Job ID = 7108750 SRX = SRX7960950 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4632513 spots for SRR11359455/SRR11359455.sra Written 4632513 spots for SRR11359455/SRR11359455.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: 00:02:01 4632513 reads; of these: 4632513 (100.00%) were unpaired; of these: 840679 (18.15%) aligned 0 times 1837773 (39.67%) aligned exactly 1 time 1954061 (42.18%) aligned >1 times 81.85% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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] 2624829 / 3791834 = 0.6922 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 Jul 2020 13:43:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.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 Jul 2020 13:43:06: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:43:06: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:43:14: 1000000 INFO @ Wed, 22 Jul 2020 13:43:16: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:43:16: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:43:16: #1 total tags in treatment: 1167005 INFO @ Wed, 22 Jul 2020 13:43:16: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:43:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:43:16: #1 tags after filtering in treatment: 1167005 INFO @ Wed, 22 Jul 2020 13:43:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:43:16: #1 finished! INFO @ Wed, 22 Jul 2020 13:43:16: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:43:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:43:16: #2 number of paired peaks: 585 WARNING @ Wed, 22 Jul 2020 13:43:16: Fewer paired peaks (585) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 585 pairs to build model! INFO @ Wed, 22 Jul 2020 13:43:16: start model_add_line... INFO @ Wed, 22 Jul 2020 13:43:16: start X-correlation... INFO @ Wed, 22 Jul 2020 13:43:16: end of X-cor INFO @ Wed, 22 Jul 2020 13:43:16: #2 finished! INFO @ Wed, 22 Jul 2020 13:43:16: #2 predicted fragment length is 187 bps INFO @ Wed, 22 Jul 2020 13:43:16: #2 alternative fragment length(s) may be 1,162,187,209,234,247,266,314,589 bps INFO @ Wed, 22 Jul 2020 13:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.05_model.r WARNING @ Wed, 22 Jul 2020 13:43:16: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:43:16: #2 You may need to consider one of the other alternative d(s): 1,162,187,209,234,247,266,314,589 WARNING @ Wed, 22 Jul 2020 13:43:16: #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 Jul 2020 13:43:16: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:43:21: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:43:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:43:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:43:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.05_summits.bed INFO @ Wed, 22 Jul 2020 13:43:22: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (175 records, 4 fields): 2 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 Jul 2020 13:43:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.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 Jul 2020 13:43:35: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:43:35: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:43:44: 1000000 INFO @ Wed, 22 Jul 2020 13:43:45: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:43:45: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:43:45: #1 total tags in treatment: 1167005 INFO @ Wed, 22 Jul 2020 13:43:45: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:43:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:43:45: #1 tags after filtering in treatment: 1167005 INFO @ Wed, 22 Jul 2020 13:43:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:43:45: #1 finished! INFO @ Wed, 22 Jul 2020 13:43:45: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:43:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:43:45: #2 number of paired peaks: 585 WARNING @ Wed, 22 Jul 2020 13:43:45: Fewer paired peaks (585) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 585 pairs to build model! INFO @ Wed, 22 Jul 2020 13:43:45: start model_add_line... INFO @ Wed, 22 Jul 2020 13:43:45: start X-correlation... INFO @ Wed, 22 Jul 2020 13:43:45: end of X-cor INFO @ Wed, 22 Jul 2020 13:43:45: #2 finished! INFO @ Wed, 22 Jul 2020 13:43:45: #2 predicted fragment length is 187 bps INFO @ Wed, 22 Jul 2020 13:43:45: #2 alternative fragment length(s) may be 1,162,187,209,234,247,266,314,589 bps INFO @ Wed, 22 Jul 2020 13:43:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.10_model.r WARNING @ Wed, 22 Jul 2020 13:43:45: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:43:45: #2 You may need to consider one of the other alternative d(s): 1,162,187,209,234,247,266,314,589 WARNING @ Wed, 22 Jul 2020 13:43:45: #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 Jul 2020 13:43:45: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:43:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:43:50: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:43:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:43:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:43:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.10_summits.bed INFO @ Wed, 22 Jul 2020 13:43:51: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 9 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 Jul 2020 13:44:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.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 Jul 2020 13:44:06: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:44:06: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:44:14: 1000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:44:15: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:44:15: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:44:15: #1 total tags in treatment: 1167005 INFO @ Wed, 22 Jul 2020 13:44:15: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:44:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:44:15: #1 tags after filtering in treatment: 1167005 INFO @ Wed, 22 Jul 2020 13:44:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:44:15: #1 finished! INFO @ Wed, 22 Jul 2020 13:44:15: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:44:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:44:15: #2 number of paired peaks: 585 WARNING @ Wed, 22 Jul 2020 13:44:15: Fewer paired peaks (585) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 585 pairs to build model! INFO @ Wed, 22 Jul 2020 13:44:15: start model_add_line... INFO @ Wed, 22 Jul 2020 13:44:15: start X-correlation... INFO @ Wed, 22 Jul 2020 13:44:15: end of X-cor INFO @ Wed, 22 Jul 2020 13:44:15: #2 finished! INFO @ Wed, 22 Jul 2020 13:44:15: #2 predicted fragment length is 187 bps INFO @ Wed, 22 Jul 2020 13:44:15: #2 alternative fragment length(s) may be 1,162,187,209,234,247,266,314,589 bps INFO @ Wed, 22 Jul 2020 13:44:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.20_model.r WARNING @ Wed, 22 Jul 2020 13:44:15: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:44:15: #2 You may need to consider one of the other alternative d(s): 1,162,187,209,234,247,266,314,589 WARNING @ Wed, 22 Jul 2020 13:44:15: #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 Jul 2020 13:44:15: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:44:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:44:20: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:44:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:44:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:44:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960950/SRX7960950.20_summits.bed INFO @ Wed, 22 Jul 2020 13:44:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 1 millis CompletedMACS2peakCalling