Job ID = 6368552 SRX = SRX5020779 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:06 prefetch.2.10.7: 1) Downloading 'SRR8201402'... 2020-06-16T00:24:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:20 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:20 prefetch.2.10.7: 'SRR8201402' is valid 2020-06-16T00:25:20 prefetch.2.10.7: 1) 'SRR8201402' was downloaded successfully Read 6066125 spots for SRR8201402/SRR8201402.sra Written 6066125 spots for SRR8201402/SRR8201402.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: 00:01:10 6066125 reads; of these: 6066125 (100.00%) were unpaired; of these: 1461481 (24.09%) aligned 0 times 3785548 (62.40%) aligned exactly 1 time 819096 (13.50%) aligned >1 times 75.91% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 453834 / 4604644 = 0.0986 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 09:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.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 09:28:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:41: 1000000 INFO @ Tue, 16 Jun 2020 09:28:47: 2000000 INFO @ Tue, 16 Jun 2020 09:28:53: 3000000 INFO @ Tue, 16 Jun 2020 09:28:59: 4000000 INFO @ Tue, 16 Jun 2020 09:29:00: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:00: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:00: #1 total tags in treatment: 4150810 INFO @ Tue, 16 Jun 2020 09:29:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:00: #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 09:29:00: #1 tags after filtering in treatment: 4150810 INFO @ Tue, 16 Jun 2020 09:29:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:00: #2 number of paired peaks: 464 WARNING @ Tue, 16 Jun 2020 09:29:00: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:00: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 09:29:00: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 16 Jun 2020 09:29:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.05_model.r WARNING @ Tue, 16 Jun 2020 09:29:00: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:00: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 16 Jun 2020 09:29:00: #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 09:29:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:00: #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 09:29:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.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 09:29:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:11: 1000000 INFO @ Tue, 16 Jun 2020 09:29:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (589 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:17: 2000000 INFO @ Tue, 16 Jun 2020 09:29:23: 3000000 INFO @ Tue, 16 Jun 2020 09:29:30: 4000000 INFO @ Tue, 16 Jun 2020 09:29:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:30: #1 total tags in treatment: 4150810 INFO @ Tue, 16 Jun 2020 09:29:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:30: #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 09:29:31: #1 tags after filtering in treatment: 4150810 INFO @ Tue, 16 Jun 2020 09:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:31: #2 number of paired peaks: 464 WARNING @ Tue, 16 Jun 2020 09:29:31: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:31: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 09:29:31: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 16 Jun 2020 09:29:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.10_model.r WARNING @ Tue, 16 Jun 2020 09:29:31: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:31: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 16 Jun 2020 09:29:31: #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 09:29:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:31: #3 Pre-compute pvalue-qvalue table... 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 09:29:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.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 09:29:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:44: 1000000 INFO @ Tue, 16 Jun 2020 09:29:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.10_summits.bed INFO @ Tue, 16 Jun 2020 09:29:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (360 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:51: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:29:59: 3000000 INFO @ Tue, 16 Jun 2020 09:30:06: 4000000 INFO @ Tue, 16 Jun 2020 09:30:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:30:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:30:07: #1 total tags in treatment: 4150810 INFO @ Tue, 16 Jun 2020 09:30:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:07: #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 09:30:07: #1 tags after filtering in treatment: 4150810 INFO @ Tue, 16 Jun 2020 09:30:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:07: #2 number of paired peaks: 464 WARNING @ Tue, 16 Jun 2020 09:30:07: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:08: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 09:30:08: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 16 Jun 2020 09:30:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.20_model.r WARNING @ Tue, 16 Jun 2020 09:30:08: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:08: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 16 Jun 2020 09:30:08: #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 09:30:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020779/SRX5020779.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 1 millis CompletedMACS2peakCalling