Job ID = 6368472 SRX = SRX5020702 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:23:18 prefetch.2.10.7: 1) Downloading 'SRR8201325'... 2020-06-16T00:23:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:13 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:13 prefetch.2.10.7: 'SRR8201325' is valid 2020-06-16T00:24:13 prefetch.2.10.7: 1) 'SRR8201325' was downloaded successfully Read 5738369 spots for SRR8201325/SRR8201325.sra Written 5738369 spots for SRR8201325/SRR8201325.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: 00:01:17 5738369 reads; of these: 5738369 (100.00%) were unpaired; of these: 54069 (0.94%) aligned 0 times 4747094 (82.73%) aligned exactly 1 time 937206 (16.33%) aligned >1 times 99.06% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 301027 / 5684300 = 0.0530 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 09:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.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 09:27:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:59: 1000000 INFO @ Tue, 16 Jun 2020 09:28:05: 2000000 INFO @ Tue, 16 Jun 2020 09:28:11: 3000000 INFO @ Tue, 16 Jun 2020 09:28:17: 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 09:28:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.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 09:28:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:23: 5000000 INFO @ Tue, 16 Jun 2020 09:28:26: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:28:26: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:28:26: #1 total tags in treatment: 5383273 INFO @ Tue, 16 Jun 2020 09:28:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:26: #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 09:28:26: #1 tags after filtering in treatment: 5383273 INFO @ Tue, 16 Jun 2020 09:28:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:26: #2 number of paired peaks: 366 WARNING @ Tue, 16 Jun 2020 09:28:26: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:26: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:28:26: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 16 Jun 2020 09:28:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.05_model.r WARNING @ Tue, 16 Jun 2020 09:28:26: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:26: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 16 Jun 2020 09:28:26: #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 09:28:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:28: 1000000 INFO @ Tue, 16 Jun 2020 09:28:34: 2000000 INFO @ Tue, 16 Jun 2020 09:28:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:40: 3000000 INFO @ Tue, 16 Jun 2020 09:28:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.05_summits.bed INFO @ Tue, 16 Jun 2020 09:28:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (614 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:28:47: 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 09:28:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.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 09:28:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:53: 5000000 INFO @ Tue, 16 Jun 2020 09:28:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:28:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:28:55: #1 total tags in treatment: 5383273 INFO @ Tue, 16 Jun 2020 09:28:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:55: #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 09:28:55: #1 tags after filtering in treatment: 5383273 INFO @ Tue, 16 Jun 2020 09:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:56: #2 number of paired peaks: 366 WARNING @ Tue, 16 Jun 2020 09:28:56: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:56: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:28:56: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 16 Jun 2020 09:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.10_model.r WARNING @ Tue, 16 Jun 2020 09:28:56: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:56: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 16 Jun 2020 09:28:56: #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 09:28:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:58: 1000000 INFO @ Tue, 16 Jun 2020 09:29:04: 2000000 INFO @ Tue, 16 Jun 2020 09:29:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:10: 3000000 INFO @ Tue, 16 Jun 2020 09:29:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.10_summits.bed INFO @ Tue, 16 Jun 2020 09:29:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:17: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:29:23: 5000000 INFO @ Tue, 16 Jun 2020 09:29:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:25: #1 total tags in treatment: 5383273 INFO @ Tue, 16 Jun 2020 09:29:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:25: #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 09:29:26: #1 tags after filtering in treatment: 5383273 INFO @ Tue, 16 Jun 2020 09:29:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:26: #2 number of paired peaks: 366 WARNING @ Tue, 16 Jun 2020 09:29:26: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:26: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:29:26: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 16 Jun 2020 09:29:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.20_model.r WARNING @ Tue, 16 Jun 2020 09:29:26: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:26: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 16 Jun 2020 09:29:26: #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 09:29:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:29:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020702/SRX5020702.20_summits.bed INFO @ Tue, 16 Jun 2020 09:29:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (101 records, 4 fields): 1 millis CompletedMACS2peakCalling