Job ID = 6365852 SRX = SRX003818 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:29:14 prefetch.2.10.7: 1) Downloading 'SRR015058'... 2020-06-15T22:29:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:40:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:40:47 prefetch.2.10.7: 1) 'SRR015058' was downloaded successfully Read 15218948 spots for SRR015058/SRR015058.sra Written 15218948 spots for SRR015058/SRR015058.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: 00:01:13 15218948 reads; of these: 15218948 (100.00%) were unpaired; of these: 11004827 (72.31%) aligned 0 times 3712686 (24.40%) aligned exactly 1 time 501435 (3.29%) aligned >1 times 27.69% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 408616 / 4214121 = 0.0970 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 07:44:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.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 07:44:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:38: 1000000 INFO @ Tue, 16 Jun 2020 07:44:43: 2000000 INFO @ Tue, 16 Jun 2020 07:44:49: 3000000 INFO @ Tue, 16 Jun 2020 07:44:53: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:44:53: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:44:53: #1 total tags in treatment: 3805505 INFO @ Tue, 16 Jun 2020 07:44:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:53: #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 07:44:53: #1 tags after filtering in treatment: 3805505 INFO @ Tue, 16 Jun 2020 07:44:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:53: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:53: #2 number of paired peaks: 2817 INFO @ Tue, 16 Jun 2020 07:44:53: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:53: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:53: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:53: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:53: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 07:44:53: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 16 Jun 2020 07:44:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.05_model.r INFO @ Tue, 16 Jun 2020 07:44:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:53: #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 07:45:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.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 07:45:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:09: 1000000 INFO @ Tue, 16 Jun 2020 07:45:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.05_summits.bed INFO @ Tue, 16 Jun 2020 07:45:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7876 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:45:15: 2000000 INFO @ Tue, 16 Jun 2020 07:45:21: 3000000 INFO @ Tue, 16 Jun 2020 07:45:26: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:45:26: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:45:26: #1 total tags in treatment: 3805505 INFO @ Tue, 16 Jun 2020 07:45:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:26: #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 07:45:26: #1 tags after filtering in treatment: 3805505 INFO @ Tue, 16 Jun 2020 07:45:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:27: #2 number of paired peaks: 2817 INFO @ Tue, 16 Jun 2020 07:45:27: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:27: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:27: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:27: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:27: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 07:45:27: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 16 Jun 2020 07:45:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.10_model.r INFO @ Tue, 16 Jun 2020 07:45:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:27: #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 07:45:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.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 07:45:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:38: 1000000 INFO @ Tue, 16 Jun 2020 07:45:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.10_summits.bed INFO @ Tue, 16 Jun 2020 07:45:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3950 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:45:44: 2000000 INFO @ Tue, 16 Jun 2020 07:45:49: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:45:53: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:45:53: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:45:53: #1 total tags in treatment: 3805505 INFO @ Tue, 16 Jun 2020 07:45:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:53: #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 07:45:53: #1 tags after filtering in treatment: 3805505 INFO @ Tue, 16 Jun 2020 07:45:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:53: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:54: #2 number of paired peaks: 2817 INFO @ Tue, 16 Jun 2020 07:45:54: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:54: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:54: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:54: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:54: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 07:45:54: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 16 Jun 2020 07:45:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.20_model.r INFO @ Tue, 16 Jun 2020 07:45:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:46:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:46:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:46:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:46:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003818/SRX003818.20_summits.bed INFO @ Tue, 16 Jun 2020 07:46:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1629 records, 4 fields): 3 millis CompletedMACS2peakCalling