Job ID = 6367554 SRX = SRX331310 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:26:51 prefetch.2.10.7: 1) Downloading 'SRR947547'... 2020-06-15T23:26:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:27:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:27:11 prefetch.2.10.7: 'SRR947547' is valid 2020-06-15T23:27:11 prefetch.2.10.7: 1) 'SRR947547' was downloaded successfully Read 3243937 spots for SRR947547/SRR947547.sra Written 3243937 spots for SRR947547/SRR947547.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: 00:00:20 3243937 reads; of these: 3243937 (100.00%) were unpaired; of these: 1210378 (37.31%) aligned 0 times 1823089 (56.20%) aligned exactly 1 time 210470 (6.49%) aligned >1 times 62.69% overall alignment rate Time searching: 00:00:20 Overall time: 00:00:20 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] 321776 / 2033559 = 0.1582 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 08:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.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 08:28:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:36: 1000000 INFO @ Tue, 16 Jun 2020 08:28:40: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:40: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:40: #1 total tags in treatment: 1711783 INFO @ Tue, 16 Jun 2020 08:28:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:40: #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 08:28:40: #1 tags after filtering in treatment: 1711783 INFO @ Tue, 16 Jun 2020 08:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:40: #2 number of paired peaks: 3416 INFO @ Tue, 16 Jun 2020 08:28:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:40: #2 predicted fragment length is 156 bps INFO @ Tue, 16 Jun 2020 08:28:40: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 16 Jun 2020 08:28:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.05_model.r INFO @ Tue, 16 Jun 2020 08:28:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5223 records, 4 fields): 5 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 08:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.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 08:29:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:06: 1000000 INFO @ Tue, 16 Jun 2020 08:29:09: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:29:09: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:29:09: #1 total tags in treatment: 1711783 INFO @ Tue, 16 Jun 2020 08:29:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:09: #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 08:29:09: #1 tags after filtering in treatment: 1711783 INFO @ Tue, 16 Jun 2020 08:29:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:10: #2 number of paired peaks: 3416 INFO @ Tue, 16 Jun 2020 08:29:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:10: #2 predicted fragment length is 156 bps INFO @ Tue, 16 Jun 2020 08:29:10: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 16 Jun 2020 08:29:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.10_model.r INFO @ Tue, 16 Jun 2020 08:29:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.10_summits.bed INFO @ Tue, 16 Jun 2020 08:29:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2910 records, 4 fields): 4 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 08:29:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.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 08:29:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:36: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:29:40: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:29:40: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:29:40: #1 total tags in treatment: 1711783 INFO @ Tue, 16 Jun 2020 08:29:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:40: #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 08:29:40: #1 tags after filtering in treatment: 1711783 INFO @ Tue, 16 Jun 2020 08:29:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:40: #2 number of paired peaks: 3416 INFO @ Tue, 16 Jun 2020 08:29:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:40: #2 predicted fragment length is 156 bps INFO @ Tue, 16 Jun 2020 08:29:40: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 16 Jun 2020 08:29:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.20_model.r INFO @ Tue, 16 Jun 2020 08:29:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331310/SRX331310.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:46: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1283 records, 4 fields): 3 millis CompletedMACS2peakCalling