Job ID = 6366600 SRX = SRX208769 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:51:41 prefetch.2.10.7: 1) Downloading 'SRR628903'... 2020-06-15T22:51:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:02 prefetch.2.10.7: 'SRR628903' is valid 2020-06-15T22:53:02 prefetch.2.10.7: 1) 'SRR628903' was downloaded successfully Read 13454005 spots for SRR628903/SRR628903.sra Written 13454005 spots for SRR628903/SRR628903.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: 00:03:43 13454005 reads; of these: 13454005 (100.00%) were unpaired; of these: 1260757 (9.37%) aligned 0 times 10496782 (78.02%) aligned exactly 1 time 1696466 (12.61%) aligned >1 times 90.63% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3329870 / 12193248 = 0.2731 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 08:01:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.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 08:01:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:16: 1000000 INFO @ Tue, 16 Jun 2020 08:01:23: 2000000 INFO @ Tue, 16 Jun 2020 08:01:30: 3000000 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 08:01:37: 4000000 INFO @ Tue, 16 Jun 2020 08:01:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.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 08:01:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:45: 5000000 INFO @ Tue, 16 Jun 2020 08:01:46: 1000000 INFO @ Tue, 16 Jun 2020 08:01:53: 6000000 INFO @ Tue, 16 Jun 2020 08:01:53: 2000000 INFO @ Tue, 16 Jun 2020 08:02:00: 7000000 INFO @ Tue, 16 Jun 2020 08:02:00: 3000000 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 08:02:07: 4000000 INFO @ Tue, 16 Jun 2020 08:02:08: 8000000 INFO @ Tue, 16 Jun 2020 08:02:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.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 08:02:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:02:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:02:14: #1 total tags in treatment: 8863378 INFO @ Tue, 16 Jun 2020 08:02:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:14: #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 08:02:14: 5000000 INFO @ Tue, 16 Jun 2020 08:02:15: #1 tags after filtering in treatment: 8863378 INFO @ Tue, 16 Jun 2020 08:02:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:15: #2 number of paired peaks: 112 WARNING @ Tue, 16 Jun 2020 08:02:15: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:15: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:02:15: #2 alternative fragment length(s) may be 1,44,56,120,192,498 bps INFO @ Tue, 16 Jun 2020 08:02:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.05_model.r WARNING @ Tue, 16 Jun 2020 08:02:15: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:02:15: #2 You may need to consider one of the other alternative d(s): 1,44,56,120,192,498 WARNING @ Tue, 16 Jun 2020 08:02:15: #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 08:02:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:16: 1000000 INFO @ Tue, 16 Jun 2020 08:02:21: 6000000 INFO @ Tue, 16 Jun 2020 08:02:23: 2000000 INFO @ Tue, 16 Jun 2020 08:02:28: 7000000 INFO @ Tue, 16 Jun 2020 08:02:29: 3000000 INFO @ Tue, 16 Jun 2020 08:02:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:35: 8000000 INFO @ Tue, 16 Jun 2020 08:02:36: 4000000 INFO @ Tue, 16 Jun 2020 08:02:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:02:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:02:41: #1 total tags in treatment: 8863378 INFO @ Tue, 16 Jun 2020 08:02:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:41: #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 08:02:41: #1 tags after filtering in treatment: 8863378 INFO @ Tue, 16 Jun 2020 08:02:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:41: #2 number of paired peaks: 112 WARNING @ Tue, 16 Jun 2020 08:02:41: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:41: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:02:41: #2 alternative fragment length(s) may be 1,44,56,120,192,498 bps INFO @ Tue, 16 Jun 2020 08:02:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.10_model.r WARNING @ Tue, 16 Jun 2020 08:02:41: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:02:41: #2 You may need to consider one of the other alternative d(s): 1,44,56,120,192,498 WARNING @ Tue, 16 Jun 2020 08:02:41: #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 08:02:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.05_summits.bed INFO @ Tue, 16 Jun 2020 08:02:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (303 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:43: 5000000 INFO @ Tue, 16 Jun 2020 08:02:49: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:02:55: 7000000 INFO @ Tue, 16 Jun 2020 08:02:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:01: 8000000 INFO @ Tue, 16 Jun 2020 08:03:06: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:03:06: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:03:06: #1 total tags in treatment: 8863378 INFO @ Tue, 16 Jun 2020 08:03:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:06: #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 08:03:06: #1 tags after filtering in treatment: 8863378 INFO @ Tue, 16 Jun 2020 08:03:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.10_summits.bed INFO @ Tue, 16 Jun 2020 08:03:07: Done! INFO @ Tue, 16 Jun 2020 08:03:07: #2 number of paired peaks: 112 WARNING @ Tue, 16 Jun 2020 08:03:07: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:07: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:03:07: #2 alternative fragment length(s) may be 1,44,56,120,192,498 bps INFO @ Tue, 16 Jun 2020 08:03:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.20_model.r WARNING @ Tue, 16 Jun 2020 08:03:07: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:03:07: #2 You may need to consider one of the other alternative d(s): 1,44,56,120,192,498 WARNING @ Tue, 16 Jun 2020 08:03:07: #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 08:03:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:07: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (69 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:03:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208769/SRX208769.20_summits.bed INFO @ Tue, 16 Jun 2020 08:03:33: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 0 millis CompletedMACS2peakCalling