Job ID = 6368540 SRX = SRX5020768 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:21:36 prefetch.2.10.7: 1) Downloading 'SRR8201391'... 2020-06-16T00:21:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:54 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:54 prefetch.2.10.7: 1) 'SRR8201391' was downloaded successfully Read 12685473 spots for SRR8201391/SRR8201391.sra Written 12685473 spots for SRR8201391/SRR8201391.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: 00:03:52 12685473 reads; of these: 12685473 (100.00%) were unpaired; of these: 2931859 (23.11%) aligned 0 times 8238445 (64.94%) aligned exactly 1 time 1515169 (11.94%) aligned >1 times 76.89% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 1707839 / 9753614 = 0.1751 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 09:32:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.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 09:32:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:12: 1000000 INFO @ Tue, 16 Jun 2020 09:32:18: 2000000 INFO @ Tue, 16 Jun 2020 09:32:24: 3000000 INFO @ Tue, 16 Jun 2020 09:32:30: 4000000 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 09:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.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 09:32:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:37: 5000000 INFO @ Tue, 16 Jun 2020 09:32:42: 1000000 INFO @ Tue, 16 Jun 2020 09:32:43: 6000000 INFO @ Tue, 16 Jun 2020 09:32:48: 2000000 INFO @ Tue, 16 Jun 2020 09:32:49: 7000000 INFO @ Tue, 16 Jun 2020 09:32:54: 3000000 INFO @ Tue, 16 Jun 2020 09:32:56: 8000000 INFO @ Tue, 16 Jun 2020 09:32:56: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:32:56: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:32:56: #1 total tags in treatment: 8045775 INFO @ Tue, 16 Jun 2020 09:32:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:56: #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 09:32:56: #1 tags after filtering in treatment: 8045775 INFO @ Tue, 16 Jun 2020 09:32:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:57: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 09:32:57: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:57: #2 predicted fragment length is 91 bps INFO @ Tue, 16 Jun 2020 09:32:57: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 16 Jun 2020 09:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.05_model.r WARNING @ Tue, 16 Jun 2020 09:32:57: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:57: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Tue, 16 Jun 2020 09:32:57: #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 09:32:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:00: 4000000 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 09:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.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 09:33:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:07: 5000000 INFO @ Tue, 16 Jun 2020 09:33:11: 1000000 INFO @ Tue, 16 Jun 2020 09:33:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:13: 6000000 INFO @ Tue, 16 Jun 2020 09:33:16: 2000000 INFO @ Tue, 16 Jun 2020 09:33:20: 7000000 INFO @ Tue, 16 Jun 2020 09:33:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.05_summits.bed INFO @ Tue, 16 Jun 2020 09:33:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (900 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:22: 3000000 INFO @ Tue, 16 Jun 2020 09:33:26: 8000000 INFO @ Tue, 16 Jun 2020 09:33:26: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:33:26: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:33:26: #1 total tags in treatment: 8045775 INFO @ Tue, 16 Jun 2020 09:33:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:26: #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 09:33:26: #1 tags after filtering in treatment: 8045775 INFO @ Tue, 16 Jun 2020 09:33:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:27: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 09:33:27: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:27: #2 predicted fragment length is 91 bps INFO @ Tue, 16 Jun 2020 09:33:27: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 16 Jun 2020 09:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.10_model.r WARNING @ Tue, 16 Jun 2020 09:33:27: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:27: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Tue, 16 Jun 2020 09:33:27: #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 09:33:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:27: 4000000 INFO @ Tue, 16 Jun 2020 09:33:33: 5000000 INFO @ Tue, 16 Jun 2020 09:33:38: 6000000 INFO @ Tue, 16 Jun 2020 09:33:43: 7000000 INFO @ Tue, 16 Jun 2020 09:33:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:49: 8000000 INFO @ Tue, 16 Jun 2020 09:33:49: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:33:49: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:33:49: #1 total tags in treatment: 8045775 INFO @ Tue, 16 Jun 2020 09:33:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:49: #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 09:33:49: #1 tags after filtering in treatment: 8045775 INFO @ Tue, 16 Jun 2020 09:33:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:50: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 09:33:50: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:50: #2 predicted fragment length is 91 bps INFO @ Tue, 16 Jun 2020 09:33:50: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 16 Jun 2020 09:33:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.20_model.r WARNING @ Tue, 16 Jun 2020 09:33:50: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:50: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Tue, 16 Jun 2020 09:33:50: #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 09:33:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.10_summits.bed INFO @ Tue, 16 Jun 2020 09:33:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (496 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:34:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:34:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020768/SRX5020768.20_summits.bed INFO @ Tue, 16 Jun 2020 09:34:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (268 records, 4 fields): 2 millis CompletedMACS2peakCalling