Job ID = 6365868 SRX = SRX005625 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:31:29 prefetch.2.10.7: 1) Downloading 'SRR017594'... 2020-06-15T22:31:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:32:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:32:02 prefetch.2.10.7: 'SRR017594' is valid 2020-06-15T22:32:02 prefetch.2.10.7: 1) 'SRR017594' was downloaded successfully Read 5707229 spots for SRR017594/SRR017594.sra Written 5707229 spots for SRR017594/SRR017594.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: 00:00:39 5707229 reads; of these: 5707229 (100.00%) were unpaired; of these: 2138623 (37.47%) aligned 0 times 3044336 (53.34%) aligned exactly 1 time 524270 (9.19%) aligned >1 times 62.53% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 1143037 / 3568606 = 0.3203 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 07:34:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.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 07:34:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:34:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:34:09: 1000000 INFO @ Tue, 16 Jun 2020 07:34:16: 2000000 INFO @ Tue, 16 Jun 2020 07:34:18: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:34:18: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:34:18: #1 total tags in treatment: 2425569 INFO @ Tue, 16 Jun 2020 07:34:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:34:18: #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 07:34:18: #1 tags after filtering in treatment: 2425569 INFO @ Tue, 16 Jun 2020 07:34:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:34:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:34:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:34:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:34:18: #2 number of paired peaks: 1455 INFO @ Tue, 16 Jun 2020 07:34:18: start model_add_line... INFO @ Tue, 16 Jun 2020 07:34:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:34:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:34:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:34:19: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 07:34:19: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 16 Jun 2020 07:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.05_model.r INFO @ Tue, 16 Jun 2020 07:34:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:34:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:34:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.05_summits.bed INFO @ Tue, 16 Jun 2020 07:34:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1611 records, 4 fields): 4 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 07:34:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.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 07:34:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:34:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:34:39: 1000000 INFO @ Tue, 16 Jun 2020 07:34:46: 2000000 INFO @ Tue, 16 Jun 2020 07:34:48: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:34:48: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:34:48: #1 total tags in treatment: 2425569 INFO @ Tue, 16 Jun 2020 07:34:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:34:48: #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 07:34:48: #1 tags after filtering in treatment: 2425569 INFO @ Tue, 16 Jun 2020 07:34:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:34:48: #1 finished! INFO @ Tue, 16 Jun 2020 07:34:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:34:48: #2 number of paired peaks: 1455 INFO @ Tue, 16 Jun 2020 07:34:48: start model_add_line... INFO @ Tue, 16 Jun 2020 07:34:48: start X-correlation... INFO @ Tue, 16 Jun 2020 07:34:48: end of X-cor INFO @ Tue, 16 Jun 2020 07:34:48: #2 finished! INFO @ Tue, 16 Jun 2020 07:34:48: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 07:34:48: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 16 Jun 2020 07:34:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.10_model.r INFO @ Tue, 16 Jun 2020 07:34:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:34:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:34:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:34:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:34:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:34:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.10_summits.bed INFO @ Tue, 16 Jun 2020 07:34:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (596 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 07:35:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.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 07:35:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:10: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:35:16: 2000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:35:18: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:35:18: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:35:18: #1 total tags in treatment: 2425569 INFO @ Tue, 16 Jun 2020 07:35:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:35:18: #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 07:35:18: #1 tags after filtering in treatment: 2425569 INFO @ Tue, 16 Jun 2020 07:35:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:35:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:35:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:35:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:35:19: #2 number of paired peaks: 1455 INFO @ Tue, 16 Jun 2020 07:35:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:35:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:35:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:35:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:35:19: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 07:35:19: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 16 Jun 2020 07:35:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.20_model.r INFO @ Tue, 16 Jun 2020 07:35:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:35:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:35:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:35:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:35:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:35:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005625/SRX005625.20_summits.bed INFO @ Tue, 16 Jun 2020 07:35:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (181 records, 4 fields): 1 millis CompletedMACS2peakCalling