Job ID = 6368792 SRX = SRX5702599 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:34 prefetch.2.10.7: 1) Downloading 'SRR8921278'... 2020-06-16T00:29:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:49 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:49 prefetch.2.10.7: 'SRR8921278' is valid 2020-06-16T00:30:49 prefetch.2.10.7: 1) 'SRR8921278' was downloaded successfully 2020-06-16T00:30:49 prefetch.2.10.7: 'SRR8921278' has 0 unresolved dependencies Read 20623272 spots for SRR8921278/SRR8921278.sra Written 20623272 spots for SRR8921278/SRR8921278.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: 00:04:30 20623272 reads; of these: 20623272 (100.00%) were unpaired; of these: 206521 (1.00%) aligned 0 times 17014600 (82.50%) aligned exactly 1 time 3402151 (16.50%) aligned >1 times 99.00% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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] 4298766 / 20416751 = 0.2106 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 09:39:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.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 09:39:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:59: 1000000 INFO @ Tue, 16 Jun 2020 09:40:04: 2000000 INFO @ Tue, 16 Jun 2020 09:40:09: 3000000 INFO @ Tue, 16 Jun 2020 09:40:14: 4000000 INFO @ Tue, 16 Jun 2020 09:40:18: 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 09:40:23: 6000000 INFO @ Tue, 16 Jun 2020 09:40:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.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 09:40:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:28: 7000000 INFO @ Tue, 16 Jun 2020 09:40:30: 1000000 INFO @ Tue, 16 Jun 2020 09:40:33: 8000000 INFO @ Tue, 16 Jun 2020 09:40:35: 2000000 INFO @ Tue, 16 Jun 2020 09:40:38: 9000000 INFO @ Tue, 16 Jun 2020 09:40:40: 3000000 INFO @ Tue, 16 Jun 2020 09:40:43: 10000000 INFO @ Tue, 16 Jun 2020 09:40:45: 4000000 INFO @ Tue, 16 Jun 2020 09:40:48: 11000000 INFO @ Tue, 16 Jun 2020 09:40:50: 5000000 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 09:40:53: 12000000 INFO @ Tue, 16 Jun 2020 09:40:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.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 09:40:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:55: 6000000 INFO @ Tue, 16 Jun 2020 09:40:58: 13000000 INFO @ Tue, 16 Jun 2020 09:41:00: 1000000 INFO @ Tue, 16 Jun 2020 09:41:00: 7000000 INFO @ Tue, 16 Jun 2020 09:41:03: 14000000 INFO @ Tue, 16 Jun 2020 09:41:05: 2000000 INFO @ Tue, 16 Jun 2020 09:41:06: 8000000 INFO @ Tue, 16 Jun 2020 09:41:08: 15000000 INFO @ Tue, 16 Jun 2020 09:41:10: 3000000 INFO @ Tue, 16 Jun 2020 09:41:11: 9000000 INFO @ Tue, 16 Jun 2020 09:41:13: 16000000 INFO @ Tue, 16 Jun 2020 09:41:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:14: #1 total tags in treatment: 16117985 INFO @ Tue, 16 Jun 2020 09:41:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:14: #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 09:41:14: #1 tags after filtering in treatment: 16117985 INFO @ Tue, 16 Jun 2020 09:41:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:15: 4000000 INFO @ Tue, 16 Jun 2020 09:41:15: #2 number of paired peaks: 172 WARNING @ Tue, 16 Jun 2020 09:41:15: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:15: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:41:15: #2 alternative fragment length(s) may be 1,48,202,443,469,590 bps INFO @ Tue, 16 Jun 2020 09:41:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.05_model.r WARNING @ Tue, 16 Jun 2020 09:41:15: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:15: #2 You may need to consider one of the other alternative d(s): 1,48,202,443,469,590 WARNING @ Tue, 16 Jun 2020 09:41:15: #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 09:41:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:16: 10000000 INFO @ Tue, 16 Jun 2020 09:41:20: 5000000 INFO @ Tue, 16 Jun 2020 09:41:21: 11000000 INFO @ Tue, 16 Jun 2020 09:41:25: 6000000 INFO @ Tue, 16 Jun 2020 09:41:26: 12000000 INFO @ Tue, 16 Jun 2020 09:41:30: 7000000 INFO @ Tue, 16 Jun 2020 09:41:31: 13000000 INFO @ Tue, 16 Jun 2020 09:41:35: 8000000 INFO @ Tue, 16 Jun 2020 09:41:36: 14000000 INFO @ Tue, 16 Jun 2020 09:41:40: 9000000 INFO @ Tue, 16 Jun 2020 09:41:41: 15000000 INFO @ Tue, 16 Jun 2020 09:41:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:45: 10000000 INFO @ Tue, 16 Jun 2020 09:41:46: 16000000 INFO @ Tue, 16 Jun 2020 09:41:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:47: #1 total tags in treatment: 16117985 INFO @ Tue, 16 Jun 2020 09:41:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:47: #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 09:41:47: #1 tags after filtering in treatment: 16117985 INFO @ Tue, 16 Jun 2020 09:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:48: #2 number of paired peaks: 172 WARNING @ Tue, 16 Jun 2020 09:41:48: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:48: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:41:48: #2 alternative fragment length(s) may be 1,48,202,443,469,590 bps INFO @ Tue, 16 Jun 2020 09:41:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.10_model.r WARNING @ Tue, 16 Jun 2020 09:41:48: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:48: #2 You may need to consider one of the other alternative d(s): 1,48,202,443,469,590 WARNING @ Tue, 16 Jun 2020 09:41:48: #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 09:41:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:50: 11000000 INFO @ Tue, 16 Jun 2020 09:41:55: 12000000 INFO @ Tue, 16 Jun 2020 09:41:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.05_summits.bed INFO @ Tue, 16 Jun 2020 09:41:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (564 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:00: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:42:05: 14000000 INFO @ Tue, 16 Jun 2020 09:42:10: 15000000 INFO @ Tue, 16 Jun 2020 09:42:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:16: 16000000 INFO @ Tue, 16 Jun 2020 09:42:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:16: #1 total tags in treatment: 16117985 INFO @ Tue, 16 Jun 2020 09:42:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:16: #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 09:42:17: #1 tags after filtering in treatment: 16117985 INFO @ Tue, 16 Jun 2020 09:42:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:18: #2 number of paired peaks: 172 WARNING @ Tue, 16 Jun 2020 09:42:18: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:18: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:42:18: #2 alternative fragment length(s) may be 1,48,202,443,469,590 bps INFO @ Tue, 16 Jun 2020 09:42:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.20_model.r WARNING @ Tue, 16 Jun 2020 09:42:18: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:18: #2 You may need to consider one of the other alternative d(s): 1,48,202,443,469,590 WARNING @ Tue, 16 Jun 2020 09:42:18: #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 09:42:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.10_summits.bed INFO @ Tue, 16 Jun 2020 09:42:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (296 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:42:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702599/SRX5702599.20_summits.bed INFO @ Tue, 16 Jun 2020 09:42:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (86 records, 4 fields): 1 millis CompletedMACS2peakCalling