Job ID = 6369039 SRX = SRX982103 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:42:27 prefetch.2.10.7: 1) Downloading 'SRR1956590'... 2020-06-16T00:42:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:44:35 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:44:36 prefetch.2.10.7: 'SRR1956590' is valid 2020-06-16T00:44:36 prefetch.2.10.7: 1) 'SRR1956590' was downloaded successfully Read 8813316 spots for SRR1956590/SRR1956590.sra Written 8813316 spots for SRR1956590/SRR1956590.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: 00:01:24 8813316 reads; of these: 8813316 (100.00%) were unpaired; of these: 3813039 (43.26%) aligned 0 times 4173234 (47.35%) aligned exactly 1 time 827043 (9.38%) aligned >1 times 56.74% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 236536 / 5000277 = 0.0473 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 09:48:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.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 09:48:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:16: 1000000 INFO @ Tue, 16 Jun 2020 09:48:21: 2000000 INFO @ Tue, 16 Jun 2020 09:48:27: 3000000 INFO @ Tue, 16 Jun 2020 09:48:33: 4000000 INFO @ Tue, 16 Jun 2020 09:48:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:48:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:48:37: #1 total tags in treatment: 4763741 INFO @ Tue, 16 Jun 2020 09:48:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:37: #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 09:48:37: #1 tags after filtering in treatment: 4763741 INFO @ Tue, 16 Jun 2020 09:48:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:38: #2 number of paired peaks: 360 WARNING @ Tue, 16 Jun 2020 09:48:38: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:38: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:48:38: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 16 Jun 2020 09:48:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.05_model.r WARNING @ Tue, 16 Jun 2020 09:48:38: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:38: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 16 Jun 2020 09:48:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:48:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:38: #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 09:48:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.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 09:48:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:46: 1000000 INFO @ Tue, 16 Jun 2020 09:48:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:51: 2000000 INFO @ Tue, 16 Jun 2020 09:48:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.05_summits.bed INFO @ Tue, 16 Jun 2020 09:48:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:48:57: 3000000 INFO @ Tue, 16 Jun 2020 09:49:03: 4000000 INFO @ Tue, 16 Jun 2020 09:49:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:49:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:49:07: #1 total tags in treatment: 4763741 INFO @ Tue, 16 Jun 2020 09:49:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:07: #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 09:49:07: #1 tags after filtering in treatment: 4763741 INFO @ Tue, 16 Jun 2020 09:49:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:08: #2 number of paired peaks: 360 WARNING @ Tue, 16 Jun 2020 09:49:08: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:08: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:49:08: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 16 Jun 2020 09:49:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.10_model.r WARNING @ Tue, 16 Jun 2020 09:49:08: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:08: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 16 Jun 2020 09:49:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:49:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:08: #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 09:49:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.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 09:49:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:16: 1000000 INFO @ Tue, 16 Jun 2020 09:49:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:22: 2000000 INFO @ Tue, 16 Jun 2020 09:49:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.10_summits.bed INFO @ Tue, 16 Jun 2020 09:49:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (272 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:27: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:49:33: 4000000 INFO @ Tue, 16 Jun 2020 09:49:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:49:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:49:37: #1 total tags in treatment: 4763741 INFO @ Tue, 16 Jun 2020 09:49:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:37: #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 09:49:37: #1 tags after filtering in treatment: 4763741 INFO @ Tue, 16 Jun 2020 09:49:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:38: #2 number of paired peaks: 360 WARNING @ Tue, 16 Jun 2020 09:49:38: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:38: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:49:38: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 16 Jun 2020 09:49:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.20_model.r WARNING @ Tue, 16 Jun 2020 09:49:38: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:38: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 16 Jun 2020 09:49:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:49:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:49:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982103/SRX982103.20_summits.bed INFO @ Tue, 16 Jun 2020 09:49:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (116 records, 4 fields): 1 millis CompletedMACS2peakCalling