Job ID = 5790706 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,717,086 reads read : 19,717,086 reads written : 19,717,086 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:14 19717086 reads; of these: 19717086 (100.00%) were unpaired; of these: 4510207 (22.87%) aligned 0 times 11449058 (58.07%) aligned exactly 1 time 3757821 (19.06%) aligned >1 times 77.13% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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_rmdupse_core] 3329192 / 15206879 = 0.2189 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 06:37:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.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 06:37:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:37:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:37:14: 1000000 INFO @ Wed, 22 Apr 2020 06:37:20: 2000000 INFO @ Wed, 22 Apr 2020 06:37:27: 3000000 INFO @ Wed, 22 Apr 2020 06:37:33: 4000000 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 06:37:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.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 06:37:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:37:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:37:39: 5000000 INFO @ Wed, 22 Apr 2020 06:37:44: 1000000 INFO @ Wed, 22 Apr 2020 06:37:46: 6000000 INFO @ Wed, 22 Apr 2020 06:37:50: 2000000 INFO @ Wed, 22 Apr 2020 06:37:53: 7000000 INFO @ Wed, 22 Apr 2020 06:37:56: 3000000 INFO @ Wed, 22 Apr 2020 06:37:59: 8000000 INFO @ Wed, 22 Apr 2020 06:38:03: 4000000 INFO @ Wed, 22 Apr 2020 06:38:06: 9000000 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 06:38:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.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 06:38:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:38:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:38:09: 5000000 INFO @ Wed, 22 Apr 2020 06:38:13: 10000000 INFO @ Wed, 22 Apr 2020 06:38:15: 1000000 INFO @ Wed, 22 Apr 2020 06:38:15: 6000000 INFO @ Wed, 22 Apr 2020 06:38:19: 11000000 INFO @ Wed, 22 Apr 2020 06:38:22: 7000000 INFO @ Wed, 22 Apr 2020 06:38:22: 2000000 INFO @ Wed, 22 Apr 2020 06:38:26: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:38:26: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:38:26: #1 total tags in treatment: 11877687 INFO @ Wed, 22 Apr 2020 06:38:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:38:26: #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 06:38:26: #1 tags after filtering in treatment: 11877498 INFO @ Wed, 22 Apr 2020 06:38:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:38:26: #1 finished! INFO @ Wed, 22 Apr 2020 06:38:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:38:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:38:28: 8000000 INFO @ Wed, 22 Apr 2020 06:38:28: #2 number of paired peaks: 39264 INFO @ Wed, 22 Apr 2020 06:38:28: start model_add_line... INFO @ Wed, 22 Apr 2020 06:38:28: start X-correlation... INFO @ Wed, 22 Apr 2020 06:38:28: end of X-cor INFO @ Wed, 22 Apr 2020 06:38:28: #2 finished! INFO @ Wed, 22 Apr 2020 06:38:28: #2 predicted fragment length is 202 bps INFO @ Wed, 22 Apr 2020 06:38:28: #2 alternative fragment length(s) may be 202 bps INFO @ Wed, 22 Apr 2020 06:38:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.05_model.r INFO @ Wed, 22 Apr 2020 06:38:28: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:38:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:38:29: 3000000 INFO @ Wed, 22 Apr 2020 06:38:34: 9000000 INFO @ Wed, 22 Apr 2020 06:38:35: 4000000 INFO @ Wed, 22 Apr 2020 06:38:40: 10000000 INFO @ Wed, 22 Apr 2020 06:38:42: 5000000 INFO @ Wed, 22 Apr 2020 06:38:46: 11000000 INFO @ Wed, 22 Apr 2020 06:38:49: 6000000 INFO @ Wed, 22 Apr 2020 06:38:52: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:38:52: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:38:52: #1 total tags in treatment: 11877687 INFO @ Wed, 22 Apr 2020 06:38:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:38:52: #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 06:38:52: #1 tags after filtering in treatment: 11877498 INFO @ Wed, 22 Apr 2020 06:38:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:38:52: #1 finished! INFO @ Wed, 22 Apr 2020 06:38:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:38:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:38:54: #2 number of paired peaks: 39264 INFO @ Wed, 22 Apr 2020 06:38:54: start model_add_line... INFO @ Wed, 22 Apr 2020 06:38:54: start X-correlation... INFO @ Wed, 22 Apr 2020 06:38:54: end of X-cor INFO @ Wed, 22 Apr 2020 06:38:54: #2 finished! INFO @ Wed, 22 Apr 2020 06:38:54: #2 predicted fragment length is 202 bps INFO @ Wed, 22 Apr 2020 06:38:54: #2 alternative fragment length(s) may be 202 bps INFO @ Wed, 22 Apr 2020 06:38:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.10_model.r INFO @ Wed, 22 Apr 2020 06:38:54: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:38:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:38:55: 7000000 INFO @ Wed, 22 Apr 2020 06:38:57: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:39:01: 8000000 INFO @ Wed, 22 Apr 2020 06:39:07: 9000000 INFO @ Wed, 22 Apr 2020 06:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:39:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:39:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.05_summits.bed INFO @ Wed, 22 Apr 2020 06:39:11: Done! pass1 - making usageList (99 chroms): 2 millis pass2 - checking and writing primary data (14587 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:39:14: 10000000 INFO @ Wed, 22 Apr 2020 06:39:20: 11000000 INFO @ Wed, 22 Apr 2020 06:39:22: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:39:25: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:39:25: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:39:25: #1 total tags in treatment: 11877687 INFO @ Wed, 22 Apr 2020 06:39:25: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:39:25: #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 06:39:26: #1 tags after filtering in treatment: 11877498 INFO @ Wed, 22 Apr 2020 06:39:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:39:26: #1 finished! INFO @ Wed, 22 Apr 2020 06:39:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:39:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:39:28: #2 number of paired peaks: 39264 INFO @ Wed, 22 Apr 2020 06:39:28: start model_add_line... INFO @ Wed, 22 Apr 2020 06:39:28: start X-correlation... INFO @ Wed, 22 Apr 2020 06:39:28: end of X-cor INFO @ Wed, 22 Apr 2020 06:39:28: #2 finished! INFO @ Wed, 22 Apr 2020 06:39:28: #2 predicted fragment length is 202 bps INFO @ Wed, 22 Apr 2020 06:39:28: #2 alternative fragment length(s) may be 202 bps INFO @ Wed, 22 Apr 2020 06:39:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.20_model.r INFO @ Wed, 22 Apr 2020 06:39:28: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:39:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:39:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:39:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:39:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.10_summits.bed INFO @ Wed, 22 Apr 2020 06:39:36: Done! pass1 - making usageList (84 chroms): 2 millis pass2 - checking and writing primary data (11535 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:39:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:40:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:40:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:40:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761737/SRX5761737.20_summits.bed INFO @ Wed, 22 Apr 2020 06:40:10: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (8973 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。