Job ID = 6366074 SRX = SRX059246 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:49:07 prefetch.2.10.7: 1) Downloading 'SRR190686'... 2020-06-15T22:49:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:36 prefetch.2.10.7: 'SRR190686' is valid 2020-06-15T22:49:36 prefetch.2.10.7: 1) 'SRR190686' was downloaded successfully Read 4391606 spots for SRR190686/SRR190686.sra Written 4391606 spots for SRR190686/SRR190686.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: 00:00:41 4391606 reads; of these: 4391606 (100.00%) were unpaired; of these: 69971 (1.59%) aligned 0 times 3569933 (81.29%) aligned exactly 1 time 751702 (17.12%) aligned >1 times 98.41% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 1028057 / 4321635 = 0.2379 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 07:51:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.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 07:51:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:00: 1000000 INFO @ Tue, 16 Jun 2020 07:52:05: 2000000 INFO @ Tue, 16 Jun 2020 07:52:09: 3000000 INFO @ Tue, 16 Jun 2020 07:52:10: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:52:10: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:52:10: #1 total tags in treatment: 3293578 INFO @ Tue, 16 Jun 2020 07:52:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:10: #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 07:52:10: #1 tags after filtering in treatment: 3293578 INFO @ Tue, 16 Jun 2020 07:52:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:10: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:10: #2 number of paired peaks: 1848 INFO @ Tue, 16 Jun 2020 07:52:10: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:10: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:10: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:10: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:10: #2 predicted fragment length is 240 bps INFO @ Tue, 16 Jun 2020 07:52:10: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 16 Jun 2020 07:52:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.05_model.r INFO @ Tue, 16 Jun 2020 07:52:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.05_summits.bed INFO @ Tue, 16 Jun 2020 07:52:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3113 records, 4 fields): 5 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 07:52:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.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 07:52:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:30: 1000000 INFO @ Tue, 16 Jun 2020 07:52:34: 2000000 INFO @ Tue, 16 Jun 2020 07:52:39: 3000000 INFO @ Tue, 16 Jun 2020 07:52:40: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:52:40: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:52:40: #1 total tags in treatment: 3293578 INFO @ Tue, 16 Jun 2020 07:52:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:40: #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 07:52:40: #1 tags after filtering in treatment: 3293578 INFO @ Tue, 16 Jun 2020 07:52:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:40: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:40: #2 number of paired peaks: 1848 INFO @ Tue, 16 Jun 2020 07:52:40: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:40: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:40: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:40: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:40: #2 predicted fragment length is 240 bps INFO @ Tue, 16 Jun 2020 07:52:40: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 16 Jun 2020 07:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.10_model.r INFO @ Tue, 16 Jun 2020 07:52:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.10_summits.bed INFO @ Tue, 16 Jun 2020 07:52:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2070 records, 4 fields): 3 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 07:52:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.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 07:52:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:00: 1000000 INFO @ Tue, 16 Jun 2020 07:53:05: 2000000 INFO @ Tue, 16 Jun 2020 07:53:09: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:53:10: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:53:10: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:53:10: #1 total tags in treatment: 3293578 INFO @ Tue, 16 Jun 2020 07:53:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:10: #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 07:53:10: #1 tags after filtering in treatment: 3293578 INFO @ Tue, 16 Jun 2020 07:53:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:10: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:10: #2 number of paired peaks: 1848 INFO @ Tue, 16 Jun 2020 07:53:10: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:10: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:10: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:10: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:10: #2 predicted fragment length is 240 bps INFO @ Tue, 16 Jun 2020 07:53:10: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 16 Jun 2020 07:53:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.20_model.r INFO @ Tue, 16 Jun 2020 07:53:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:53:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059246/SRX059246.20_summits.bed INFO @ Tue, 16 Jun 2020 07:53:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1200 records, 4 fields): 3 millis CompletedMACS2peakCalling