Job ID = 6366808 SRX = SRX234915 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:00:38 prefetch.2.10.7: 1) Downloading 'SRR707559'... 2020-06-15T23:00:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:13 prefetch.2.10.7: 'SRR707559' is valid 2020-06-15T23:01:13 prefetch.2.10.7: 1) 'SRR707559' was downloaded successfully Read 7466694 spots for SRR707559/SRR707559.sra Written 7466694 spots for SRR707559/SRR707559.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 7466694 reads; of these: 7466694 (100.00%) were unpaired; of these: 2432482 (32.58%) aligned 0 times 4215421 (56.46%) aligned exactly 1 time 818791 (10.97%) aligned >1 times 67.42% 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] 324478 / 5034212 = 0.0645 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 08:04:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.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 08:04:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:23: 1000000 INFO @ Tue, 16 Jun 2020 08:04:29: 2000000 INFO @ Tue, 16 Jun 2020 08:04:35: 3000000 INFO @ Tue, 16 Jun 2020 08:04:42: 4000000 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 08:04:46: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:04:46: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:04:46: #1 total tags in treatment: 4709734 INFO @ Tue, 16 Jun 2020 08:04:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:46: #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 08:04:46: #1 tags after filtering in treatment: 4709734 INFO @ Tue, 16 Jun 2020 08:04:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:46: #2 number of paired peaks: 425 WARNING @ Tue, 16 Jun 2020 08:04:46: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:47: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:04:47: #2 alternative fragment length(s) may be 3,34,564,570,572 bps INFO @ Tue, 16 Jun 2020 08:04:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.05_model.r WARNING @ Tue, 16 Jun 2020 08:04:47: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:47: #2 You may need to consider one of the other alternative d(s): 3,34,564,570,572 WARNING @ Tue, 16 Jun 2020 08:04:47: #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 08:04:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.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 08:04:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:53: 1000000 INFO @ Tue, 16 Jun 2020 08:04:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:58: 2000000 INFO @ Tue, 16 Jun 2020 08:05:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.05_summits.bed INFO @ Tue, 16 Jun 2020 08:05:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (500 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:05:04: 3000000 INFO @ Tue, 16 Jun 2020 08:05:10: 4000000 INFO @ Tue, 16 Jun 2020 08:05:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:05:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:05:13: #1 total tags in treatment: 4709734 INFO @ Tue, 16 Jun 2020 08:05:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:13: #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 08:05:14: #1 tags after filtering in treatment: 4709734 INFO @ Tue, 16 Jun 2020 08:05:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:14: #2 number of paired peaks: 425 WARNING @ Tue, 16 Jun 2020 08:05:14: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:14: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:05:14: #2 alternative fragment length(s) may be 3,34,564,570,572 bps INFO @ Tue, 16 Jun 2020 08:05:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.10_model.r WARNING @ Tue, 16 Jun 2020 08:05:14: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:14: #2 You may need to consider one of the other alternative d(s): 3,34,564,570,572 WARNING @ Tue, 16 Jun 2020 08:05:14: #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 08:05:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:14: #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 08:05:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.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 08:05:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:23: 1000000 INFO @ Tue, 16 Jun 2020 08:05:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:29: 2000000 INFO @ Tue, 16 Jun 2020 08:05:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.10_summits.bed INFO @ Tue, 16 Jun 2020 08:05:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (227 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:05:34: 3000000 INFO @ Tue, 16 Jun 2020 08:05:40: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:05:44: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:05:44: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:05:44: #1 total tags in treatment: 4709734 INFO @ Tue, 16 Jun 2020 08:05:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:44: #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 08:05:44: #1 tags after filtering in treatment: 4709734 INFO @ Tue, 16 Jun 2020 08:05:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:44: #2 number of paired peaks: 425 WARNING @ Tue, 16 Jun 2020 08:05:44: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:44: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:05:44: #2 alternative fragment length(s) may be 3,34,564,570,572 bps INFO @ Tue, 16 Jun 2020 08:05:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.20_model.r WARNING @ Tue, 16 Jun 2020 08:05:44: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:44: #2 You may need to consider one of the other alternative d(s): 3,34,564,570,572 WARNING @ Tue, 16 Jun 2020 08:05:44: #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 08:05:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:05:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234915/SRX234915.20_summits.bed INFO @ Tue, 16 Jun 2020 08:06:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 millis CompletedMACS2peakCalling