Job ID = 6367208 SRX = SRX2985928 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:41:59 prefetch.2.10.7: 1) Downloading 'SRR5807078'... 2020-06-15T23:41:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:20 prefetch.2.10.7: 1) 'SRR5807078' was downloaded successfully 2020-06-15T23:45:20 prefetch.2.10.7: 'SRR5807078' has 0 unresolved dependencies Read 42454831 spots for SRR5807078/SRR5807078.sra Written 42454831 spots for SRR5807078/SRR5807078.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: 00:10:43 42454831 reads; of these: 42454831 (100.00%) were unpaired; of these: 1021986 (2.41%) aligned 0 times 32364910 (76.23%) aligned exactly 1 time 9067935 (21.36%) aligned >1 times 97.59% overall alignment rate Time searching: 00:10:43 Overall time: 00:10:43 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 20 files... [bam_rmdupse_core] 11946956 / 41432845 = 0.2883 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 09:05:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.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 09:05:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:07: 1000000 INFO @ Tue, 16 Jun 2020 09:05:14: 2000000 INFO @ Tue, 16 Jun 2020 09:05:21: 3000000 INFO @ Tue, 16 Jun 2020 09:05:27: 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 09:05:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.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 09:05:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:34: 5000000 INFO @ Tue, 16 Jun 2020 09:05:37: 1000000 INFO @ Tue, 16 Jun 2020 09:05:41: 6000000 INFO @ Tue, 16 Jun 2020 09:05:43: 2000000 INFO @ Tue, 16 Jun 2020 09:05:47: 7000000 INFO @ Tue, 16 Jun 2020 09:05:49: 3000000 INFO @ Tue, 16 Jun 2020 09:05:54: 8000000 INFO @ Tue, 16 Jun 2020 09:05:55: 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 09:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.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 09:06:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:00: 9000000 INFO @ Tue, 16 Jun 2020 09:06:02: 5000000 INFO @ Tue, 16 Jun 2020 09:06:07: 1000000 INFO @ Tue, 16 Jun 2020 09:06:07: 10000000 INFO @ Tue, 16 Jun 2020 09:06:08: 6000000 INFO @ Tue, 16 Jun 2020 09:06:13: 2000000 INFO @ Tue, 16 Jun 2020 09:06:14: 11000000 INFO @ Tue, 16 Jun 2020 09:06:14: 7000000 INFO @ Tue, 16 Jun 2020 09:06:19: 3000000 INFO @ Tue, 16 Jun 2020 09:06:20: 12000000 INFO @ Tue, 16 Jun 2020 09:06:21: 8000000 INFO @ Tue, 16 Jun 2020 09:06:26: 4000000 INFO @ Tue, 16 Jun 2020 09:06:27: 9000000 INFO @ Tue, 16 Jun 2020 09:06:27: 13000000 INFO @ Tue, 16 Jun 2020 09:06:32: 5000000 INFO @ Tue, 16 Jun 2020 09:06:33: 10000000 INFO @ Tue, 16 Jun 2020 09:06:33: 14000000 INFO @ Tue, 16 Jun 2020 09:06:38: 6000000 INFO @ Tue, 16 Jun 2020 09:06:40: 11000000 INFO @ Tue, 16 Jun 2020 09:06:40: 15000000 INFO @ Tue, 16 Jun 2020 09:06:44: 7000000 INFO @ Tue, 16 Jun 2020 09:06:46: 12000000 INFO @ Tue, 16 Jun 2020 09:06:47: 16000000 INFO @ Tue, 16 Jun 2020 09:06:51: 8000000 INFO @ Tue, 16 Jun 2020 09:06:52: 13000000 INFO @ Tue, 16 Jun 2020 09:06:53: 17000000 INFO @ Tue, 16 Jun 2020 09:06:57: 9000000 INFO @ Tue, 16 Jun 2020 09:06:58: 14000000 INFO @ Tue, 16 Jun 2020 09:07:00: 18000000 INFO @ Tue, 16 Jun 2020 09:07:03: 10000000 INFO @ Tue, 16 Jun 2020 09:07:04: 15000000 INFO @ Tue, 16 Jun 2020 09:07:06: 19000000 INFO @ Tue, 16 Jun 2020 09:07:09: 11000000 INFO @ Tue, 16 Jun 2020 09:07:11: 16000000 INFO @ Tue, 16 Jun 2020 09:07:13: 20000000 INFO @ Tue, 16 Jun 2020 09:07:16: 12000000 INFO @ Tue, 16 Jun 2020 09:07:17: 17000000 INFO @ Tue, 16 Jun 2020 09:07:19: 21000000 INFO @ Tue, 16 Jun 2020 09:07:22: 13000000 INFO @ Tue, 16 Jun 2020 09:07:23: 18000000 INFO @ Tue, 16 Jun 2020 09:07:26: 22000000 INFO @ Tue, 16 Jun 2020 09:07:28: 14000000 INFO @ Tue, 16 Jun 2020 09:07:29: 19000000 INFO @ Tue, 16 Jun 2020 09:07:32: 23000000 INFO @ Tue, 16 Jun 2020 09:07:34: 15000000 INFO @ Tue, 16 Jun 2020 09:07:35: 20000000 INFO @ Tue, 16 Jun 2020 09:07:39: 24000000 INFO @ Tue, 16 Jun 2020 09:07:40: 16000000 INFO @ Tue, 16 Jun 2020 09:07:41: 21000000 INFO @ Tue, 16 Jun 2020 09:07:45: 25000000 INFO @ Tue, 16 Jun 2020 09:07:46: 17000000 INFO @ Tue, 16 Jun 2020 09:07:47: 22000000 INFO @ Tue, 16 Jun 2020 09:07:52: 26000000 INFO @ Tue, 16 Jun 2020 09:07:53: 18000000 INFO @ Tue, 16 Jun 2020 09:07:53: 23000000 INFO @ Tue, 16 Jun 2020 09:07:58: 27000000 INFO @ Tue, 16 Jun 2020 09:07:59: 19000000 INFO @ Tue, 16 Jun 2020 09:08:00: 24000000 INFO @ Tue, 16 Jun 2020 09:08:05: 20000000 INFO @ Tue, 16 Jun 2020 09:08:05: 28000000 INFO @ Tue, 16 Jun 2020 09:08:06: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:08:11: 21000000 INFO @ Tue, 16 Jun 2020 09:08:11: 29000000 INFO @ Tue, 16 Jun 2020 09:08:12: 26000000 INFO @ Tue, 16 Jun 2020 09:08:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:08:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:08:15: #1 total tags in treatment: 29485889 INFO @ Tue, 16 Jun 2020 09:08:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:15: #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 09:08:15: #1 tags after filtering in treatment: 29485889 INFO @ Tue, 16 Jun 2020 09:08:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:17: 22000000 INFO @ Tue, 16 Jun 2020 09:08:17: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 09:08:17: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:17: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:08:17: #2 alternative fragment length(s) may be 1,14,42,509,594 bps INFO @ Tue, 16 Jun 2020 09:08:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.05_model.r WARNING @ Tue, 16 Jun 2020 09:08:17: #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 09:08:17: #2 You may need to consider one of the other alternative d(s): 1,14,42,509,594 WARNING @ Tue, 16 Jun 2020 09:08:17: #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 09:08:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:18: 27000000 INFO @ Tue, 16 Jun 2020 09:08:23: 23000000 INFO @ Tue, 16 Jun 2020 09:08:24: 28000000 INFO @ Tue, 16 Jun 2020 09:08:29: 24000000 INFO @ Tue, 16 Jun 2020 09:08:30: 29000000 INFO @ Tue, 16 Jun 2020 09:08:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:08:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:08:33: #1 total tags in treatment: 29485889 INFO @ Tue, 16 Jun 2020 09:08:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:33: #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 09:08:33: #1 tags after filtering in treatment: 29485889 INFO @ Tue, 16 Jun 2020 09:08:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:35: 25000000 INFO @ Tue, 16 Jun 2020 09:08:35: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 09:08:35: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:36: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:08:36: #2 alternative fragment length(s) may be 1,14,42,509,594 bps INFO @ Tue, 16 Jun 2020 09:08:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.10_model.r WARNING @ Tue, 16 Jun 2020 09:08:36: #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 09:08:36: #2 You may need to consider one of the other alternative d(s): 1,14,42,509,594 WARNING @ Tue, 16 Jun 2020 09:08:36: #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 09:08:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:41: 26000000 INFO @ Tue, 16 Jun 2020 09:08:46: 27000000 INFO @ Tue, 16 Jun 2020 09:08:52: 28000000 INFO @ Tue, 16 Jun 2020 09:08:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:57: 29000000 INFO @ Tue, 16 Jun 2020 09:09:00: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:09:00: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:09:00: #1 total tags in treatment: 29485889 INFO @ Tue, 16 Jun 2020 09:09:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:00: #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 09:09:01: #1 tags after filtering in treatment: 29485889 INFO @ Tue, 16 Jun 2020 09:09:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:02: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 09:09:02: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:03: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:09:03: #2 alternative fragment length(s) may be 1,14,42,509,594 bps INFO @ Tue, 16 Jun 2020 09:09:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.20_model.r WARNING @ Tue, 16 Jun 2020 09:09:03: #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 09:09:03: #2 You may need to consider one of the other alternative d(s): 1,14,42,509,594 WARNING @ Tue, 16 Jun 2020 09:09:03: #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 09:09:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:09:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.05_summits.bed INFO @ Tue, 16 Jun 2020 09:09:14: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:09:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.10_summits.bed INFO @ Tue, 16 Jun 2020 09:09:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:09:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2985928/SRX2985928.20_summits.bed INFO @ Tue, 16 Jun 2020 09:10:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling