Job ID = 6368803 SRX = SRX5709768 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:31:15 prefetch.2.10.7: 1) Downloading 'SRR8928718'... 2020-06-16T00:31:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:33:35 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:33:35 prefetch.2.10.7: 1) 'SRR8928718' was downloaded successfully 2020-06-16T00:33:35 prefetch.2.10.7: 'SRR8928718' has 0 unresolved dependencies Read 30203719 spots for SRR8928718/SRR8928718.sra Written 30203719 spots for SRR8928718/SRR8928718.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: 00:06:00 30203719 reads; of these: 30203719 (100.00%) were unpaired; of these: 4768861 (15.79%) aligned 0 times 21201844 (70.20%) aligned exactly 1 time 4233014 (14.01%) aligned >1 times 84.21% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 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 12 files... [bam_rmdupse_core] 9557992 / 25434858 = 0.3758 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 09:46:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.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 09:46:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:39: 1000000 INFO @ Tue, 16 Jun 2020 09:46:45: 2000000 INFO @ Tue, 16 Jun 2020 09:46:51: 3000000 INFO @ Tue, 16 Jun 2020 09:46:57: 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 09:47:03: 5000000 INFO @ Tue, 16 Jun 2020 09:47:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.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 09:47:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:08: 6000000 INFO @ Tue, 16 Jun 2020 09:47:09: 1000000 INFO @ Tue, 16 Jun 2020 09:47:14: 7000000 INFO @ Tue, 16 Jun 2020 09:47:15: 2000000 INFO @ Tue, 16 Jun 2020 09:47:20: 8000000 INFO @ Tue, 16 Jun 2020 09:47:20: 3000000 INFO @ Tue, 16 Jun 2020 09:47:26: 9000000 INFO @ Tue, 16 Jun 2020 09:47:26: 4000000 INFO @ Tue, 16 Jun 2020 09:47:31: 5000000 INFO @ Tue, 16 Jun 2020 09:47:31: 10000000 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 09:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.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 09:47:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:37: 6000000 INFO @ Tue, 16 Jun 2020 09:47:37: 11000000 INFO @ Tue, 16 Jun 2020 09:47:39: 1000000 INFO @ Tue, 16 Jun 2020 09:47:42: 7000000 INFO @ Tue, 16 Jun 2020 09:47:43: 12000000 INFO @ Tue, 16 Jun 2020 09:47:45: 2000000 INFO @ Tue, 16 Jun 2020 09:47:48: 8000000 INFO @ Tue, 16 Jun 2020 09:47:49: 13000000 INFO @ Tue, 16 Jun 2020 09:47:51: 3000000 INFO @ Tue, 16 Jun 2020 09:47:54: 9000000 INFO @ Tue, 16 Jun 2020 09:47:54: 14000000 INFO @ Tue, 16 Jun 2020 09:47:56: 4000000 INFO @ Tue, 16 Jun 2020 09:48:00: 10000000 INFO @ Tue, 16 Jun 2020 09:48:00: 15000000 INFO @ Tue, 16 Jun 2020 09:48:02: 5000000 INFO @ Tue, 16 Jun 2020 09:48:05: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:48:05: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:48:05: #1 total tags in treatment: 15876866 INFO @ Tue, 16 Jun 2020 09:48:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:05: #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 09:48:05: 11000000 INFO @ Tue, 16 Jun 2020 09:48:06: #1 tags after filtering in treatment: 15876866 INFO @ Tue, 16 Jun 2020 09:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:07: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 09:48:07: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:07: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:48:07: #2 alternative fragment length(s) may be 1,32 bps INFO @ Tue, 16 Jun 2020 09:48:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.05_model.r WARNING @ Tue, 16 Jun 2020 09:48:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:07: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Tue, 16 Jun 2020 09:48:07: #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 09:48:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:08: 6000000 INFO @ Tue, 16 Jun 2020 09:48:11: 12000000 INFO @ Tue, 16 Jun 2020 09:48:13: 7000000 INFO @ Tue, 16 Jun 2020 09:48:17: 13000000 INFO @ Tue, 16 Jun 2020 09:48:19: 8000000 INFO @ Tue, 16 Jun 2020 09:48:23: 14000000 INFO @ Tue, 16 Jun 2020 09:48:25: 9000000 INFO @ Tue, 16 Jun 2020 09:48:28: 15000000 INFO @ Tue, 16 Jun 2020 09:48:31: 10000000 INFO @ Tue, 16 Jun 2020 09:48:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:34: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:48:34: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:48:34: #1 total tags in treatment: 15876866 INFO @ Tue, 16 Jun 2020 09:48:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:34: #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 09:48:34: #1 tags after filtering in treatment: 15876866 INFO @ Tue, 16 Jun 2020 09:48:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:35: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 09:48:35: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:35: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:48:35: #2 alternative fragment length(s) may be 1,32 bps INFO @ Tue, 16 Jun 2020 09:48:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.10_model.r WARNING @ Tue, 16 Jun 2020 09:48:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:35: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Tue, 16 Jun 2020 09:48:35: #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 09:48:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:36: 11000000 INFO @ Tue, 16 Jun 2020 09:48:42: 12000000 INFO @ Tue, 16 Jun 2020 09:48:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.05_summits.bed INFO @ Tue, 16 Jun 2020 09:48:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:48:48: 13000000 INFO @ Tue, 16 Jun 2020 09:48:53: 14000000 INFO @ Tue, 16 Jun 2020 09:48:59: 15000000 INFO @ Tue, 16 Jun 2020 09:49:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:04: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:49:04: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:49:04: #1 total tags in treatment: 15876866 INFO @ Tue, 16 Jun 2020 09:49:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:04: #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 09:49:04: #1 tags after filtering in treatment: 15876866 INFO @ Tue, 16 Jun 2020 09:49:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:05: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 09:49:05: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:05: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:49:05: #2 alternative fragment length(s) may be 1,32 bps INFO @ Tue, 16 Jun 2020 09:49:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.20_model.r WARNING @ Tue, 16 Jun 2020 09:49:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:05: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Tue, 16 Jun 2020 09:49:05: #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 09:49:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.10_summits.bed INFO @ Tue, 16 Jun 2020 09:49:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:49:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709768/SRX5709768.20_summits.bed INFO @ Tue, 16 Jun 2020 09:49:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling