Job ID = 6366094 SRX = SRX059272 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:32:51 prefetch.2.10.7: 1) Downloading 'SRR190712'... 2020-06-15T22:32:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:33:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:33:25 prefetch.2.10.7: 'SRR190712' is valid 2020-06-15T22:33:25 prefetch.2.10.7: 1) 'SRR190712' was downloaded successfully Read 8055605 spots for SRR190712/SRR190712.sra Written 8055605 spots for SRR190712/SRR190712.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: 00:00:51 8055605 reads; of these: 8055605 (100.00%) were unpaired; of these: 3625148 (45.00%) aligned 0 times 3180093 (39.48%) aligned exactly 1 time 1250364 (15.52%) aligned >1 times 55.00% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 1929064 / 4430457 = 0.4354 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 07:35:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.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 07:35:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:00: 1000000 INFO @ Tue, 16 Jun 2020 07:36:05: 2000000 INFO @ Tue, 16 Jun 2020 07:36:07: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:36:07: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:36:07: #1 total tags in treatment: 2501393 INFO @ Tue, 16 Jun 2020 07:36:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:07: #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 07:36:07: #1 tags after filtering in treatment: 2501393 INFO @ Tue, 16 Jun 2020 07:36:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:07: #2 number of paired peaks: 1852 INFO @ Tue, 16 Jun 2020 07:36:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:07: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 07:36:07: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 16 Jun 2020 07:36:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.05_model.r INFO @ Tue, 16 Jun 2020 07:36:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:36:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.05_summits.bed INFO @ Tue, 16 Jun 2020 07:36:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1971 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 07:36:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.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 07:36:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:30: 1000000 INFO @ Tue, 16 Jun 2020 07:36:35: 2000000 INFO @ Tue, 16 Jun 2020 07:36:37: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:36:37: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:36:37: #1 total tags in treatment: 2501393 INFO @ Tue, 16 Jun 2020 07:36:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:37: #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 07:36:37: #1 tags after filtering in treatment: 2501393 INFO @ Tue, 16 Jun 2020 07:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:37: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:37: #2 number of paired peaks: 1852 INFO @ Tue, 16 Jun 2020 07:36:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:37: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 07:36:37: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 16 Jun 2020 07:36:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.10_model.r INFO @ Tue, 16 Jun 2020 07:36:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:36:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.10_summits.bed INFO @ Tue, 16 Jun 2020 07:36:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1703 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 07:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.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 07:36:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:37:00: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:37:05: 2000000 INFO @ Tue, 16 Jun 2020 07:37:07: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:37:07: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:37:07: #1 total tags in treatment: 2501393 INFO @ Tue, 16 Jun 2020 07:37:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:07: #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 07:37:07: #1 tags after filtering in treatment: 2501393 INFO @ Tue, 16 Jun 2020 07:37:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:07: #2 number of paired peaks: 1852 INFO @ Tue, 16 Jun 2020 07:37:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:07: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 07:37:07: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 16 Jun 2020 07:37:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.20_model.r INFO @ Tue, 16 Jun 2020 07:37:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:37:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059272/SRX059272.20_summits.bed INFO @ Tue, 16 Jun 2020 07:37:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1433 records, 4 fields): 3 millis CompletedMACS2peakCalling