Job ID = 6366257 SRX = SRX094515 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:32:21 prefetch.2.10.7: 1) Downloading 'SRR340089'... 2020-06-15T22:32:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:33:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:33:00 prefetch.2.10.7: 'SRR340089' is valid 2020-06-15T22:33:00 prefetch.2.10.7: 1) 'SRR340089' was downloaded successfully Read 3221462 spots for SRR340089/SRR340089.sra Written 3221462 spots for SRR340089/SRR340089.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: 00:00:15 3221462 reads; of these: 3221462 (100.00%) were unpaired; of these: 2548392 (79.11%) aligned 0 times 551532 (17.12%) aligned exactly 1 time 121538 (3.77%) aligned >1 times 20.89% overall alignment rate Time searching: 00:00:15 Overall time: 00:00:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 365775 / 673070 = 0.5434 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 07:34:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.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 07:34:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:34:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:34:07: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:34:07: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:34:07: #1 total tags in treatment: 307295 INFO @ Tue, 16 Jun 2020 07:34:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:34:07: #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 07:34:07: #1 tags after filtering in treatment: 307295 INFO @ Tue, 16 Jun 2020 07:34:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:34:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:34:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:34:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:34:07: #2 number of paired peaks: 1396 INFO @ Tue, 16 Jun 2020 07:34:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:34:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:34:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:34:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:34:07: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 07:34:07: #2 alternative fragment length(s) may be 101,554,590 bps INFO @ Tue, 16 Jun 2020 07:34:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.05_model.r INFO @ Tue, 16 Jun 2020 07:34:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:34:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:34:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:34:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:34:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:34:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.05_summits.bed INFO @ Tue, 16 Jun 2020 07:34:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 1 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 07:34:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.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 07:34:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:34:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:34:37: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:34:37: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:34:37: #1 total tags in treatment: 307295 INFO @ Tue, 16 Jun 2020 07:34:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:34:37: #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 07:34:37: #1 tags after filtering in treatment: 307295 INFO @ Tue, 16 Jun 2020 07:34:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:34:37: #1 finished! INFO @ Tue, 16 Jun 2020 07:34:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:34:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:34:37: #2 number of paired peaks: 1396 INFO @ Tue, 16 Jun 2020 07:34:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:34:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:34:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:34:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:34:37: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 07:34:37: #2 alternative fragment length(s) may be 101,554,590 bps INFO @ Tue, 16 Jun 2020 07:34:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.10_model.r INFO @ Tue, 16 Jun 2020 07:34:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:34:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:34:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:34:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:34:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:34:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.10_summits.bed INFO @ Tue, 16 Jun 2020 07:34:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (73 records, 4 fields): 1 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 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:35:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.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 07:35:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:05: #1 read treatment tags... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:35:07: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:35:07: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:35:07: #1 total tags in treatment: 307295 INFO @ Tue, 16 Jun 2020 07:35:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:35:07: #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 07:35:07: #1 tags after filtering in treatment: 307295 INFO @ Tue, 16 Jun 2020 07:35:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:35:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:35:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:35:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:35:07: #2 number of paired peaks: 1396 INFO @ Tue, 16 Jun 2020 07:35:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:35:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:35:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:35:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:35:07: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 07:35:07: #2 alternative fragment length(s) may be 101,554,590 bps INFO @ Tue, 16 Jun 2020 07:35:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.20_model.r INFO @ Tue, 16 Jun 2020 07:35:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:35:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:35:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:35:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:35:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:35:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX094515/SRX094515.20_summits.bed INFO @ Tue, 16 Jun 2020 07:35:08: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (33 records, 4 fields): 2 millis CompletedMACS2peakCalling