Job ID = 6366809 SRX = SRX234916 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:03:23 prefetch.2.10.7: 1) Downloading 'SRR707560'... 2020-06-15T23:03:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:40 prefetch.2.10.7: 'SRR707560' is valid 2020-06-15T23:03:40 prefetch.2.10.7: 1) 'SRR707560' was downloaded successfully Read 1318376 spots for SRR707560/SRR707560.sra Written 1318376 spots for SRR707560/SRR707560.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: 00:00:09 1318376 reads; of these: 1318376 (100.00%) were unpaired; of these: 642440 (48.73%) aligned 0 times 567719 (43.06%) aligned exactly 1 time 108217 (8.21%) aligned >1 times 51.27% overall alignment rate Time searching: 00:00:09 Overall time: 00:00:09 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] 114594 / 675936 = 0.1695 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 08:04:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.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 08:04:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:35: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:04:35: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:04:35: #1 total tags in treatment: 561342 INFO @ Tue, 16 Jun 2020 08:04:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:35: #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 08:04:36: #1 tags after filtering in treatment: 561342 INFO @ Tue, 16 Jun 2020 08:04:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:36: #2 number of paired peaks: 841 WARNING @ Tue, 16 Jun 2020 08:04:36: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:36: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:04:36: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:04:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.05_model.r INFO @ Tue, 16 Jun 2020 08:04:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.05_summits.bed INFO @ Tue, 16 Jun 2020 08:04:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (263 records, 4 fields): 3 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 08:05:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.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 08:05:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:05: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:05:05: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:05:05: #1 total tags in treatment: 561342 INFO @ Tue, 16 Jun 2020 08:05:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:05: #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 08:05:06: #1 tags after filtering in treatment: 561342 INFO @ Tue, 16 Jun 2020 08:05:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:06: #2 number of paired peaks: 841 WARNING @ Tue, 16 Jun 2020 08:05:06: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:06: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:05:06: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:05:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.10_model.r INFO @ Tue, 16 Jun 2020 08:05:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.10_summits.bed INFO @ Tue, 16 Jun 2020 08:05:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (95 records, 4 fields): 1 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 08:05:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.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 08:05:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:33: #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 08:05:36: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:05:36: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:05:36: #1 total tags in treatment: 561342 INFO @ Tue, 16 Jun 2020 08:05:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:36: #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 08:05:36: #1 tags after filtering in treatment: 561342 INFO @ Tue, 16 Jun 2020 08:05:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:36: #2 number of paired peaks: 841 WARNING @ Tue, 16 Jun 2020 08:05:36: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:36: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:05:36: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:05:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.20_model.r INFO @ Tue, 16 Jun 2020 08:05:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234916/SRX234916.20_summits.bed INFO @ Tue, 16 Jun 2020 08:05:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (17 records, 4 fields): 1 millis CompletedMACS2peakCalling