Job ID = 6455036 SRX = SRX2642387 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:50:40 prefetch.2.10.7: 1) Downloading 'SRR5345727'... 2020-06-21T09:50:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:51:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:51:40 prefetch.2.10.7: 'SRR5345727' is valid 2020-06-21T09:51:40 prefetch.2.10.7: 1) 'SRR5345727' was downloaded successfully 2020-06-21T09:51:40 prefetch.2.10.7: 'SRR5345727' has 0 unresolved dependencies Read 2773549 spots for SRR5345727/SRR5345727.sra Written 2773549 spots for SRR5345727/SRR5345727.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 2773549 reads; of these: 2773549 (100.00%) were unpaired; of these: 452656 (16.32%) aligned 0 times 1715268 (61.84%) aligned exactly 1 time 605625 (21.84%) aligned >1 times 83.68% 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: 1870 sequences. [bam_rmdupse_core] 135007 / 2320893 = 0.0582 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 18:54:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.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 18:54:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:40: 1000000 INFO @ Sun, 21 Jun 2020 18:54:50: 2000000 INFO @ Sun, 21 Jun 2020 18:54:52: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 18:54:52: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 18:54:52: #1 total tags in treatment: 2185886 INFO @ Sun, 21 Jun 2020 18:54:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:52: #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 18:54:52: #1 tags after filtering in treatment: 2185814 INFO @ Sun, 21 Jun 2020 18:54:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:53: #2 number of paired peaks: 713 WARNING @ Sun, 21 Jun 2020 18:54:53: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sun, 21 Jun 2020 18:54:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:53: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 18:54:53: #2 alternative fragment length(s) may be 107 bps INFO @ Sun, 21 Jun 2020 18:54:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.05_model.r WARNING @ Sun, 21 Jun 2020 18:54:53: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:54:53: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Sun, 21 Jun 2020 18:54:53: #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 18:54:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:58: #3 Call peaks for each chromosome... 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 18:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.05_summits.bed INFO @ Sun, 21 Jun 2020 18:55:00: Done! pass1 - making usageList (383 chroms): 1 millis pass2 - checking and writing primary data (691 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:55:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.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 18:55:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:09: 1000000 INFO @ Sun, 21 Jun 2020 18:55:18: 2000000 INFO @ Sun, 21 Jun 2020 18:55:19: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 18:55:19: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 18:55:19: #1 total tags in treatment: 2185886 INFO @ Sun, 21 Jun 2020 18:55:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:19: #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 18:55:19: #1 tags after filtering in treatment: 2185814 INFO @ Sun, 21 Jun 2020 18:55:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:20: #2 number of paired peaks: 713 WARNING @ Sun, 21 Jun 2020 18:55:20: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sun, 21 Jun 2020 18:55:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:20: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 18:55:20: #2 alternative fragment length(s) may be 107 bps INFO @ Sun, 21 Jun 2020 18:55:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.10_model.r WARNING @ Sun, 21 Jun 2020 18:55:20: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:55:20: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Sun, 21 Jun 2020 18:55:20: #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 18:55:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:55:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.10_summits.bed INFO @ Sun, 21 Jun 2020 18:55:28: Done! pass1 - making usageList (240 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 18:55:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.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 18:55:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:39: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:55:48: 2000000 INFO @ Sun, 21 Jun 2020 18:55:49: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 18:55:49: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 18:55:49: #1 total tags in treatment: 2185886 INFO @ Sun, 21 Jun 2020 18:55:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:49: #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 18:55:49: #1 tags after filtering in treatment: 2185814 INFO @ Sun, 21 Jun 2020 18:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:50: #2 number of paired peaks: 713 WARNING @ Sun, 21 Jun 2020 18:55:50: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sun, 21 Jun 2020 18:55:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:50: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 18:55:50: #2 alternative fragment length(s) may be 107 bps INFO @ Sun, 21 Jun 2020 18:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.20_model.r WARNING @ Sun, 21 Jun 2020 18:55:50: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:55:50: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Sun, 21 Jun 2020 18:55:50: #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 18:55:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:55:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642387/SRX2642387.20_summits.bed INFO @ Sun, 21 Jun 2020 18:55:58: Done! pass1 - making usageList (103 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 5 millis CompletedMACS2peakCalling