Job ID = 5790867 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 691,000 reads read : 1,382,000 reads written : 691,000 reads 0-length : 691,000 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:07 691000 reads; of these: 691000 (100.00%) were unpaired; of these: 213 (0.03%) aligned 0 times 603924 (87.40%) aligned exactly 1 time 86863 (12.57%) aligned >1 times 99.97% overall alignment rate Time searching: 00:00:07 Overall time: 00:00:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 67135 / 690787 = 0.0972 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 @ Wed, 22 Apr 2020 07:59:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Apr 2020 07:59:03: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:59:03: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:59:06: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 07:59:06: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 07:59:06: #1 total tags in treatment: 623652 INFO @ Wed, 22 Apr 2020 07:59:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:59:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:59:06: #1 tags after filtering in treatment: 623652 INFO @ Wed, 22 Apr 2020 07:59:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:59:06: #1 finished! INFO @ Wed, 22 Apr 2020 07:59:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:59:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:59:06: #2 number of paired peaks: 211 WARNING @ Wed, 22 Apr 2020 07:59:06: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Wed, 22 Apr 2020 07:59:06: start model_add_line... INFO @ Wed, 22 Apr 2020 07:59:06: start X-correlation... INFO @ Wed, 22 Apr 2020 07:59:06: end of X-cor INFO @ Wed, 22 Apr 2020 07:59:06: #2 finished! INFO @ Wed, 22 Apr 2020 07:59:06: #2 predicted fragment length is 117 bps INFO @ Wed, 22 Apr 2020 07:59:06: #2 alternative fragment length(s) may be 117 bps INFO @ Wed, 22 Apr 2020 07:59:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.05_model.r WARNING @ Wed, 22 Apr 2020 07:59:06: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:59:06: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Wed, 22 Apr 2020 07:59:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:59:06: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:59:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:59:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:59:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:59:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:59:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.05_summits.bed INFO @ Wed, 22 Apr 2020 07:59:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (580 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 @ Wed, 22 Apr 2020 07:59:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Apr 2020 07:59:33: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:59:33: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:59:36: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 07:59:36: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 07:59:36: #1 total tags in treatment: 623652 INFO @ Wed, 22 Apr 2020 07:59:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:59:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:59:36: #1 tags after filtering in treatment: 623652 INFO @ Wed, 22 Apr 2020 07:59:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:59:36: #1 finished! INFO @ Wed, 22 Apr 2020 07:59:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:59:36: #2 number of paired peaks: 211 WARNING @ Wed, 22 Apr 2020 07:59:36: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Wed, 22 Apr 2020 07:59:36: start model_add_line... INFO @ Wed, 22 Apr 2020 07:59:36: start X-correlation... INFO @ Wed, 22 Apr 2020 07:59:36: end of X-cor INFO @ Wed, 22 Apr 2020 07:59:36: #2 finished! INFO @ Wed, 22 Apr 2020 07:59:36: #2 predicted fragment length is 117 bps INFO @ Wed, 22 Apr 2020 07:59:36: #2 alternative fragment length(s) may be 117 bps INFO @ Wed, 22 Apr 2020 07:59:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.10_model.r WARNING @ Wed, 22 Apr 2020 07:59:36: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:59:36: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Wed, 22 Apr 2020 07:59:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:59:36: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:59:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:59:38: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:59:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:59:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:59:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.10_summits.bed INFO @ Wed, 22 Apr 2020 07:59:38: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (303 records, 4 fields): 3 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 @ Wed, 22 Apr 2020 08:00:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Apr 2020 08:00:03: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:00:03: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:00:07: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:00:07: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:00:07: #1 total tags in treatment: 623652 INFO @ Wed, 22 Apr 2020 08:00:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:00:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:00:07: #1 tags after filtering in treatment: 623652 INFO @ Wed, 22 Apr 2020 08:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:00:07: #1 finished! INFO @ Wed, 22 Apr 2020 08:00:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:00:07: #2 number of paired peaks: 211 WARNING @ Wed, 22 Apr 2020 08:00:07: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Wed, 22 Apr 2020 08:00:07: start model_add_line... INFO @ Wed, 22 Apr 2020 08:00:07: start X-correlation... INFO @ Wed, 22 Apr 2020 08:00:07: end of X-cor INFO @ Wed, 22 Apr 2020 08:00:07: #2 finished! INFO @ Wed, 22 Apr 2020 08:00:07: #2 predicted fragment length is 117 bps INFO @ Wed, 22 Apr 2020 08:00:07: #2 alternative fragment length(s) may be 117 bps INFO @ Wed, 22 Apr 2020 08:00:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.20_model.r WARNING @ Wed, 22 Apr 2020 08:00:07: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:00:07: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Wed, 22 Apr 2020 08:00:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:00:07: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:00:07: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:00:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:00:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550806/SRX5550806.20_summits.bed INFO @ Wed, 22 Apr 2020 08:00:09: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (135 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。