Job ID = 6367423 SRX = SRX331182 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:41:44 prefetch.2.10.7: 1) Downloading 'SRR947414'... 2020-06-15T23:41:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:43:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:43:11 prefetch.2.10.7: 'SRR947414' is valid 2020-06-15T23:43:11 prefetch.2.10.7: 1) 'SRR947414' was downloaded successfully Read 8202913 spots for SRR947414/SRR947414.sra Written 8202913 spots for SRR947414/SRR947414.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: 00:01:03 8202913 reads; of these: 8202913 (100.00%) were unpaired; of these: 2588585 (31.56%) aligned 0 times 4693637 (57.22%) aligned exactly 1 time 920691 (11.22%) aligned >1 times 68.44% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 522056 / 5614328 = 0.0930 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 08:46:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.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 08:46:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:46:15: 1000000 INFO @ Tue, 16 Jun 2020 08:46:22: 2000000 INFO @ Tue, 16 Jun 2020 08:46:28: 3000000 INFO @ Tue, 16 Jun 2020 08:46:34: 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 08:46:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.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 08:46:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:46:40: 5000000 INFO @ Tue, 16 Jun 2020 08:46:41: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:46:41: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:46:41: #1 total tags in treatment: 5092272 INFO @ Tue, 16 Jun 2020 08:46:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:41: #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 08:46:41: #1 tags after filtering in treatment: 5092272 INFO @ Tue, 16 Jun 2020 08:46:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:41: #2 number of paired peaks: 443 WARNING @ Tue, 16 Jun 2020 08:46:41: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Tue, 16 Jun 2020 08:46:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:41: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:46:41: #2 alternative fragment length(s) may be 4,38,64,537,565,578 bps INFO @ Tue, 16 Jun 2020 08:46:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.05_model.r WARNING @ Tue, 16 Jun 2020 08:46:41: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:46:41: #2 You may need to consider one of the other alternative d(s): 4,38,64,537,565,578 WARNING @ Tue, 16 Jun 2020 08:46:41: #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 08:46:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:46: 1000000 INFO @ Tue, 16 Jun 2020 08:46:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:52: 2000000 INFO @ Tue, 16 Jun 2020 08:46:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.05_summits.bed INFO @ Tue, 16 Jun 2020 08:46:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (761 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:58: 3000000 INFO @ Tue, 16 Jun 2020 08:47:05: 4000000 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 08:47:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.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 08:47:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:11: 5000000 INFO @ Tue, 16 Jun 2020 08:47:12: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:47:12: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:47:12: #1 total tags in treatment: 5092272 INFO @ Tue, 16 Jun 2020 08:47:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:12: #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 08:47:12: #1 tags after filtering in treatment: 5092272 INFO @ Tue, 16 Jun 2020 08:47:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:12: #2 number of paired peaks: 443 WARNING @ Tue, 16 Jun 2020 08:47:12: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:12: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:47:12: #2 alternative fragment length(s) may be 4,38,64,537,565,578 bps INFO @ Tue, 16 Jun 2020 08:47:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.10_model.r WARNING @ Tue, 16 Jun 2020 08:47:12: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:47:12: #2 You may need to consider one of the other alternative d(s): 4,38,64,537,565,578 WARNING @ Tue, 16 Jun 2020 08:47:12: #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 08:47:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:47:15: 1000000 INFO @ Tue, 16 Jun 2020 08:47:21: 2000000 INFO @ Tue, 16 Jun 2020 08:47:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:26: 3000000 INFO @ Tue, 16 Jun 2020 08:47:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.10_summits.bed INFO @ Tue, 16 Jun 2020 08:47:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (295 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:47:32: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:47:37: 5000000 INFO @ Tue, 16 Jun 2020 08:47:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:47:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:47:37: #1 total tags in treatment: 5092272 INFO @ Tue, 16 Jun 2020 08:47:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:37: #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 08:47:37: #1 tags after filtering in treatment: 5092272 INFO @ Tue, 16 Jun 2020 08:47:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:38: #2 number of paired peaks: 443 WARNING @ Tue, 16 Jun 2020 08:47:38: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:38: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:47:38: #2 alternative fragment length(s) may be 4,38,64,537,565,578 bps INFO @ Tue, 16 Jun 2020 08:47:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.20_model.r WARNING @ Tue, 16 Jun 2020 08:47:38: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:47:38: #2 You may need to consider one of the other alternative d(s): 4,38,64,537,565,578 WARNING @ Tue, 16 Jun 2020 08:47:38: #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 08:47:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:47:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331182/SRX331182.20_summits.bed INFO @ Tue, 16 Jun 2020 08:47:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (81 records, 4 fields): 1 millis CompletedMACS2peakCalling