Job ID = 6366807 SRX = SRX234914 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:04:53 prefetch.2.10.7: 1) Downloading 'SRR707558'... 2020-06-15T23:04:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:05:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:05:25 prefetch.2.10.7: 'SRR707558' is valid 2020-06-15T23:05:25 prefetch.2.10.7: 1) 'SRR707558' was downloaded successfully Read 6807499 spots for SRR707558/SRR707558.sra Written 6807499 spots for SRR707558/SRR707558.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: 00:00:58 6807499 reads; of these: 6807499 (100.00%) were unpaired; of these: 1817561 (26.70%) aligned 0 times 4183607 (61.46%) aligned exactly 1 time 806331 (11.84%) aligned >1 times 73.30% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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] 385809 / 4989938 = 0.0773 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 08:08:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.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 08:08:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:19: 1000000 INFO @ Tue, 16 Jun 2020 08:08:24: 2000000 INFO @ Tue, 16 Jun 2020 08:08:30: 3000000 INFO @ Tue, 16 Jun 2020 08:08:35: 4000000 INFO @ Tue, 16 Jun 2020 08:08:38: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:08:38: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:08:38: #1 total tags in treatment: 4604129 INFO @ Tue, 16 Jun 2020 08:08:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:38: #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 08:08:38: #1 tags after filtering in treatment: 4604129 INFO @ Tue, 16 Jun 2020 08:08:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:38: #2 number of paired peaks: 429 WARNING @ Tue, 16 Jun 2020 08:08:38: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:38: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:08:38: #2 alternative fragment length(s) may be 3,30,489,561,577 bps INFO @ Tue, 16 Jun 2020 08:08:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.05_model.r WARNING @ Tue, 16 Jun 2020 08:08:38: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:38: #2 You may need to consider one of the other alternative d(s): 3,30,489,561,577 WARNING @ Tue, 16 Jun 2020 08:08:38: #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 08:08:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:38: #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 08:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.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 08:08:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:49: 1000000 INFO @ Tue, 16 Jun 2020 08:08:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (472 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:54: 2000000 INFO @ Tue, 16 Jun 2020 08:09:00: 3000000 INFO @ Tue, 16 Jun 2020 08:09:05: 4000000 INFO @ Tue, 16 Jun 2020 08:09:08: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:09:08: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:09:08: #1 total tags in treatment: 4604129 INFO @ Tue, 16 Jun 2020 08:09:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:08: #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 08:09:08: #1 tags after filtering in treatment: 4604129 INFO @ Tue, 16 Jun 2020 08:09:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:09: #2 number of paired peaks: 429 WARNING @ Tue, 16 Jun 2020 08:09:09: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:09: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:09:09: #2 alternative fragment length(s) may be 3,30,489,561,577 bps INFO @ Tue, 16 Jun 2020 08:09:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.10_model.r WARNING @ Tue, 16 Jun 2020 08:09:09: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:09:09: #2 You may need to consider one of the other alternative d(s): 3,30,489,561,577 WARNING @ Tue, 16 Jun 2020 08:09:09: #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 08:09:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:09: #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 08:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.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 08:09:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:19: 1000000 INFO @ Tue, 16 Jun 2020 08:09:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.10_summits.bed INFO @ Tue, 16 Jun 2020 08:09:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (234 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:09:24: 2000000 INFO @ Tue, 16 Jun 2020 08:09:30: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:09:35: 4000000 INFO @ Tue, 16 Jun 2020 08:09:38: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:09:38: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:09:38: #1 total tags in treatment: 4604129 INFO @ Tue, 16 Jun 2020 08:09:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:38: #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 08:09:38: #1 tags after filtering in treatment: 4604129 INFO @ Tue, 16 Jun 2020 08:09:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:38: #2 number of paired peaks: 429 WARNING @ Tue, 16 Jun 2020 08:09:38: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:38: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:09:38: #2 alternative fragment length(s) may be 3,30,489,561,577 bps INFO @ Tue, 16 Jun 2020 08:09:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.20_model.r WARNING @ Tue, 16 Jun 2020 08:09:38: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:09:38: #2 You may need to consider one of the other alternative d(s): 3,30,489,561,577 WARNING @ Tue, 16 Jun 2020 08:09:38: #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 08:09:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:09:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234914/SRX234914.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (41 records, 4 fields): 0 millis CompletedMACS2peakCalling