:15: #1 total tags in treatment: 23542454 INFO @ Wed, 22 Apr 2020 05:32:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:32:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:32:16: #1 tags after filtering in treatment: 23542325 INFO @ Wed, 22 Apr 2020 05:32:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:32:16: #1 finished! INFO @ Wed, 22 Apr 2020 05:32:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:32:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:32:18: #2 number of paired peaks: 23375 INFO @ Wed, 22 Apr 2020 05:32:18: start model_add_line... INFO @ Wed, 22 Apr 2020 05:32:18: 18000000 INFO @ Wed, 22 Apr 2020 05:32:19: start X-correlation... INFO @ Wed, 22 Apr 2020 05:32:19: end of X-cor INFO @ Wed, 22 Apr 2020 05:32:19: #2 finished! INFO @ Wed, 22 Apr 2020 05:32:19: #2 predicted fragment length is 174 bps INFO @ Wed, 22 Apr 2020 05:32:19: #2 alternative fragment length(s) may be 174 bps INFO @ Wed, 22 Apr 2020 05:32:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.10_model.r INFO @ Wed, 22 Apr 2020 05:32:19: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:32:23: 19000000 INFO @ Wed, 22 Apr 2020 05:32:28: 20000000 INFO @ Wed, 22 Apr 2020 05:32:32: 21000000 INFO @ Wed, 22 Apr 2020 05:32:37: 22000000 INFO @ Wed, 22 Apr 2020 05:32:39: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:32:41: 23000000 INFO @ Wed, 22 Apr 2020 05:32:44: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:32:44: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:32:44: #1 total tags in treatment: 23542454 INFO @ Wed, 22 Apr 2020 05:32:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:32:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:32:45: #1 tags after filtering in treatment: 23542325 INFO @ Wed, 22 Apr 2020 05:32:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:32:45: #1 finished! INFO @ Wed, 22 Apr 2020 05:32:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:32:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:32:47: #2 number of paired peaks: 23375 INFO @ Wed, 22 Apr 2020 05:32:47: start model_add_line... INFO @ Wed, 22 Apr 2020 05:32:48: start X-correlation... INFO @ Wed, 22 Apr 2020 05:32:48: end of X-cor INFO @ Wed, 22 Apr 2020 05:32:48: #2 finished! INFO @ Wed, 22 Apr 2020 05:32:48: #2 predicted fragment length is 174 bps INFO @ Wed, 22 Apr 2020 05:32:48: #2 alternative fragment length(s) may be 174 bps INFO @ Wed, 22 Apr 2020 05:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.20_model.r INFO @ Wed, 22 Apr 2020 05:32:48: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:32:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:33:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:33:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:33:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.05_summits.bed INFO @ Wed, 22 Apr 2020 05:33:09: Done! pass1 - making usageList (123 chroms): 3 millis pass2 - checking and writing primary data (17918 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:33:10: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:33:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:33:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:33:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.10_summits.bed INFO @ Wed, 22 Apr 2020 05:33:36: Done! pass1 - making usageList (106 chroms): 2 millis pass2 - checking and writing primary data (15521 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:33:41: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:34:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:34:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:34:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761697/SRX5761697.20_summits.bed INFO @ Wed, 22 Apr 2020 05:34:07: Done! pass1 - making usageList (87 chroms): 2 millis pass2 - checking and writing primary data (13100 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。