Job ID = 6455508 SRX = SRX287842 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:26:36 prefetch.2.10.7: 1) Downloading 'SRR870031'... 2020-06-21T10:26:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:29:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:29:51 prefetch.2.10.7: 'SRR870031' is valid 2020-06-21T10:29:51 prefetch.2.10.7: 1) 'SRR870031' was downloaded successfully Read 13389851 spots for SRR870031/SRR870031.sra Written 13389851 spots for SRR870031/SRR870031.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: 00:04:00 13389851 reads; of these: 13389851 (100.00%) were unpaired; of these: 961621 (7.18%) aligned 0 times 8386963 (62.64%) aligned exactly 1 time 4041267 (30.18%) aligned >1 times 92.82% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2019402 / 12428230 = 0.1625 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 @ Sun, 21 Jun 2020 19:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 19:38:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:11: 1000000 INFO @ Sun, 21 Jun 2020 19:38:17: 2000000 INFO @ Sun, 21 Jun 2020 19:38:23: 3000000 INFO @ Sun, 21 Jun 2020 19:38:29: 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 @ Sun, 21 Jun 2020 19:38:34: 5000000 INFO @ Sun, 21 Jun 2020 19:38:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 19:38:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:40: 6000000 INFO @ Sun, 21 Jun 2020 19:38:42: 1000000 INFO @ Sun, 21 Jun 2020 19:38:46: 7000000 INFO @ Sun, 21 Jun 2020 19:38:48: 2000000 INFO @ Sun, 21 Jun 2020 19:38:53: 8000000 INFO @ Sun, 21 Jun 2020 19:38:53: 3000000 INFO @ Sun, 21 Jun 2020 19:38:59: 9000000 INFO @ Sun, 21 Jun 2020 19:38:59: 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 @ Sun, 21 Jun 2020 19:39:05: 5000000 INFO @ Sun, 21 Jun 2020 19:39:05: 10000000 INFO @ Sun, 21 Jun 2020 19:39:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 19:39:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:39:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:39:08: #1 total tags in treatment: 10408828 INFO @ Sun, 21 Jun 2020 19:39:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:39:08: #1 tags after filtering in treatment: 10408827 INFO @ Sun, 21 Jun 2020 19:39:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:09: #2 number of paired peaks: 842 WARNING @ Sun, 21 Jun 2020 19:39:09: Fewer paired peaks (842) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 842 pairs to build model! INFO @ Sun, 21 Jun 2020 19:39:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:09: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:39:09: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:39:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.05_model.r WARNING @ Sun, 21 Jun 2020 19:39:09: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:39:09: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:39:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:39:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:39:11: 6000000 INFO @ Sun, 21 Jun 2020 19:39:11: 1000000 INFO @ Sun, 21 Jun 2020 19:39:17: 2000000 INFO @ Sun, 21 Jun 2020 19:39:17: 7000000 INFO @ Sun, 21 Jun 2020 19:39:22: 3000000 INFO @ Sun, 21 Jun 2020 19:39:23: 8000000 INFO @ Sun, 21 Jun 2020 19:39:27: 4000000 INFO @ Sun, 21 Jun 2020 19:39:30: 9000000 INFO @ Sun, 21 Jun 2020 19:39:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:32: 5000000 INFO @ Sun, 21 Jun 2020 19:39:36: 10000000 INFO @ Sun, 21 Jun 2020 19:39:38: 6000000 INFO @ Sun, 21 Jun 2020 19:39:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:39:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:39:39: #1 total tags in treatment: 10408828 INFO @ Sun, 21 Jun 2020 19:39:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:39:39: #1 tags after filtering in treatment: 10408827 INFO @ Sun, 21 Jun 2020 19:39:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:40: #2 number of paired peaks: 842 WARNING @ Sun, 21 Jun 2020 19:39:40: Fewer paired peaks (842) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 842 pairs to build model! INFO @ Sun, 21 Jun 2020 19:39:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.05_summits.bed INFO @ Sun, 21 Jun 2020 19:39:40: Done! INFO @ Sun, 21 Jun 2020 19:39:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:40: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:39:40: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:39:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.10_model.r WARNING @ Sun, 21 Jun 2020 19:39:40: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:39:40: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:39:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:39:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:40: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (623 chroms): 1 millis pass2 - checking and writing primary data (2171 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:39:43: 7000000 INFO @ Sun, 21 Jun 2020 19:39:48: 8000000 INFO @ Sun, 21 Jun 2020 19:39:53: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:39:59: 10000000 INFO @ Sun, 21 Jun 2020 19:40:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:40:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:40:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:40:01: #1 total tags in treatment: 10408828 INFO @ Sun, 21 Jun 2020 19:40:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:40:01: #1 tags after filtering in treatment: 10408827 INFO @ Sun, 21 Jun 2020 19:40:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:01: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:02: #2 number of paired peaks: 842 WARNING @ Sun, 21 Jun 2020 19:40:02: Fewer paired peaks (842) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 842 pairs to build model! INFO @ Sun, 21 Jun 2020 19:40:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:02: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:40:02: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:40:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.20_model.r WARNING @ Sun, 21 Jun 2020 19:40:02: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:40:02: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:40:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:40:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:40:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:40:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:40:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.10_summits.bed INFO @ Sun, 21 Jun 2020 19:40:11: Done! pass1 - making usageList (505 chroms): 2 millis pass2 - checking and writing primary data (1838 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:40:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287842/SRX287842.20_summits.bed INFO @ Sun, 21 Jun 2020 19:40:33: Done! pass1 - making usageList (384 chroms): 1 millis pass2 - checking and writing primary data (903 records, 4 fields): 12 millis CompletedMACS2peakCalling