Job ID = 6507938 SRX = SRX495100 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:41:46 prefetch.2.10.7: 1) Downloading 'SRR1198632'... 2020-06-26T13:41:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:44:06 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:44:07 prefetch.2.10.7: 'SRR1198632' is valid 2020-06-26T13:44:07 prefetch.2.10.7: 1) 'SRR1198632' was downloaded successfully Read 9064871 spots for SRR1198632/SRR1198632.sra Written 9064871 spots for SRR1198632/SRR1198632.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: 00:01:46 9064871 reads; of these: 9064871 (100.00%) were unpaired; of these: 159054 (1.75%) aligned 0 times 6207207 (68.48%) aligned exactly 1 time 2698610 (29.77%) aligned >1 times 98.25% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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] 4653587 / 8905817 = 0.5225 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 @ Fri, 26 Jun 2020 22:48:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.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 @ Fri, 26 Jun 2020 22:48:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:48:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:48:37: 1000000 INFO @ Fri, 26 Jun 2020 22:48:43: 2000000 INFO @ Fri, 26 Jun 2020 22:48:49: 3000000 INFO @ Fri, 26 Jun 2020 22:48:55: 4000000 INFO @ Fri, 26 Jun 2020 22:48:57: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:48:57: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:48:57: #1 total tags in treatment: 4252230 INFO @ Fri, 26 Jun 2020 22:48:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:48:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:48:57: #1 tags after filtering in treatment: 4252230 INFO @ Fri, 26 Jun 2020 22:48:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:48:57: #1 finished! INFO @ Fri, 26 Jun 2020 22:48:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:48:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:48:57: #2 number of paired peaks: 1731 INFO @ Fri, 26 Jun 2020 22:48:57: start model_add_line... INFO @ Fri, 26 Jun 2020 22:48:57: start X-correlation... INFO @ Fri, 26 Jun 2020 22:48:57: end of X-cor INFO @ Fri, 26 Jun 2020 22:48:57: #2 finished! INFO @ Fri, 26 Jun 2020 22:48:57: #2 predicted fragment length is 247 bps INFO @ Fri, 26 Jun 2020 22:48:57: #2 alternative fragment length(s) may be 247 bps INFO @ Fri, 26 Jun 2020 22:48:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.05_model.r INFO @ Fri, 26 Jun 2020 22:48:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:48:57: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 22:49:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.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 @ Fri, 26 Jun 2020 22:49:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:49:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:49:07: 1000000 INFO @ Fri, 26 Jun 2020 22:49:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:49:13: 2000000 INFO @ Fri, 26 Jun 2020 22:49:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:49:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:49:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.05_summits.bed INFO @ Fri, 26 Jun 2020 22:49:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1725 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:49:19: 3000000 INFO @ Fri, 26 Jun 2020 22:49:24: 4000000 INFO @ Fri, 26 Jun 2020 22:49:26: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:49:26: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:49:26: #1 total tags in treatment: 4252230 INFO @ Fri, 26 Jun 2020 22:49:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:49:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:49:26: #1 tags after filtering in treatment: 4252230 INFO @ Fri, 26 Jun 2020 22:49:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:49:26: #1 finished! INFO @ Fri, 26 Jun 2020 22:49:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:49:26: #2 number of paired peaks: 1731 INFO @ Fri, 26 Jun 2020 22:49:26: start model_add_line... INFO @ Fri, 26 Jun 2020 22:49:26: start X-correlation... INFO @ Fri, 26 Jun 2020 22:49:27: end of X-cor INFO @ Fri, 26 Jun 2020 22:49:27: #2 finished! INFO @ Fri, 26 Jun 2020 22:49:27: #2 predicted fragment length is 247 bps INFO @ Fri, 26 Jun 2020 22:49:27: #2 alternative fragment length(s) may be 247 bps INFO @ Fri, 26 Jun 2020 22:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.10_model.r INFO @ Fri, 26 Jun 2020 22:49:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:49:27: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 22:49:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.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 @ Fri, 26 Jun 2020 22:49:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:49:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:49:36: 1000000 INFO @ Fri, 26 Jun 2020 22:49:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:49:42: 2000000 INFO @ Fri, 26 Jun 2020 22:49:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:49:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:49:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.10_summits.bed INFO @ Fri, 26 Jun 2020 22:49:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1543 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:49:47: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:49:52: 4000000 INFO @ Fri, 26 Jun 2020 22:49:53: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:49:53: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:49:53: #1 total tags in treatment: 4252230 INFO @ Fri, 26 Jun 2020 22:49:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:49:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:49:54: #1 tags after filtering in treatment: 4252230 INFO @ Fri, 26 Jun 2020 22:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:49:54: #1 finished! INFO @ Fri, 26 Jun 2020 22:49:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:49:54: #2 number of paired peaks: 1731 INFO @ Fri, 26 Jun 2020 22:49:54: start model_add_line... INFO @ Fri, 26 Jun 2020 22:49:54: start X-correlation... INFO @ Fri, 26 Jun 2020 22:49:54: end of X-cor INFO @ Fri, 26 Jun 2020 22:49:54: #2 finished! INFO @ Fri, 26 Jun 2020 22:49:54: #2 predicted fragment length is 247 bps INFO @ Fri, 26 Jun 2020 22:49:54: #2 alternative fragment length(s) may be 247 bps INFO @ Fri, 26 Jun 2020 22:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.20_model.r INFO @ Fri, 26 Jun 2020 22:49:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:49:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:50:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:50:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:50:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:50:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495100/SRX495100.20_summits.bed INFO @ Fri, 26 Jun 2020 22:50:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1378 records, 4 fields): 4 millis CompletedMACS2peakCalling