Job ID = 6366966 SRX = SRX2576665 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:11:46 prefetch.2.10.7: 1) Downloading 'SRR5272622'... 2020-06-15T23:11:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:47 prefetch.2.10.7: 'SRR5272622' is valid 2020-06-15T23:12:47 prefetch.2.10.7: 1) 'SRR5272622' was downloaded successfully 2020-06-15T23:12:47 prefetch.2.10.7: 'SRR5272622' has 0 unresolved dependencies Read 12133544 spots for SRR5272622/SRR5272622.sra Written 12133544 spots for SRR5272622/SRR5272622.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: 00:02:55 12133544 reads; of these: 12133544 (100.00%) were unpaired; of these: 290511 (2.39%) aligned 0 times 9570427 (78.88%) aligned exactly 1 time 2272606 (18.73%) aligned >1 times 97.61% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2664113 / 11843033 = 0.2250 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 08:19:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.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 08:19:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:13: 1000000 INFO @ Tue, 16 Jun 2020 08:19:18: 2000000 INFO @ Tue, 16 Jun 2020 08:19:23: 3000000 INFO @ Tue, 16 Jun 2020 08:19:28: 4000000 INFO @ Tue, 16 Jun 2020 08:19:33: 5000000 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 08:19:38: 6000000 INFO @ Tue, 16 Jun 2020 08:19:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.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 08:19:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:43: 7000000 INFO @ Tue, 16 Jun 2020 08:19:43: 1000000 INFO @ Tue, 16 Jun 2020 08:19:48: 8000000 INFO @ Tue, 16 Jun 2020 08:19:49: 2000000 INFO @ Tue, 16 Jun 2020 08:19:54: 9000000 INFO @ Tue, 16 Jun 2020 08:19:54: 3000000 INFO @ Tue, 16 Jun 2020 08:19:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:19:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:19:55: #1 total tags in treatment: 9178920 INFO @ Tue, 16 Jun 2020 08:19:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:55: #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 08:19:55: #1 tags after filtering in treatment: 9178920 INFO @ Tue, 16 Jun 2020 08:19:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:55: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 08:19:55: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:55: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 08:19:55: #2 alternative fragment length(s) may be 4,55,577 bps INFO @ Tue, 16 Jun 2020 08:19:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.05_model.r WARNING @ Tue, 16 Jun 2020 08:19:55: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:55: #2 You may need to consider one of the other alternative d(s): 4,55,577 WARNING @ Tue, 16 Jun 2020 08:19:55: #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 08:19:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:59: 4000000 INFO @ Tue, 16 Jun 2020 08:20:04: 5000000 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 08:20:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.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 08:20:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:09: 6000000 INFO @ Tue, 16 Jun 2020 08:20:13: 1000000 INFO @ Tue, 16 Jun 2020 08:20:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:14: 7000000 INFO @ Tue, 16 Jun 2020 08:20:18: 2000000 INFO @ Tue, 16 Jun 2020 08:20:19: 8000000 INFO @ Tue, 16 Jun 2020 08:20:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1615 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:23: 3000000 INFO @ Tue, 16 Jun 2020 08:20:24: 9000000 INFO @ Tue, 16 Jun 2020 08:20:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:20:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:20:25: #1 total tags in treatment: 9178920 INFO @ Tue, 16 Jun 2020 08:20:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:25: #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 08:20:25: #1 tags after filtering in treatment: 9178920 INFO @ Tue, 16 Jun 2020 08:20:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:26: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 08:20:26: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:26: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 08:20:26: #2 alternative fragment length(s) may be 4,55,577 bps INFO @ Tue, 16 Jun 2020 08:20:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.10_model.r WARNING @ Tue, 16 Jun 2020 08:20:26: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:26: #2 You may need to consider one of the other alternative d(s): 4,55,577 WARNING @ Tue, 16 Jun 2020 08:20:26: #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 08:20:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:28: 4000000 INFO @ Tue, 16 Jun 2020 08:20:33: 5000000 INFO @ Tue, 16 Jun 2020 08:20:38: 6000000 INFO @ Tue, 16 Jun 2020 08:20:43: 7000000 INFO @ Tue, 16 Jun 2020 08:20:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:48: 8000000 INFO @ Tue, 16 Jun 2020 08:20:53: 9000000 INFO @ Tue, 16 Jun 2020 08:20:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.10_summits.bed INFO @ Tue, 16 Jun 2020 08:20:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (640 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:20:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:20:54: #1 total tags in treatment: 9178920 INFO @ Tue, 16 Jun 2020 08:20:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:54: #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 08:20:54: #1 tags after filtering in treatment: 9178920 INFO @ Tue, 16 Jun 2020 08:20:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:55: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 08:20:55: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:55: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 08:20:55: #2 alternative fragment length(s) may be 4,55,577 bps INFO @ Tue, 16 Jun 2020 08:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.20_model.r WARNING @ Tue, 16 Jun 2020 08:20:55: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:55: #2 You may need to consider one of the other alternative d(s): 4,55,577 WARNING @ Tue, 16 Jun 2020 08:20:55: #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 08:20:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:21:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:21:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576665/SRX2576665.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 1 millis CompletedMACS2peakCalling