Job ID = 6365898 SRX = SRX015096 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:29:44 prefetch.2.10.7: 1) Downloading 'SRR032440'... 2020-06-15T22:29:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:30:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:30:08 prefetch.2.10.7: 'SRR032440' is valid 2020-06-15T22:30:08 prefetch.2.10.7: 1) 'SRR032440' was downloaded successfully Read 3099942 spots for SRR032440/SRR032440.sra Written 3099942 spots for SRR032440/SRR032440.sra 2020-06-15T22:30:27 prefetch.2.10.7: 1) Downloading 'SRR032441'... 2020-06-15T22:30:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:30:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:30:46 prefetch.2.10.7: 'SRR032441' is valid 2020-06-15T22:30:46 prefetch.2.10.7: 1) 'SRR032441' was downloaded successfully Read 1978701 spots for SRR032441/SRR032441.sra Written 1978701 spots for SRR032441/SRR032441.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:29 5078643 reads; of these: 5078643 (100.00%) were unpaired; of these: 4251110 (83.71%) aligned 0 times 730863 (14.39%) aligned exactly 1 time 96670 (1.90%) aligned >1 times 16.29% overall alignment rate Time searching: 00:00:30 Overall time: 00:00:30 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] 55206 / 827533 = 0.0667 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 07:32:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.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 07:32:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:12: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:32:12: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:32:12: #1 total tags in treatment: 772327 INFO @ Tue, 16 Jun 2020 07:32:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:32:12: #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 07:32:12: #1 tags after filtering in treatment: 772327 INFO @ Tue, 16 Jun 2020 07:32:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:32:12: #1 finished! INFO @ Tue, 16 Jun 2020 07:32:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:32:12: #2 number of paired peaks: 2016 INFO @ Tue, 16 Jun 2020 07:32:12: start model_add_line... INFO @ Tue, 16 Jun 2020 07:32:12: start X-correlation... INFO @ Tue, 16 Jun 2020 07:32:12: end of X-cor INFO @ Tue, 16 Jun 2020 07:32:12: #2 finished! INFO @ Tue, 16 Jun 2020 07:32:12: #2 predicted fragment length is 190 bps INFO @ Tue, 16 Jun 2020 07:32:12: #2 alternative fragment length(s) may be 190 bps INFO @ Tue, 16 Jun 2020 07:32:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.05_model.r INFO @ Tue, 16 Jun 2020 07:32:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:32:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:32:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:32:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:32:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:32:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.05_summits.bed INFO @ Tue, 16 Jun 2020 07:32:15: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1452 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 07:32:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.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 07:32:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:42: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:32:42: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:32:42: #1 total tags in treatment: 772327 INFO @ Tue, 16 Jun 2020 07:32:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:32:42: #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 07:32:42: #1 tags after filtering in treatment: 772327 INFO @ Tue, 16 Jun 2020 07:32:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:32:42: #1 finished! INFO @ Tue, 16 Jun 2020 07:32:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:32:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:32:42: #2 number of paired peaks: 2016 INFO @ Tue, 16 Jun 2020 07:32:42: start model_add_line... INFO @ Tue, 16 Jun 2020 07:32:42: start X-correlation... INFO @ Tue, 16 Jun 2020 07:32:42: end of X-cor INFO @ Tue, 16 Jun 2020 07:32:42: #2 finished! INFO @ Tue, 16 Jun 2020 07:32:42: #2 predicted fragment length is 190 bps INFO @ Tue, 16 Jun 2020 07:32:42: #2 alternative fragment length(s) may be 190 bps INFO @ Tue, 16 Jun 2020 07:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.10_model.r INFO @ Tue, 16 Jun 2020 07:32:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:32:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:32:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:32:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:32:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:32:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.10_summits.bed INFO @ Tue, 16 Jun 2020 07:32:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (553 records, 4 fields): 2 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 07:33:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.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 07:33:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:33:07: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:33:12: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:33:12: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:33:12: #1 total tags in treatment: 772327 INFO @ Tue, 16 Jun 2020 07:33:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:33:12: #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 07:33:12: #1 tags after filtering in treatment: 772327 INFO @ Tue, 16 Jun 2020 07:33:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:33:12: #1 finished! INFO @ Tue, 16 Jun 2020 07:33:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:33:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:33:12: #2 number of paired peaks: 2016 INFO @ Tue, 16 Jun 2020 07:33:12: start model_add_line... INFO @ Tue, 16 Jun 2020 07:33:12: start X-correlation... INFO @ Tue, 16 Jun 2020 07:33:12: end of X-cor INFO @ Tue, 16 Jun 2020 07:33:12: #2 finished! INFO @ Tue, 16 Jun 2020 07:33:12: #2 predicted fragment length is 190 bps INFO @ Tue, 16 Jun 2020 07:33:12: #2 alternative fragment length(s) may be 190 bps INFO @ Tue, 16 Jun 2020 07:33:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.20_model.r INFO @ Tue, 16 Jun 2020 07:33:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:33:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:33:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:33:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:33:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:33:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX015096/SRX015096.20_summits.bed INFO @ Tue, 16 Jun 2020 07:33:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (118 records, 4 fields): 1 millis CompletedMACS2peakCalling