Job ID = 6366026 SRX = SRX054254 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:44:52 prefetch.2.10.7: 1) Downloading 'SRR164261'... 2020-06-15T22:44:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:45:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:45:41 prefetch.2.10.7: 'SRR164261' is valid 2020-06-15T22:45:41 prefetch.2.10.7: 1) 'SRR164261' was downloaded successfully Read 5858168 spots for SRR164261/SRR164261.sra Written 5858168 spots for SRR164261/SRR164261.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: 00:00:34 5858168 reads; of these: 5858168 (100.00%) were unpaired; of these: 3786353 (64.63%) aligned 0 times 1824210 (31.14%) aligned exactly 1 time 247605 (4.23%) aligned >1 times 35.37% overall alignment rate Time searching: 00:00:34 Overall time: 00:00:34 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] 285313 / 2071815 = 0.1377 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 07:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.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 07:47:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:47:38: 1000000 INFO @ Tue, 16 Jun 2020 07:47:42: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:47:42: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:47:42: #1 total tags in treatment: 1786502 INFO @ Tue, 16 Jun 2020 07:47:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:42: #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 07:47:42: #1 tags after filtering in treatment: 1786502 INFO @ Tue, 16 Jun 2020 07:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:42: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:43: #2 number of paired peaks: 1059 INFO @ Tue, 16 Jun 2020 07:47:43: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:43: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:43: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:43: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:43: #2 predicted fragment length is 171 bps INFO @ Tue, 16 Jun 2020 07:47:43: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 16 Jun 2020 07:47:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.05_model.r INFO @ Tue, 16 Jun 2020 07:47:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.05_summits.bed INFO @ Tue, 16 Jun 2020 07:47:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2491 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 07:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.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 07:48:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:08: 1000000 INFO @ Tue, 16 Jun 2020 07:48:12: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:48:12: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:48:12: #1 total tags in treatment: 1786502 INFO @ Tue, 16 Jun 2020 07:48:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:12: #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 07:48:12: #1 tags after filtering in treatment: 1786502 INFO @ Tue, 16 Jun 2020 07:48:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:12: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:13: #2 number of paired peaks: 1059 INFO @ Tue, 16 Jun 2020 07:48:13: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:13: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:13: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:13: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:13: #2 predicted fragment length is 171 bps INFO @ Tue, 16 Jun 2020 07:48:13: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 16 Jun 2020 07:48:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.10_model.r INFO @ Tue, 16 Jun 2020 07:48:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:48:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.10_summits.bed INFO @ Tue, 16 Jun 2020 07:48:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1034 records, 4 fields): 3 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 07:48:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.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 07:48:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:38: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:48:42: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:48:42: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:48:42: #1 total tags in treatment: 1786502 INFO @ Tue, 16 Jun 2020 07:48:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:42: #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 07:48:42: #1 tags after filtering in treatment: 1786502 INFO @ Tue, 16 Jun 2020 07:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:42: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:42: #2 number of paired peaks: 1059 INFO @ Tue, 16 Jun 2020 07:48:42: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:43: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:43: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:43: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:43: #2 predicted fragment length is 171 bps INFO @ Tue, 16 Jun 2020 07:48:43: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 16 Jun 2020 07:48:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.20_model.r INFO @ Tue, 16 Jun 2020 07:48:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:48:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054254/SRX054254.20_summits.bed INFO @ Tue, 16 Jun 2020 07:48:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 1 millis CompletedMACS2peakCalling