Job ID = 6366024 SRX = SRX054252 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:45:22 prefetch.2.10.7: 1) Downloading 'SRR164258'... 2020-06-15T22:45:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:45:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:45:52 prefetch.2.10.7: 'SRR164258' is valid 2020-06-15T22:45:52 prefetch.2.10.7: 1) 'SRR164258' was downloaded successfully Read 2829693 spots for SRR164258/SRR164258.sra Written 2829693 spots for SRR164258/SRR164258.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: 00:00:16 2829693 reads; of these: 2829693 (100.00%) were unpaired; of these: 2041436 (72.14%) aligned 0 times 685059 (24.21%) aligned exactly 1 time 103198 (3.65%) aligned >1 times 27.86% overall alignment rate Time searching: 00:00:16 Overall time: 00:00:16 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] 30753 / 788257 = 0.0390 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 07:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.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 07:47:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:47:06: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:47:06: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:47:06: #1 total tags in treatment: 757504 INFO @ Tue, 16 Jun 2020 07:47:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:06: #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 07:47:06: #1 tags after filtering in treatment: 757504 INFO @ Tue, 16 Jun 2020 07:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:06: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:06: #2 number of paired peaks: 672 WARNING @ Tue, 16 Jun 2020 07:47:06: Fewer paired peaks (672) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 672 pairs to build model! INFO @ Tue, 16 Jun 2020 07:47:06: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:06: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:06: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:06: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:06: #2 predicted fragment length is 121 bps INFO @ Tue, 16 Jun 2020 07:47:06: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 16 Jun 2020 07:47:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.05_model.r INFO @ Tue, 16 Jun 2020 07:47:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.05_summits.bed INFO @ Tue, 16 Jun 2020 07:47:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 1 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 07:47:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.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 07:47:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:47:36: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:47:36: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:47:36: #1 total tags in treatment: 757504 INFO @ Tue, 16 Jun 2020 07:47:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:36: #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 07:47:36: #1 tags after filtering in treatment: 757504 INFO @ Tue, 16 Jun 2020 07:47:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:36: #2 number of paired peaks: 672 WARNING @ Tue, 16 Jun 2020 07:47:36: Fewer paired peaks (672) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 672 pairs to build model! INFO @ Tue, 16 Jun 2020 07:47:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:36: #2 predicted fragment length is 121 bps INFO @ Tue, 16 Jun 2020 07:47:36: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 16 Jun 2020 07:47:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.10_model.r INFO @ Tue, 16 Jun 2020 07:47:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.10_summits.bed INFO @ Tue, 16 Jun 2020 07:47:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (52 records, 4 fields): 0 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 07:48:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.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 07:48:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:01: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:48:06: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:48:06: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:48:06: #1 total tags in treatment: 757504 INFO @ Tue, 16 Jun 2020 07:48:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:06: #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 07:48:06: #1 tags after filtering in treatment: 757504 INFO @ Tue, 16 Jun 2020 07:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:06: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:06: #2 number of paired peaks: 672 WARNING @ Tue, 16 Jun 2020 07:48:06: Fewer paired peaks (672) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 672 pairs to build model! INFO @ Tue, 16 Jun 2020 07:48:06: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:06: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:06: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:06: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:06: #2 predicted fragment length is 121 bps INFO @ Tue, 16 Jun 2020 07:48:06: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 16 Jun 2020 07:48:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.20_model.r INFO @ Tue, 16 Jun 2020 07:48:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:48:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054252/SRX054252.20_summits.bed INFO @ Tue, 16 Jun 2020 07:48:09: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 0 millis CompletedMACS2peakCalling