Job ID = 6366144 SRX = SRX065660 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:43:37 prefetch.2.10.7: 1) Downloading 'SRR217366'... 2020-06-15T22:43:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:44:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:44:14 prefetch.2.10.7: 'SRR217366' is valid 2020-06-15T22:44:14 prefetch.2.10.7: 1) 'SRR217366' was downloaded successfully Read 7263691 spots for SRR217366/SRR217366.sra Written 7263691 spots for SRR217366/SRR217366.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: 00:00:43 7263691 reads; of these: 7263691 (100.00%) were unpaired; of these: 4581751 (63.08%) aligned 0 times 2363737 (32.54%) aligned exactly 1 time 318203 (4.38%) aligned >1 times 36.92% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 325752 / 2681940 = 0.1215 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 07:46:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.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 07:46:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:46:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:46:28: 1000000 INFO @ Tue, 16 Jun 2020 07:46:34: 2000000 INFO @ Tue, 16 Jun 2020 07:46:35: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:46:35: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:46:35: #1 total tags in treatment: 2356188 INFO @ Tue, 16 Jun 2020 07:46:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:46:35: #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 07:46:35: #1 tags after filtering in treatment: 2356188 INFO @ Tue, 16 Jun 2020 07:46:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:46:35: #1 finished! INFO @ Tue, 16 Jun 2020 07:46:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:46:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:46:36: #2 number of paired peaks: 3039 INFO @ Tue, 16 Jun 2020 07:46:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:46:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:46:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:46:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:46:36: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 07:46:36: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 16 Jun 2020 07:46:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.05_model.r INFO @ Tue, 16 Jun 2020 07:46:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:46:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:46:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:46:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:46:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:46:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.05_summits.bed INFO @ Tue, 16 Jun 2020 07:46:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7053 records, 4 fields): 9 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 07:46:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.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 07:46:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:46:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:46:58: 1000000 INFO @ Tue, 16 Jun 2020 07:47:05: 2000000 INFO @ Tue, 16 Jun 2020 07:47:07: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:47:07: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:47:07: #1 total tags in treatment: 2356188 INFO @ Tue, 16 Jun 2020 07:47:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:07: #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 07:47:07: #1 tags after filtering in treatment: 2356188 INFO @ Tue, 16 Jun 2020 07:47:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:07: #2 number of paired peaks: 3039 INFO @ Tue, 16 Jun 2020 07:47:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:07: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 07:47:07: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 16 Jun 2020 07:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.10_model.r INFO @ Tue, 16 Jun 2020 07:47:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.10_summits.bed INFO @ Tue, 16 Jun 2020 07:47:17: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4288 records, 4 fields): 5 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 07:47:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.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 07:47:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:47:29: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:47:35: 2000000 INFO @ Tue, 16 Jun 2020 07:47:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:47:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:47:37: #1 total tags in treatment: 2356188 INFO @ Tue, 16 Jun 2020 07:47:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:37: #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 07:47:37: #1 tags after filtering in treatment: 2356188 INFO @ Tue, 16 Jun 2020 07:47:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:37: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:38: #2 number of paired peaks: 3039 INFO @ Tue, 16 Jun 2020 07:47:38: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:38: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:38: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:38: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:38: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 07:47:38: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 16 Jun 2020 07:47:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.20_model.r INFO @ Tue, 16 Jun 2020 07:47:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:47:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065660/SRX065660.20_summits.bed INFO @ Tue, 16 Jun 2020 07:47:46: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1787 records, 4 fields): 4 millis CompletedMACS2peakCalling