Job ID = 6368393 SRX = SRX495072 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:15:06 prefetch.2.10.7: 1) Downloading 'SRR1198604'... 2020-06-16T00:15:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:17:38 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:17:38 prefetch.2.10.7: 1) 'SRR1198604' was downloaded successfully Read 22611426 spots for SRR1198604/SRR1198604.sra Written 22611426 spots for SRR1198604/SRR1198604.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: 00:05:34 22611426 reads; of these: 22611426 (100.00%) were unpaired; of these: 914408 (4.04%) aligned 0 times 17441858 (77.14%) aligned exactly 1 time 4255160 (18.82%) aligned >1 times 95.96% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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_sort_core] merging from 12 files... [bam_rmdupse_core] 7458440 / 21697018 = 0.3438 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 09:29:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.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 09:29:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:42: 1000000 INFO @ Tue, 16 Jun 2020 09:29:48: 2000000 INFO @ Tue, 16 Jun 2020 09:29:54: 3000000 INFO @ Tue, 16 Jun 2020 09:29:59: 4000000 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 09:30:05: 5000000 INFO @ Tue, 16 Jun 2020 09:30:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.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 09:30:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:11: 6000000 INFO @ Tue, 16 Jun 2020 09:30:13: 1000000 INFO @ Tue, 16 Jun 2020 09:30:17: 7000000 INFO @ Tue, 16 Jun 2020 09:30:19: 2000000 INFO @ Tue, 16 Jun 2020 09:30:23: 8000000 INFO @ Tue, 16 Jun 2020 09:30:25: 3000000 INFO @ Tue, 16 Jun 2020 09:30:29: 9000000 INFO @ Tue, 16 Jun 2020 09:30:32: 4000000 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 09:30:35: 10000000 INFO @ Tue, 16 Jun 2020 09:30:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.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 09:30:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:38: 5000000 INFO @ Tue, 16 Jun 2020 09:30:42: 11000000 INFO @ Tue, 16 Jun 2020 09:30:43: 1000000 INFO @ Tue, 16 Jun 2020 09:30:44: 6000000 INFO @ Tue, 16 Jun 2020 09:30:48: 12000000 INFO @ Tue, 16 Jun 2020 09:30:49: 2000000 INFO @ Tue, 16 Jun 2020 09:30:51: 7000000 INFO @ Tue, 16 Jun 2020 09:30:54: 13000000 INFO @ Tue, 16 Jun 2020 09:30:56: 3000000 INFO @ Tue, 16 Jun 2020 09:30:57: 8000000 INFO @ Tue, 16 Jun 2020 09:31:00: 14000000 INFO @ Tue, 16 Jun 2020 09:31:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:31:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:31:02: #1 total tags in treatment: 14238578 INFO @ Tue, 16 Jun 2020 09:31:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:02: #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 09:31:02: #1 tags after filtering in treatment: 14238578 INFO @ Tue, 16 Jun 2020 09:31:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:02: 4000000 INFO @ Tue, 16 Jun 2020 09:31:03: #2 number of paired peaks: 675 WARNING @ Tue, 16 Jun 2020 09:31:03: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:03: #2 predicted fragment length is 116 bps INFO @ Tue, 16 Jun 2020 09:31:03: #2 alternative fragment length(s) may be 116 bps INFO @ Tue, 16 Jun 2020 09:31:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.05_model.r INFO @ Tue, 16 Jun 2020 09:31:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:03: 9000000 INFO @ Tue, 16 Jun 2020 09:31:08: 5000000 INFO @ Tue, 16 Jun 2020 09:31:09: 10000000 INFO @ Tue, 16 Jun 2020 09:31:15: 6000000 INFO @ Tue, 16 Jun 2020 09:31:15: 11000000 INFO @ Tue, 16 Jun 2020 09:31:21: 7000000 INFO @ Tue, 16 Jun 2020 09:31:22: 12000000 INFO @ Tue, 16 Jun 2020 09:31:28: 13000000 INFO @ Tue, 16 Jun 2020 09:31:28: 8000000 INFO @ Tue, 16 Jun 2020 09:31:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:34: 14000000 INFO @ Tue, 16 Jun 2020 09:31:34: 9000000 INFO @ Tue, 16 Jun 2020 09:31:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:31:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:31:35: #1 total tags in treatment: 14238578 INFO @ Tue, 16 Jun 2020 09:31:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:35: #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 09:31:35: #1 tags after filtering in treatment: 14238578 INFO @ Tue, 16 Jun 2020 09:31:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:37: #2 number of paired peaks: 675 WARNING @ Tue, 16 Jun 2020 09:31:37: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:37: #2 predicted fragment length is 116 bps INFO @ Tue, 16 Jun 2020 09:31:37: #2 alternative fragment length(s) may be 116 bps INFO @ Tue, 16 Jun 2020 09:31:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.10_model.r INFO @ Tue, 16 Jun 2020 09:31:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:40: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:31:46: 11000000 INFO @ Tue, 16 Jun 2020 09:31:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.05_summits.bed INFO @ Tue, 16 Jun 2020 09:31:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2612 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:52: 12000000 INFO @ Tue, 16 Jun 2020 09:31:58: 13000000 INFO @ Tue, 16 Jun 2020 09:32:04: 14000000 INFO @ Tue, 16 Jun 2020 09:32:06: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:32:06: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:32:06: #1 total tags in treatment: 14238578 INFO @ Tue, 16 Jun 2020 09:32:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:06: #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 09:32:06: #1 tags after filtering in treatment: 14238578 INFO @ Tue, 16 Jun 2020 09:32:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:07: #2 number of paired peaks: 675 WARNING @ Tue, 16 Jun 2020 09:32:07: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:07: #2 predicted fragment length is 116 bps INFO @ Tue, 16 Jun 2020 09:32:07: #2 alternative fragment length(s) may be 116 bps INFO @ Tue, 16 Jun 2020 09:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.20_model.r INFO @ Tue, 16 Jun 2020 09:32:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1807 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495072/SRX495072.20_summits.bed INFO @ Tue, 16 Jun 2020 09:32:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1165 records, 4 fields): 3 millis CompletedMACS2peakCalling