Job ID = 6366014 SRX = SRX054206 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:45:07 prefetch.2.10.7: 1) Downloading 'SRR163972'... 2020-06-15T22:45:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:45:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:45:55 prefetch.2.10.7: 'SRR163972' is valid 2020-06-15T22:45:55 prefetch.2.10.7: 1) 'SRR163972' was downloaded successfully Read 6132744 spots for SRR163972/SRR163972.sra Written 6132744 spots for SRR163972/SRR163972.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: 00:00:53 6132744 reads; of these: 6132744 (100.00%) were unpaired; of these: 2028352 (33.07%) aligned 0 times 3608525 (58.84%) aligned exactly 1 time 495867 (8.09%) aligned >1 times 66.93% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 283229 / 4104392 = 0.0690 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 07:48:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.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 07:48:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:50: 1000000 INFO @ Tue, 16 Jun 2020 07:48:55: 2000000 INFO @ Tue, 16 Jun 2020 07:49:01: 3000000 INFO @ Tue, 16 Jun 2020 07:49:06: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:49:06: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:49:06: #1 total tags in treatment: 3821163 INFO @ Tue, 16 Jun 2020 07:49:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:06: #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 07:49:06: #1 tags after filtering in treatment: 3821163 INFO @ Tue, 16 Jun 2020 07:49:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:06: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:07: #2 number of paired peaks: 210 WARNING @ Tue, 16 Jun 2020 07:49:07: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 16 Jun 2020 07:49:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:07: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 07:49:07: #2 alternative fragment length(s) may be 3,35,64,66,91,119,547,598 bps INFO @ Tue, 16 Jun 2020 07:49:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.05_model.r WARNING @ Tue, 16 Jun 2020 07:49:07: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:49:07: #2 You may need to consider one of the other alternative d(s): 3,35,64,66,91,119,547,598 WARNING @ Tue, 16 Jun 2020 07:49:07: #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 07:49:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:07: #3 Pre-compute pvalue-qvalue table... 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 07:49:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.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 07:49:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:49:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.05_summits.bed INFO @ Tue, 16 Jun 2020 07:49:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:49:22: 1000000 INFO @ Tue, 16 Jun 2020 07:49:30: 2000000 INFO @ Tue, 16 Jun 2020 07:49:37: 3000000 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 07:49:44: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:49:44: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:49:44: #1 total tags in treatment: 3821163 INFO @ Tue, 16 Jun 2020 07:49:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:44: #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 07:49:44: #1 tags after filtering in treatment: 3821163 INFO @ Tue, 16 Jun 2020 07:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:44: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:44: #2 number of paired peaks: 210 WARNING @ Tue, 16 Jun 2020 07:49:44: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 16 Jun 2020 07:49:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.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 07:49:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:49:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:44: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 07:49:44: #2 alternative fragment length(s) may be 3,35,64,66,91,119,547,598 bps INFO @ Tue, 16 Jun 2020 07:49:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.10_model.r WARNING @ Tue, 16 Jun 2020 07:49:44: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:49:44: #2 You may need to consider one of the other alternative d(s): 3,35,64,66,91,119,547,598 WARNING @ Tue, 16 Jun 2020 07:49:44: #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 07:49:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:49:50: 1000000 INFO @ Tue, 16 Jun 2020 07:49:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:56: 2000000 INFO @ Tue, 16 Jun 2020 07:49:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.10_summits.bed INFO @ Tue, 16 Jun 2020 07:49:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:50:02: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:50:07: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:50:07: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:50:07: #1 total tags in treatment: 3821163 INFO @ Tue, 16 Jun 2020 07:50:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:07: #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 07:50:08: #1 tags after filtering in treatment: 3821163 INFO @ Tue, 16 Jun 2020 07:50:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:08: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:08: #2 number of paired peaks: 210 WARNING @ Tue, 16 Jun 2020 07:50:08: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:08: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:08: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:08: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:08: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:08: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 07:50:08: #2 alternative fragment length(s) may be 3,35,64,66,91,119,547,598 bps INFO @ Tue, 16 Jun 2020 07:50:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.20_model.r WARNING @ Tue, 16 Jun 2020 07:50:08: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:50:08: #2 You may need to consider one of the other alternative d(s): 3,35,64,66,91,119,547,598 WARNING @ Tue, 16 Jun 2020 07:50:08: #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 07:50:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:50:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054206/SRX054206.20_summits.bed INFO @ Tue, 16 Jun 2020 07:50:21: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling