Job ID = 6368564 SRX = SRX5020790 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:16:06 prefetch.2.10.7: 1) Downloading 'SRR8201413'... 2020-06-16T00:16:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:55 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:56 prefetch.2.10.7: 'SRR8201413' is valid 2020-06-16T00:16:56 prefetch.2.10.7: 1) 'SRR8201413' was downloaded successfully Read 5515691 spots for SRR8201413/SRR8201413.sra Written 5515691 spots for SRR8201413/SRR8201413.sra 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:10 5515691 reads; of these: 5515691 (100.00%) were unpaired; of these: 441397 (8.00%) aligned 0 times 4356682 (78.99%) aligned exactly 1 time 717612 (13.01%) aligned >1 times 92.00% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 566392 / 5074294 = 0.1116 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 @ Tue, 16 Jun 2020 09:20:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:20:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:16: 1000000 INFO @ Tue, 16 Jun 2020 09:20:22: 2000000 INFO @ Tue, 16 Jun 2020 09:20:28: 3000000 INFO @ Tue, 16 Jun 2020 09:20:33: 4000000 INFO @ Tue, 16 Jun 2020 09:20:36: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:36: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:36: #1 total tags in treatment: 4507902 INFO @ Tue, 16 Jun 2020 09:20:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:20:36: #1 tags after filtering in treatment: 4507902 INFO @ Tue, 16 Jun 2020 09:20:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:37: #2 number of paired peaks: 1617 INFO @ Tue, 16 Jun 2020 09:20:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:37: #2 predicted fragment length is 181 bps INFO @ Tue, 16 Jun 2020 09:20:37: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 16 Jun 2020 09:20:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.05_model.r INFO @ Tue, 16 Jun 2020 09:20:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:37: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 16 Jun 2020 09:20:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:20:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:47: 1000000 INFO @ Tue, 16 Jun 2020 09:20:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1702 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:53: 2000000 INFO @ Tue, 16 Jun 2020 09:20:59: 3000000 INFO @ Tue, 16 Jun 2020 09:21:05: 4000000 INFO @ Tue, 16 Jun 2020 09:21:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:21:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:21:07: #1 total tags in treatment: 4507902 INFO @ Tue, 16 Jun 2020 09:21:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:21:07: #1 tags after filtering in treatment: 4507902 INFO @ Tue, 16 Jun 2020 09:21:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:08: #2 number of paired peaks: 1617 INFO @ Tue, 16 Jun 2020 09:21:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:08: #2 predicted fragment length is 181 bps INFO @ Tue, 16 Jun 2020 09:21:08: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 16 Jun 2020 09:21:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.10_model.r INFO @ Tue, 16 Jun 2020 09:21:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:08: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 16 Jun 2020 09:21:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:21:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:16: 1000000 INFO @ Tue, 16 Jun 2020 09:21:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:21: 2000000 INFO @ Tue, 16 Jun 2020 09:21:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1045 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:27: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:21:33: 4000000 INFO @ Tue, 16 Jun 2020 09:21:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:21:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:21:35: #1 total tags in treatment: 4507902 INFO @ Tue, 16 Jun 2020 09:21:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:21:35: #1 tags after filtering in treatment: 4507902 INFO @ Tue, 16 Jun 2020 09:21:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:36: #2 number of paired peaks: 1617 INFO @ Tue, 16 Jun 2020 09:21:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:36: #2 predicted fragment length is 181 bps INFO @ Tue, 16 Jun 2020 09:21:36: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 16 Jun 2020 09:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.20_model.r INFO @ Tue, 16 Jun 2020 09:21:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:21:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020790/SRX5020790.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (558 records, 4 fields): 1 millis CompletedMACS2peakCalling