Job ID = 6368395 SRX = SRX495074 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:17:25 prefetch.2.10.7: 1) Downloading 'SRR1198606'... 2020-06-16T00:17:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:19:29 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:19:29 prefetch.2.10.7: 1) 'SRR1198606' was downloaded successfully Read 13809537 spots for SRR1198606/SRR1198606.sra Written 13809537 spots for SRR1198606/SRR1198606.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: 00:02:17 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 2268837 (16.43%) aligned 0 times 9710141 (70.31%) aligned exactly 1 time 1830559 (13.26%) aligned >1 times 83.57% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 1988096 / 11540700 = 0.1723 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 09:25:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.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 09:25:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:32: 1000000 INFO @ Tue, 16 Jun 2020 09:25:37: 2000000 INFO @ Tue, 16 Jun 2020 09:25:42: 3000000 INFO @ Tue, 16 Jun 2020 09:25:47: 4000000 INFO @ Tue, 16 Jun 2020 09:25:51: 5000000 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 09:25:56: 6000000 INFO @ Tue, 16 Jun 2020 09:25:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.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 09:25:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:01: 7000000 INFO @ Tue, 16 Jun 2020 09:26:02: 1000000 INFO @ Tue, 16 Jun 2020 09:26:07: 8000000 INFO @ Tue, 16 Jun 2020 09:26:07: 2000000 INFO @ Tue, 16 Jun 2020 09:26:12: 9000000 INFO @ Tue, 16 Jun 2020 09:26:12: 3000000 INFO @ Tue, 16 Jun 2020 09:26:15: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:26:15: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:26:15: #1 total tags in treatment: 9552604 INFO @ Tue, 16 Jun 2020 09:26:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:15: #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 09:26:15: #1 tags after filtering in treatment: 9552604 INFO @ Tue, 16 Jun 2020 09:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:15: #2 number of paired peaks: 292 WARNING @ Tue, 16 Jun 2020 09:26:15: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:16: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:26:16: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 16 Jun 2020 09:26:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.05_model.r WARNING @ Tue, 16 Jun 2020 09:26:16: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:16: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 16 Jun 2020 09:26:16: #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 09:26:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:17: 4000000 INFO @ Tue, 16 Jun 2020 09:26:22: 5000000 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 09:26:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.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 09:26:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:27: 6000000 INFO @ Tue, 16 Jun 2020 09:26:32: 1000000 INFO @ Tue, 16 Jun 2020 09:26:32: 7000000 INFO @ Tue, 16 Jun 2020 09:26:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:37: 2000000 INFO @ Tue, 16 Jun 2020 09:26:37: 8000000 INFO @ Tue, 16 Jun 2020 09:26:42: 3000000 INFO @ Tue, 16 Jun 2020 09:26:43: 9000000 INFO @ Tue, 16 Jun 2020 09:26:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.05_summits.bed INFO @ Tue, 16 Jun 2020 09:26:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (589 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:46: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:26:46: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:26:46: #1 total tags in treatment: 9552604 INFO @ Tue, 16 Jun 2020 09:26:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:46: #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 09:26:46: #1 tags after filtering in treatment: 9552604 INFO @ Tue, 16 Jun 2020 09:26:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:46: #2 number of paired peaks: 292 WARNING @ Tue, 16 Jun 2020 09:26:46: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:47: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:26:47: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 16 Jun 2020 09:26:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.10_model.r WARNING @ Tue, 16 Jun 2020 09:26:47: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:47: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 16 Jun 2020 09:26:47: #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 09:26:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:48: 4000000 INFO @ Tue, 16 Jun 2020 09:26:52: 5000000 INFO @ Tue, 16 Jun 2020 09:26:57: 6000000 INFO @ Tue, 16 Jun 2020 09:27:02: 7000000 INFO @ Tue, 16 Jun 2020 09:27:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:08: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:27:13: 9000000 INFO @ Tue, 16 Jun 2020 09:27:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.10_summits.bed INFO @ Tue, 16 Jun 2020 09:27:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (289 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:27:16: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:27:16: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:27:16: #1 total tags in treatment: 9552604 INFO @ Tue, 16 Jun 2020 09:27:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:16: #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 09:27:16: #1 tags after filtering in treatment: 9552604 INFO @ Tue, 16 Jun 2020 09:27:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:17: #2 number of paired peaks: 292 WARNING @ Tue, 16 Jun 2020 09:27:17: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:17: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:27:17: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 16 Jun 2020 09:27:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.20_model.r WARNING @ Tue, 16 Jun 2020 09:27:17: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:27:17: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 16 Jun 2020 09:27:17: #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 09:27:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:27:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495074/SRX495074.20_summits.bed INFO @ Tue, 16 Jun 2020 09:27:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 1 millis CompletedMACS2peakCalling