Job ID = 6455026 SRX = SRX2642377 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:52:55 prefetch.2.10.7: 1) Downloading 'SRR5345717'... 2020-06-21T09:52:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:53:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:53:53 prefetch.2.10.7: 'SRR5345717' is valid 2020-06-21T09:53:53 prefetch.2.10.7: 1) 'SRR5345717' was downloaded successfully 2020-06-21T09:53:53 prefetch.2.10.7: 'SRR5345717' has 0 unresolved dependencies Read 2751401 spots for SRR5345717/SRR5345717.sra Written 2751401 spots for SRR5345717/SRR5345717.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 2751401 reads; of these: 2751401 (100.00%) were unpaired; of these: 450426 (16.37%) aligned 0 times 1733159 (62.99%) aligned exactly 1 time 567816 (20.64%) aligned >1 times 83.63% 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] 147336 / 2300975 = 0.0640 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 18:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.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 18:56:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:57: 1000000 INFO @ Sun, 21 Jun 2020 18:57:05: 2000000 INFO @ Sun, 21 Jun 2020 18:57:07: #1 tag size is determined as 99 bps INFO @ Sun, 21 Jun 2020 18:57:07: #1 tag size = 99 INFO @ Sun, 21 Jun 2020 18:57:07: #1 total tags in treatment: 2153639 INFO @ Sun, 21 Jun 2020 18:57:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:07: #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 18:57:07: #1 tags after filtering in treatment: 2153558 INFO @ Sun, 21 Jun 2020 18:57:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:07: #2 number of paired peaks: 2353 INFO @ Sun, 21 Jun 2020 18:57:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:07: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 18:57:07: #2 alternative fragment length(s) may be 131 bps INFO @ Sun, 21 Jun 2020 18:57:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.05_model.r WARNING @ Sun, 21 Jun 2020 18:57:07: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:57:07: #2 You may need to consider one of the other alternative d(s): 131 WARNING @ Sun, 21 Jun 2020 18:57:07: #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 18:57:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.05_summits.bed INFO @ Sun, 21 Jun 2020 18:57:15: Done! pass1 - making usageList (385 chroms): 1 millis pass2 - checking and writing primary data (716 records, 4 fields): 11 millis CompletedMACS2peakCalling 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 18:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.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 18:57:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:26: 1000000 INFO @ Sun, 21 Jun 2020 18:57:34: 2000000 INFO @ Sun, 21 Jun 2020 18:57:35: #1 tag size is determined as 99 bps INFO @ Sun, 21 Jun 2020 18:57:35: #1 tag size = 99 INFO @ Sun, 21 Jun 2020 18:57:35: #1 total tags in treatment: 2153639 INFO @ Sun, 21 Jun 2020 18:57:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:35: #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 18:57:35: #1 tags after filtering in treatment: 2153558 INFO @ Sun, 21 Jun 2020 18:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:36: #2 number of paired peaks: 2353 INFO @ Sun, 21 Jun 2020 18:57:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:36: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 18:57:36: #2 alternative fragment length(s) may be 131 bps INFO @ Sun, 21 Jun 2020 18:57:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.10_model.r WARNING @ Sun, 21 Jun 2020 18:57:36: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:57:36: #2 You may need to consider one of the other alternative d(s): 131 WARNING @ Sun, 21 Jun 2020 18:57:36: #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 18:57:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.10_summits.bed INFO @ Sun, 21 Jun 2020 18:57:43: Done! pass1 - making usageList (250 chroms): 1 millis pass2 - checking and writing primary data (378 records, 4 fields): 8 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 18:57:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.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 18:57:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:56: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:58:04: 2000000 INFO @ Sun, 21 Jun 2020 18:58:05: #1 tag size is determined as 99 bps INFO @ Sun, 21 Jun 2020 18:58:05: #1 tag size = 99 INFO @ Sun, 21 Jun 2020 18:58:05: #1 total tags in treatment: 2153639 INFO @ Sun, 21 Jun 2020 18:58:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:58:06: #1 tags after filtering in treatment: 2153558 INFO @ Sun, 21 Jun 2020 18:58:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:06: #2 number of paired peaks: 2353 INFO @ Sun, 21 Jun 2020 18:58:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:06: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 18:58:06: #2 alternative fragment length(s) may be 131 bps INFO @ Sun, 21 Jun 2020 18:58:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.20_model.r WARNING @ Sun, 21 Jun 2020 18:58:06: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:58:06: #2 You may need to consider one of the other alternative d(s): 131 WARNING @ Sun, 21 Jun 2020 18:58:06: #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 18:58:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642377/SRX2642377.20_summits.bed INFO @ Sun, 21 Jun 2020 18:58:14: Done! pass1 - making usageList (109 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 5 millis CompletedMACS2peakCalling