Job ID = 6366550 SRX = SRX188616 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:50:26 prefetch.2.10.7: 1) Downloading 'SRR573723'... 2020-06-15T22:50:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:50:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:50:51 prefetch.2.10.7: 'SRR573723' is valid 2020-06-15T22:50:51 prefetch.2.10.7: 1) 'SRR573723' was downloaded successfully Read 3175883 spots for SRR573723/SRR573723.sra Written 3175883 spots for SRR573723/SRR573723.sra 2020-06-15T22:51:11 prefetch.2.10.7: 1) Downloading 'SRR573724'... 2020-06-15T22:51:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:51:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:51:40 prefetch.2.10.7: 'SRR573724' is valid 2020-06-15T22:51:40 prefetch.2.10.7: 1) 'SRR573724' was downloaded successfully Read 4085478 spots for SRR573724/SRR573724.sra Written 4085478 spots for SRR573724/SRR573724.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: 00:00:38 7261361 reads; of these: 7261361 (100.00%) were unpaired; of these: 5933883 (81.72%) aligned 0 times 1180203 (16.25%) aligned exactly 1 time 147275 (2.03%) aligned >1 times 18.28% overall alignment rate Time searching: 00:00:38 Overall time: 00:00:38 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] 77328 / 1327478 = 0.0583 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 07:53:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.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 07:53:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:31: 1000000 INFO @ Tue, 16 Jun 2020 07:53:33: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:53:33: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:53:33: #1 total tags in treatment: 1250150 INFO @ Tue, 16 Jun 2020 07:53:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:33: #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 07:53:33: #1 tags after filtering in treatment: 1250150 INFO @ Tue, 16 Jun 2020 07:53:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:33: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:33: #2 number of paired peaks: 263 WARNING @ Tue, 16 Jun 2020 07:53:33: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:33: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:33: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:33: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:33: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:33: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 07:53:33: #2 alternative fragment length(s) may be 40,65,107,125,179,442,479,536 bps INFO @ Tue, 16 Jun 2020 07:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.05_model.r WARNING @ Tue, 16 Jun 2020 07:53:33: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:33: #2 You may need to consider one of the other alternative d(s): 40,65,107,125,179,442,479,536 WARNING @ Tue, 16 Jun 2020 07:53:33: #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 07:53:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.05_summits.bed INFO @ Tue, 16 Jun 2020 07:53:37: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (50 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:53:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.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 07:53:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:03: 1000000 INFO @ Tue, 16 Jun 2020 07:54:05: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:54:05: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:54:05: #1 total tags in treatment: 1250150 INFO @ Tue, 16 Jun 2020 07:54:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:05: #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 07:54:05: #1 tags after filtering in treatment: 1250150 INFO @ Tue, 16 Jun 2020 07:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:05: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:05: #2 number of paired peaks: 263 WARNING @ Tue, 16 Jun 2020 07:54:05: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:05: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:05: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:05: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:05: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:05: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 07:54:05: #2 alternative fragment length(s) may be 40,65,107,125,179,442,479,536 bps INFO @ Tue, 16 Jun 2020 07:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.10_model.r WARNING @ Tue, 16 Jun 2020 07:54:05: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:54:05: #2 You may need to consider one of the other alternative d(s): 40,65,107,125,179,442,479,536 WARNING @ Tue, 16 Jun 2020 07:54:05: #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 07:54:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:54:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.10_summits.bed INFO @ Tue, 16 Jun 2020 07:54:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (18 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:54:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.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 07:54:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:26: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:54:32: 1000000 INFO @ Tue, 16 Jun 2020 07:54:33: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:54:33: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:54:33: #1 total tags in treatment: 1250150 INFO @ Tue, 16 Jun 2020 07:54:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:33: #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 07:54:33: #1 tags after filtering in treatment: 1250150 INFO @ Tue, 16 Jun 2020 07:54:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:33: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:34: #2 number of paired peaks: 263 WARNING @ Tue, 16 Jun 2020 07:54:34: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:34: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:34: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:34: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:34: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:34: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 07:54:34: #2 alternative fragment length(s) may be 40,65,107,125,179,442,479,536 bps INFO @ Tue, 16 Jun 2020 07:54:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.20_model.r WARNING @ Tue, 16 Jun 2020 07:54:34: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:54:34: #2 You may need to consider one of the other alternative d(s): 40,65,107,125,179,442,479,536 WARNING @ Tue, 16 Jun 2020 07:54:34: #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 07:54:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:54:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188616/SRX188616.20_summits.bed INFO @ Tue, 16 Jun 2020 07:54:38: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling