Job ID = 6366612 SRX = SRX208776 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:57:09 prefetch.2.10.7: 1) Downloading 'SRR628910'... 2020-06-15T22:57:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:57 prefetch.2.10.7: 'SRR628910' is valid 2020-06-15T22:57:57 prefetch.2.10.7: 1) 'SRR628910' was downloaded successfully Read 11387508 spots for SRR628910/SRR628910.sra Written 11387508 spots for SRR628910/SRR628910.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: 00:03:23 11387508 reads; of these: 11387508 (100.00%) were unpaired; of these: 1207648 (10.61%) aligned 0 times 8807277 (77.34%) aligned exactly 1 time 1372583 (12.05%) aligned >1 times 89.39% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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 8 files... [bam_rmdupse_core] 5785068 / 10179860 = 0.5683 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 08:04:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.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 08:04:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:39: 1000000 INFO @ Tue, 16 Jun 2020 08:04:45: 2000000 INFO @ Tue, 16 Jun 2020 08:04:50: 3000000 INFO @ Tue, 16 Jun 2020 08:04:56: 4000000 INFO @ Tue, 16 Jun 2020 08:04:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:04:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:04:58: #1 total tags in treatment: 4394792 INFO @ Tue, 16 Jun 2020 08:04:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:58: #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 08:04:58: #1 tags after filtering in treatment: 4394792 INFO @ Tue, 16 Jun 2020 08:04:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:58: #2 number of paired peaks: 340 WARNING @ Tue, 16 Jun 2020 08:04:58: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:58: #2 predicted fragment length is 212 bps INFO @ Tue, 16 Jun 2020 08:04:58: #2 alternative fragment length(s) may be 212 bps INFO @ Tue, 16 Jun 2020 08:04:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.05_model.r INFO @ Tue, 16 Jun 2020 08:04:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:58: #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 @ Tue, 16 Jun 2020 08:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.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 08:05:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:09: 1000000 INFO @ Tue, 16 Jun 2020 08:05:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.05_summits.bed INFO @ Tue, 16 Jun 2020 08:05:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (866 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:05:15: 2000000 INFO @ Tue, 16 Jun 2020 08:05:21: 3000000 INFO @ Tue, 16 Jun 2020 08:05:26: 4000000 INFO @ Tue, 16 Jun 2020 08:05:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:05:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:05:28: #1 total tags in treatment: 4394792 INFO @ Tue, 16 Jun 2020 08:05:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:28: #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 08:05:28: #1 tags after filtering in treatment: 4394792 INFO @ Tue, 16 Jun 2020 08:05:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:29: #2 number of paired peaks: 340 WARNING @ Tue, 16 Jun 2020 08:05:29: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:29: #2 predicted fragment length is 212 bps INFO @ Tue, 16 Jun 2020 08:05:29: #2 alternative fragment length(s) may be 212 bps INFO @ Tue, 16 Jun 2020 08:05:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.10_model.r INFO @ Tue, 16 Jun 2020 08:05:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:29: #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 @ Tue, 16 Jun 2020 08:05:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.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 08:05:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:40: 1000000 INFO @ Tue, 16 Jun 2020 08:05:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.10_summits.bed INFO @ Tue, 16 Jun 2020 08:05:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (532 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:05:46: 2000000 INFO @ Tue, 16 Jun 2020 08:05:52: 3000000 INFO @ Tue, 16 Jun 2020 08:05:57: 4000000 INFO @ Tue, 16 Jun 2020 08:06:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:06:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:06:00: #1 total tags in treatment: 4394792 INFO @ Tue, 16 Jun 2020 08:06:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:00: #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 08:06:00: #1 tags after filtering in treatment: 4394792 INFO @ Tue, 16 Jun 2020 08:06:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:00: #2 number of paired peaks: 340 WARNING @ Tue, 16 Jun 2020 08:06:00: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:00: #2 predicted fragment length is 212 bps INFO @ Tue, 16 Jun 2020 08:06:00: #2 alternative fragment length(s) may be 212 bps INFO @ Tue, 16 Jun 2020 08:06:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.20_model.r INFO @ Tue, 16 Jun 2020 08:06:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:00: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:06:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:06:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208776/SRX208776.20_summits.bed INFO @ Tue, 16 Jun 2020 08:06:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 1 millis CompletedMACS2peakCalling