Job ID = 6366057 SRX = SRX059229 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:38:06 prefetch.2.10.7: 1) Downloading 'SRR190669'... 2020-06-15T22:38:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:40:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:40:24 prefetch.2.10.7: 1) 'SRR190669' was downloaded successfully Read 20333805 spots for SRR190669/SRR190669.sra Written 20333805 spots for SRR190669/SRR190669.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: 00:03:54 20333805 reads; of these: 20333805 (100.00%) were unpaired; of these: 241920 (1.19%) aligned 0 times 16212157 (79.73%) aligned exactly 1 time 3879728 (19.08%) aligned >1 times 98.81% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 2867093 / 20091885 = 0.1427 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 07:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.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 07:50:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:43: 1000000 INFO @ Tue, 16 Jun 2020 07:50:48: 2000000 INFO @ Tue, 16 Jun 2020 07:50:53: 3000000 INFO @ Tue, 16 Jun 2020 07:50:59: 4000000 INFO @ Tue, 16 Jun 2020 07:51:04: 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 07:51:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.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 07:51:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:10: 6000000 INFO @ Tue, 16 Jun 2020 07:51:12: 1000000 INFO @ Tue, 16 Jun 2020 07:51:15: 7000000 INFO @ Tue, 16 Jun 2020 07:51:18: 2000000 INFO @ Tue, 16 Jun 2020 07:51:21: 8000000 INFO @ Tue, 16 Jun 2020 07:51:24: 3000000 INFO @ Tue, 16 Jun 2020 07:51:26: 9000000 INFO @ Tue, 16 Jun 2020 07:51:29: 4000000 INFO @ Tue, 16 Jun 2020 07:51:32: 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 07:51:35: 5000000 INFO @ Tue, 16 Jun 2020 07:51:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.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 07:51:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:38: 11000000 INFO @ Tue, 16 Jun 2020 07:51:42: 6000000 INFO @ Tue, 16 Jun 2020 07:51:43: 1000000 INFO @ Tue, 16 Jun 2020 07:51:44: 12000000 INFO @ Tue, 16 Jun 2020 07:51:49: 7000000 INFO @ Tue, 16 Jun 2020 07:51:49: 2000000 INFO @ Tue, 16 Jun 2020 07:51:50: 13000000 INFO @ Tue, 16 Jun 2020 07:51:55: 3000000 INFO @ Tue, 16 Jun 2020 07:51:55: 8000000 INFO @ Tue, 16 Jun 2020 07:51:56: 14000000 INFO @ Tue, 16 Jun 2020 07:52:01: 4000000 INFO @ Tue, 16 Jun 2020 07:52:01: 9000000 INFO @ Tue, 16 Jun 2020 07:52:02: 15000000 INFO @ Tue, 16 Jun 2020 07:52:06: 5000000 INFO @ Tue, 16 Jun 2020 07:52:07: 10000000 INFO @ Tue, 16 Jun 2020 07:52:08: 16000000 INFO @ Tue, 16 Jun 2020 07:52:13: 6000000 INFO @ Tue, 16 Jun 2020 07:52:14: 17000000 INFO @ Tue, 16 Jun 2020 07:52:14: 11000000 INFO @ Tue, 16 Jun 2020 07:52:15: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:52:15: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:52:15: #1 total tags in treatment: 17224792 INFO @ Tue, 16 Jun 2020 07:52:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:15: #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 07:52:15: #1 tags after filtering in treatment: 17224792 INFO @ Tue, 16 Jun 2020 07:52:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:15: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:16: #2 number of paired peaks: 212 WARNING @ Tue, 16 Jun 2020 07:52:16: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:16: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:17: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:17: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:17: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:17: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:52:17: #2 alternative fragment length(s) may be 1,19,23,39,523,543,563,576 bps INFO @ Tue, 16 Jun 2020 07:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.05_model.r WARNING @ Tue, 16 Jun 2020 07:52:17: #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 07:52:17: #2 You may need to consider one of the other alternative d(s): 1,19,23,39,523,543,563,576 WARNING @ Tue, 16 Jun 2020 07:52:17: #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 07:52:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:19: 7000000 INFO @ Tue, 16 Jun 2020 07:52:20: 12000000 INFO @ Tue, 16 Jun 2020 07:52:24: 8000000 INFO @ Tue, 16 Jun 2020 07:52:26: 13000000 INFO @ Tue, 16 Jun 2020 07:52:30: 9000000 INFO @ Tue, 16 Jun 2020 07:52:33: 14000000 INFO @ Tue, 16 Jun 2020 07:52:36: 10000000 INFO @ Tue, 16 Jun 2020 07:52:39: 15000000 INFO @ Tue, 16 Jun 2020 07:52:43: 11000000 INFO @ Tue, 16 Jun 2020 07:52:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:45: 16000000 INFO @ Tue, 16 Jun 2020 07:52:49: 12000000 INFO @ Tue, 16 Jun 2020 07:52:51: 17000000 INFO @ Tue, 16 Jun 2020 07:52:53: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:52:53: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:52:53: #1 total tags in treatment: 17224792 INFO @ Tue, 16 Jun 2020 07:52:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:53: #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 07:52:53: #1 tags after filtering in treatment: 17224792 INFO @ Tue, 16 Jun 2020 07:52:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:53: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:54: #2 number of paired peaks: 212 WARNING @ Tue, 16 Jun 2020 07:52:54: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:54: start model_add_line... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:52:54: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:54: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:54: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:54: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:52:54: #2 alternative fragment length(s) may be 1,19,23,39,523,543,563,576 bps INFO @ Tue, 16 Jun 2020 07:52:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.10_model.r WARNING @ Tue, 16 Jun 2020 07:52:54: #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 07:52:54: #2 You may need to consider one of the other alternative d(s): 1,19,23,39,523,543,563,576 WARNING @ Tue, 16 Jun 2020 07:52:54: #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 07:52:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:55: 13000000 INFO @ Tue, 16 Jun 2020 07:53:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.05_summits.bed INFO @ Tue, 16 Jun 2020 07:53:00: Done! pass1 - making usageList (0 chroms): 12 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:03: 14000000 INFO @ Tue, 16 Jun 2020 07:53:09: 15000000 INFO @ Tue, 16 Jun 2020 07:53:15: 16000000 INFO @ Tue, 16 Jun 2020 07:53:20: 17000000 INFO @ Tue, 16 Jun 2020 07:53:22: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:53:22: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:53:22: #1 total tags in treatment: 17224792 INFO @ Tue, 16 Jun 2020 07:53:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:22: #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 07:53:22: #1 tags after filtering in treatment: 17224792 INFO @ Tue, 16 Jun 2020 07:53:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:22: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:23: #2 number of paired peaks: 212 WARNING @ Tue, 16 Jun 2020 07:53:23: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:23: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:23: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:23: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:23: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:23: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:53:23: #2 alternative fragment length(s) may be 1,19,23,39,523,543,563,576 bps INFO @ Tue, 16 Jun 2020 07:53:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.20_model.r WARNING @ Tue, 16 Jun 2020 07:53:23: #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 07:53:23: #2 You may need to consider one of the other alternative d(s): 1,19,23,39,523,543,563,576 WARNING @ Tue, 16 Jun 2020 07:53:23: #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 07:53:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:25: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.10_summits.bed INFO @ Tue, 16 Jun 2020 07:53:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059229/SRX059229.20_summits.bed INFO @ Tue, 16 Jun 2020 07:54:04: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling