Job ID = 6366204 SRX = SRX076079 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:49:07 prefetch.2.10.7: 1) Downloading 'SRR275569'... 2020-06-15T22:49:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:50:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:50:00 prefetch.2.10.7: 'SRR275569' is valid 2020-06-15T22:50:00 prefetch.2.10.7: 1) 'SRR275569' was downloaded successfully Read 12806974 spots for SRR275569/SRR275569.sra Written 12806974 spots for SRR275569/SRR275569.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: 00:02:05 12806974 reads; of these: 12806974 (100.00%) were unpaired; of these: 1085550 (8.48%) aligned 0 times 9617421 (75.10%) aligned exactly 1 time 2104003 (16.43%) aligned >1 times 91.52% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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_rmdupse_core] 1218713 / 11721424 = 0.1040 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 07:55:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.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 07:55:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:20: 1000000 INFO @ Tue, 16 Jun 2020 07:55:25: 2000000 INFO @ Tue, 16 Jun 2020 07:55:30: 3000000 INFO @ Tue, 16 Jun 2020 07:55:34: 4000000 INFO @ Tue, 16 Jun 2020 07:55:39: 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 07:55:44: 6000000 INFO @ Tue, 16 Jun 2020 07:55:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.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 07:55:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:49: 7000000 INFO @ Tue, 16 Jun 2020 07:55:51: 1000000 INFO @ Tue, 16 Jun 2020 07:55:55: 8000000 INFO @ Tue, 16 Jun 2020 07:55:56: 2000000 INFO @ Tue, 16 Jun 2020 07:56:00: 9000000 INFO @ Tue, 16 Jun 2020 07:56:01: 3000000 INFO @ Tue, 16 Jun 2020 07:56:05: 10000000 INFO @ Tue, 16 Jun 2020 07:56:07: 4000000 INFO @ Tue, 16 Jun 2020 07:56:08: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:56:08: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:56:08: #1 total tags in treatment: 10502711 INFO @ Tue, 16 Jun 2020 07:56:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:56:08: #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 07:56:08: #1 tags after filtering in treatment: 10502711 INFO @ Tue, 16 Jun 2020 07:56:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:56:08: #1 finished! INFO @ Tue, 16 Jun 2020 07:56:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:56:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:56:09: #2 number of paired peaks: 341 WARNING @ Tue, 16 Jun 2020 07:56:09: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Tue, 16 Jun 2020 07:56:09: start model_add_line... INFO @ Tue, 16 Jun 2020 07:56:09: start X-correlation... INFO @ Tue, 16 Jun 2020 07:56:09: end of X-cor INFO @ Tue, 16 Jun 2020 07:56:09: #2 finished! INFO @ Tue, 16 Jun 2020 07:56:09: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 07:56:09: #2 alternative fragment length(s) may be 2,36,537 bps INFO @ Tue, 16 Jun 2020 07:56:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.05_model.r WARNING @ Tue, 16 Jun 2020 07:56:09: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:56:09: #2 You may need to consider one of the other alternative d(s): 2,36,537 WARNING @ Tue, 16 Jun 2020 07:56:09: #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 07:56:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:56:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:56:12: 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 07:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.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 07:56:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:17: 6000000 INFO @ Tue, 16 Jun 2020 07:56:20: 1000000 INFO @ Tue, 16 Jun 2020 07:56:22: 7000000 INFO @ Tue, 16 Jun 2020 07:56:26: 2000000 INFO @ Tue, 16 Jun 2020 07:56:28: 8000000 INFO @ Tue, 16 Jun 2020 07:56:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:56:31: 3000000 INFO @ Tue, 16 Jun 2020 07:56:33: 9000000 INFO @ Tue, 16 Jun 2020 07:56:36: 4000000 INFO @ Tue, 16 Jun 2020 07:56:39: 10000000 INFO @ Tue, 16 Jun 2020 07:56:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:56:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:56:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.05_summits.bed INFO @ Tue, 16 Jun 2020 07:56:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (616 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:56:41: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:56:41: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:56:41: #1 total tags in treatment: 10502711 INFO @ Tue, 16 Jun 2020 07:56:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:56:41: #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 07:56:42: #1 tags after filtering in treatment: 10502711 INFO @ Tue, 16 Jun 2020 07:56:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:56:42: #1 finished! INFO @ Tue, 16 Jun 2020 07:56:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:56:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:56:42: 5000000 INFO @ Tue, 16 Jun 2020 07:56:42: #2 number of paired peaks: 341 WARNING @ Tue, 16 Jun 2020 07:56:42: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Tue, 16 Jun 2020 07:56:42: start model_add_line... INFO @ Tue, 16 Jun 2020 07:56:42: start X-correlation... INFO @ Tue, 16 Jun 2020 07:56:42: end of X-cor INFO @ Tue, 16 Jun 2020 07:56:42: #2 finished! INFO @ Tue, 16 Jun 2020 07:56:42: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 07:56:42: #2 alternative fragment length(s) may be 2,36,537 bps INFO @ Tue, 16 Jun 2020 07:56:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.10_model.r WARNING @ Tue, 16 Jun 2020 07:56:42: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:56:42: #2 You may need to consider one of the other alternative d(s): 2,36,537 WARNING @ Tue, 16 Jun 2020 07:56:42: #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 07:56:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:56:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:56:47: 6000000 INFO @ Tue, 16 Jun 2020 07:56:52: 7000000 INFO @ Tue, 16 Jun 2020 07:56:57: 8000000 INFO @ Tue, 16 Jun 2020 07:57:02: 9000000 INFO @ Tue, 16 Jun 2020 07:57:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:57:07: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:57:09: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:57:09: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:57:09: #1 total tags in treatment: 10502711 INFO @ Tue, 16 Jun 2020 07:57:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:09: #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 07:57:10: #1 tags after filtering in treatment: 10502711 INFO @ Tue, 16 Jun 2020 07:57:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:10: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:10: #2 number of paired peaks: 341 WARNING @ Tue, 16 Jun 2020 07:57:10: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Tue, 16 Jun 2020 07:57:10: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:10: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:10: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:10: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:10: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 07:57:10: #2 alternative fragment length(s) may be 2,36,537 bps INFO @ Tue, 16 Jun 2020 07:57:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.20_model.r WARNING @ Tue, 16 Jun 2020 07:57:10: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:57:10: #2 You may need to consider one of the other alternative d(s): 2,36,537 WARNING @ Tue, 16 Jun 2020 07:57:10: #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 07:57:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:57:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:57:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:57:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.10_summits.bed INFO @ Tue, 16 Jun 2020 07:57:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (277 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:57:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:57:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:57:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:57:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX076079/SRX076079.20_summits.bed INFO @ Tue, 16 Jun 2020 07:57:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (95 records, 4 fields): 1 millis CompletedMACS2peakCalling