Job ID = 6455031 SRX = SRX2642382 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:38:55 prefetch.2.10.7: 1) Downloading 'SRR5345722'... 2020-06-21T09:38:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:40:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:40:14 prefetch.2.10.7: 'SRR5345722' is valid 2020-06-21T09:40:14 prefetch.2.10.7: 1) 'SRR5345722' was downloaded successfully 2020-06-21T09:40:14 prefetch.2.10.7: 'SRR5345722' has 0 unresolved dependencies Read 3236615 spots for SRR5345722/SRR5345722.sra Written 3236615 spots for SRR5345722/SRR5345722.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: 00:01:44 3236615 reads; of these: 3236615 (100.00%) were unpaired; of these: 600046 (18.54%) aligned 0 times 1901598 (58.75%) aligned exactly 1 time 734971 (22.71%) aligned >1 times 81.46% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 223816 / 2636569 = 0.0849 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 18:44:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.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 18:44:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:17: 1000000 INFO @ Sun, 21 Jun 2020 18:44:29: 2000000 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 18:44:35: #1 tag size is determined as 99 bps INFO @ Sun, 21 Jun 2020 18:44:35: #1 tag size = 99 INFO @ Sun, 21 Jun 2020 18:44:35: #1 total tags in treatment: 2412753 INFO @ Sun, 21 Jun 2020 18:44:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:35: #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 18:44:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.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 18:44:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:35: #1 tags after filtering in treatment: 2412707 INFO @ Sun, 21 Jun 2020 18:44:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:35: #2 number of paired peaks: 418 WARNING @ Sun, 21 Jun 2020 18:44:35: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Sun, 21 Jun 2020 18:44:35: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:35: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 18:44:35: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 18:44:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.05_model.r WARNING @ Sun, 21 Jun 2020 18:44:35: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:44:35: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sun, 21 Jun 2020 18:44:35: #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 18:44:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.05_summits.bed INFO @ Sun, 21 Jun 2020 18:44:44: Done! pass1 - making usageList (372 chroms): 1 millis pass2 - checking and writing primary data (685 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:44:47: 1000000 INFO @ Sun, 21 Jun 2020 18:44:59: 2000000 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 18:45:04: #1 tag size is determined as 99 bps INFO @ Sun, 21 Jun 2020 18:45:04: #1 tag size = 99 INFO @ Sun, 21 Jun 2020 18:45:04: #1 total tags in treatment: 2412753 INFO @ Sun, 21 Jun 2020 18:45:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:04: #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 18:45:05: #1 tags after filtering in treatment: 2412707 INFO @ Sun, 21 Jun 2020 18:45:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:05: #2 number of paired peaks: 418 WARNING @ Sun, 21 Jun 2020 18:45:05: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:05: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 18:45:05: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 18:45:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.10_model.r WARNING @ Sun, 21 Jun 2020 18:45:05: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:05: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sun, 21 Jun 2020 18:45:05: #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 18:45:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.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 18:45:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.10_summits.bed INFO @ Sun, 21 Jun 2020 18:45:13: Done! pass1 - making usageList (225 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:45:18: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:45:30: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:45:36: #1 tag size is determined as 99 bps INFO @ Sun, 21 Jun 2020 18:45:36: #1 tag size = 99 INFO @ Sun, 21 Jun 2020 18:45:36: #1 total tags in treatment: 2412753 INFO @ Sun, 21 Jun 2020 18:45:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:36: #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 18:45:36: #1 tags after filtering in treatment: 2412707 INFO @ Sun, 21 Jun 2020 18:45:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:36: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:37: #2 number of paired peaks: 418 WARNING @ Sun, 21 Jun 2020 18:45:37: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:37: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 18:45:37: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 18:45:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.20_model.r WARNING @ Sun, 21 Jun 2020 18:45:37: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:37: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sun, 21 Jun 2020 18:45:37: #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 18:45:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642382/SRX2642382.20_summits.bed INFO @ Sun, 21 Jun 2020 18:45:45: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 7 millis CompletedMACS2peakCalling