Job ID = 6368773 SRX = SRX554734 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:34:25 prefetch.2.10.7: 1) Downloading 'SRR1301084'... 2020-06-16T00:34:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:29 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:29 prefetch.2.10.7: 'SRR1301084' is valid 2020-06-16T00:35:29 prefetch.2.10.7: 1) 'SRR1301084' was downloaded successfully Read 7539884 spots for SRR1301084/SRR1301084.sra Written 7539884 spots for SRR1301084/SRR1301084.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: 00:02:17 7539884 reads; of these: 7539884 (100.00%) were unpaired; of these: 120364 (1.60%) aligned 0 times 5521338 (73.23%) aligned exactly 1 time 1898182 (25.18%) aligned >1 times 98.40% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 1980435 / 7419520 = 0.2669 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 09:40:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.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 09:40:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:36: 1000000 INFO @ Tue, 16 Jun 2020 09:40:42: 2000000 INFO @ Tue, 16 Jun 2020 09:40:48: 3000000 INFO @ Tue, 16 Jun 2020 09:40:54: 4000000 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 09:40:59: 5000000 INFO @ Tue, 16 Jun 2020 09:41:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.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 09:41:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:02: #1 total tags in treatment: 5439085 INFO @ Tue, 16 Jun 2020 09:41:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:02: #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 09:41:02: #1 tags after filtering in treatment: 5439085 INFO @ Tue, 16 Jun 2020 09:41:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:03: #2 number of paired peaks: 1718 INFO @ Tue, 16 Jun 2020 09:41:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:03: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 09:41:03: #2 alternative fragment length(s) may be 3,95,118 bps INFO @ Tue, 16 Jun 2020 09:41:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.05_model.r INFO @ Tue, 16 Jun 2020 09:41:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:06: 1000000 INFO @ Tue, 16 Jun 2020 09:41:12: 2000000 INFO @ Tue, 16 Jun 2020 09:41:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:19: 3000000 INFO @ Tue, 16 Jun 2020 09:41:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.05_summits.bed INFO @ Tue, 16 Jun 2020 09:41:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1201 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:25: 4000000 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 09:41:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.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 09:41:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:31: 5000000 INFO @ Tue, 16 Jun 2020 09:41:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:34: #1 total tags in treatment: 5439085 INFO @ Tue, 16 Jun 2020 09:41:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:34: #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 09:41:34: #1 tags after filtering in treatment: 5439085 INFO @ Tue, 16 Jun 2020 09:41:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:34: #2 number of paired peaks: 1718 INFO @ Tue, 16 Jun 2020 09:41:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:34: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 09:41:34: #2 alternative fragment length(s) may be 3,95,118 bps INFO @ Tue, 16 Jun 2020 09:41:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.10_model.r INFO @ Tue, 16 Jun 2020 09:41:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:36: 1000000 INFO @ Tue, 16 Jun 2020 09:41:42: 2000000 INFO @ Tue, 16 Jun 2020 09:41:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:48: 3000000 INFO @ Tue, 16 Jun 2020 09:41:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.10_summits.bed INFO @ Tue, 16 Jun 2020 09:41:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (413 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:54: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:42:00: 5000000 INFO @ Tue, 16 Jun 2020 09:42:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:03: #1 total tags in treatment: 5439085 INFO @ Tue, 16 Jun 2020 09:42:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:03: #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 09:42:03: #1 tags after filtering in treatment: 5439085 INFO @ Tue, 16 Jun 2020 09:42:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:03: #2 number of paired peaks: 1718 INFO @ Tue, 16 Jun 2020 09:42:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:03: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 09:42:03: #2 alternative fragment length(s) may be 3,95,118 bps INFO @ Tue, 16 Jun 2020 09:42:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.20_model.r INFO @ Tue, 16 Jun 2020 09:42:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:42:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554734/SRX554734.20_summits.bed INFO @ Tue, 16 Jun 2020 09:42:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 1 millis CompletedMACS2peakCalling