Job ID = 6366306 SRX = SRX1078730 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:34:36 prefetch.2.10.7: 1) Downloading 'SRR2084337'... 2020-06-15T22:34:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:35:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:35:45 prefetch.2.10.7: 'SRR2084337' is valid 2020-06-15T22:35:45 prefetch.2.10.7: 1) 'SRR2084337' was downloaded successfully Read 9405441 spots for SRR2084337/SRR2084337.sra Written 9405441 spots for SRR2084337/SRR2084337.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: 00:02:09 9405441 reads; of these: 9405441 (100.00%) were unpaired; of these: 153832 (1.64%) aligned 0 times 7689194 (81.75%) aligned exactly 1 time 1562415 (16.61%) aligned >1 times 98.36% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 744426 / 9251609 = 0.0805 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 07:41:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.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 07:41:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:30: 1000000 INFO @ Tue, 16 Jun 2020 07:41:37: 2000000 INFO @ Tue, 16 Jun 2020 07:41:43: 3000000 INFO @ Tue, 16 Jun 2020 07:41:50: 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 07:41:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.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 07:41:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:56: 5000000 INFO @ Tue, 16 Jun 2020 07:42:00: 1000000 INFO @ Tue, 16 Jun 2020 07:42:03: 6000000 INFO @ Tue, 16 Jun 2020 07:42:06: 2000000 INFO @ Tue, 16 Jun 2020 07:42:10: 7000000 INFO @ Tue, 16 Jun 2020 07:42:12: 3000000 INFO @ Tue, 16 Jun 2020 07:42:16: 8000000 INFO @ Tue, 16 Jun 2020 07:42:18: 4000000 INFO @ Tue, 16 Jun 2020 07:42:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:42:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:42:20: #1 total tags in treatment: 8507183 INFO @ Tue, 16 Jun 2020 07:42:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:20: #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 07:42:20: #1 tags after filtering in treatment: 8507183 INFO @ Tue, 16 Jun 2020 07:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:20: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:20: #2 number of paired peaks: 415 WARNING @ Tue, 16 Jun 2020 07:42:20: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:20: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:20: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:20: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:20: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:20: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 07:42:20: #2 alternative fragment length(s) may be 3,50,555 bps INFO @ Tue, 16 Jun 2020 07:42:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.05_model.r WARNING @ Tue, 16 Jun 2020 07:42:20: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:42:20: #2 You may need to consider one of the other alternative d(s): 3,50,555 WARNING @ Tue, 16 Jun 2020 07:42:20: #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 07:42:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:20: #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 07:42:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.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 07:42:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:24: 5000000 INFO @ Tue, 16 Jun 2020 07:42:30: 1000000 INFO @ Tue, 16 Jun 2020 07:42:30: 6000000 INFO @ Tue, 16 Jun 2020 07:42:36: 2000000 INFO @ Tue, 16 Jun 2020 07:42:37: 7000000 INFO @ Tue, 16 Jun 2020 07:42:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:42: 3000000 INFO @ Tue, 16 Jun 2020 07:42:42: 8000000 INFO @ Tue, 16 Jun 2020 07:42:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:42:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:42:45: #1 total tags in treatment: 8507183 INFO @ Tue, 16 Jun 2020 07:42:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:45: #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 07:42:46: #1 tags after filtering in treatment: 8507183 INFO @ Tue, 16 Jun 2020 07:42:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:46: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:46: #2 number of paired peaks: 415 WARNING @ Tue, 16 Jun 2020 07:42:46: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:46: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:46: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:46: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:46: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:46: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 07:42:46: #2 alternative fragment length(s) may be 3,50,555 bps INFO @ Tue, 16 Jun 2020 07:42:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.10_model.r WARNING @ Tue, 16 Jun 2020 07:42:46: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:42:46: #2 You may need to consider one of the other alternative d(s): 3,50,555 WARNING @ Tue, 16 Jun 2020 07:42:46: #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 07:42:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:42:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.05_summits.bed INFO @ Tue, 16 Jun 2020 07:42:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (647 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:42:48: 4000000 INFO @ Tue, 16 Jun 2020 07:42:53: 5000000 INFO @ Tue, 16 Jun 2020 07:42:59: 6000000 INFO @ Tue, 16 Jun 2020 07:43:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:05: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:43:11: 8000000 INFO @ Tue, 16 Jun 2020 07:43:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.10_summits.bed INFO @ Tue, 16 Jun 2020 07:43:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:43:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:43:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:43:14: #1 total tags in treatment: 8507183 INFO @ Tue, 16 Jun 2020 07:43:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:14: #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 07:43:14: #1 tags after filtering in treatment: 8507183 INFO @ Tue, 16 Jun 2020 07:43:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:14: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:15: #2 number of paired peaks: 415 WARNING @ Tue, 16 Jun 2020 07:43:15: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Tue, 16 Jun 2020 07:43:15: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:15: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:15: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:15: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:15: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 07:43:15: #2 alternative fragment length(s) may be 3,50,555 bps INFO @ Tue, 16 Jun 2020 07:43:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.20_model.r WARNING @ Tue, 16 Jun 2020 07:43:15: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:43:15: #2 You may need to consider one of the other alternative d(s): 3,50,555 WARNING @ Tue, 16 Jun 2020 07:43:15: #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 07:43:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:43:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078730/SRX1078730.20_summits.bed INFO @ Tue, 16 Jun 2020 07:43:41: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (187 records, 4 fields): 1 millis CompletedMACS2peakCalling