Job ID = 6365890 SRX = SRX012298 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:42:37 prefetch.2.10.7: 1) Downloading 'SRR029217'... 2020-06-15T22:42:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:50:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:50:08 prefetch.2.10.7: 1) 'SRR029217' was downloaded successfully Read 7829986 spots for SRR029217/SRR029217.sra Written 7829986 spots for SRR029217/SRR029217.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: 00:01:07 7829986 reads; of these: 7829986 (100.00%) were unpaired; of these: 2245020 (28.67%) aligned 0 times 4162349 (53.16%) aligned exactly 1 time 1422617 (18.17%) aligned >1 times 71.33% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1638011 / 5584966 = 0.2933 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 07:53:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.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 07:53:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:22: 1000000 INFO @ Tue, 16 Jun 2020 07:53:28: 2000000 INFO @ Tue, 16 Jun 2020 07:53:33: 3000000 INFO @ Tue, 16 Jun 2020 07:53:37: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:53:37: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:53:37: #1 total tags in treatment: 3946955 INFO @ Tue, 16 Jun 2020 07:53:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:37: #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 07:53:38: #1 tags after filtering in treatment: 3946955 INFO @ Tue, 16 Jun 2020 07:53:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:38: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:38: #2 number of paired peaks: 820 WARNING @ Tue, 16 Jun 2020 07:53:38: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:38: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:38: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:38: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:38: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:38: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 07:53:38: #2 alternative fragment length(s) may be 2,47,58,77,84,97,573,597 bps INFO @ Tue, 16 Jun 2020 07:53:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.05_model.r WARNING @ Tue, 16 Jun 2020 07:53:38: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:38: #2 You may need to consider one of the other alternative d(s): 2,47,58,77,84,97,573,597 WARNING @ Tue, 16 Jun 2020 07:53:38: #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 07:53:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:38: #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 07:53:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.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 07:53:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.05_summits.bed INFO @ Tue, 16 Jun 2020 07:53:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (260 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:53: 1000000 INFO @ Tue, 16 Jun 2020 07:53:58: 2000000 INFO @ Tue, 16 Jun 2020 07:54:03: 3000000 INFO @ Tue, 16 Jun 2020 07:54:08: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:54:08: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:54:08: #1 total tags in treatment: 3946955 INFO @ Tue, 16 Jun 2020 07:54:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:08: #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 07:54:08: #1 tags after filtering in treatment: 3946955 INFO @ Tue, 16 Jun 2020 07:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:08: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:08: #2 number of paired peaks: 820 WARNING @ Tue, 16 Jun 2020 07:54:08: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:08: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:08: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:08: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:08: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:08: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 07:54:08: #2 alternative fragment length(s) may be 2,47,58,77,84,97,573,597 bps INFO @ Tue, 16 Jun 2020 07:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.10_model.r WARNING @ Tue, 16 Jun 2020 07:54:08: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:54:08: #2 You may need to consider one of the other alternative d(s): 2,47,58,77,84,97,573,597 WARNING @ Tue, 16 Jun 2020 07:54:08: #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 07:54:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:08: #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 07:54:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.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 07:54:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.10_summits.bed INFO @ Tue, 16 Jun 2020 07:54:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (89 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:23: 1000000 INFO @ Tue, 16 Jun 2020 07:54:28: 2000000 INFO @ Tue, 16 Jun 2020 07:54:33: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:54:38: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:54:38: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:54:38: #1 total tags in treatment: 3946955 INFO @ Tue, 16 Jun 2020 07:54:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:38: #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 07:54:38: #1 tags after filtering in treatment: 3946955 INFO @ Tue, 16 Jun 2020 07:54:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:38: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:38: #2 number of paired peaks: 820 WARNING @ Tue, 16 Jun 2020 07:54:38: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:38: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:38: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:38: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:38: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:38: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 07:54:38: #2 alternative fragment length(s) may be 2,47,58,77,84,97,573,597 bps INFO @ Tue, 16 Jun 2020 07:54:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.20_model.r WARNING @ Tue, 16 Jun 2020 07:54:38: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:54:38: #2 You may need to consider one of the other alternative d(s): 2,47,58,77,84,97,573,597 WARNING @ Tue, 16 Jun 2020 07:54:38: #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 07:54:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:54:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX012298/SRX012298.20_summits.bed INFO @ Tue, 16 Jun 2020 07:54:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (20 records, 4 fields): 1 millis CompletedMACS2peakCalling