Job ID = 6458324 SRX = SRX5011074 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:21:22 prefetch.2.10.7: 1) Downloading 'SRR8191523'... 2020-06-21T12:21:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:22:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:23:00 prefetch.2.10.7: 'SRR8191523' is valid 2020-06-21T12:23:00 prefetch.2.10.7: 1) 'SRR8191523' was downloaded successfully 2020-06-21T12:23:00 prefetch.2.10.7: 'SRR8191523' has 0 unresolved dependencies Read 21860819 spots for SRR8191523/SRR8191523.sra Written 21860819 spots for SRR8191523/SRR8191523.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:46 21860819 reads; of these: 21860819 (100.00%) were unpaired; of these: 3121800 (14.28%) aligned 0 times 14769963 (67.56%) aligned exactly 1 time 3969056 (18.16%) aligned >1 times 85.72% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 12409222 / 18739019 = 0.6622 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 21:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.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 21:31:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:31:57: 1000000 INFO @ Sun, 21 Jun 2020 21:32:03: 2000000 INFO @ Sun, 21 Jun 2020 21:32:08: 3000000 INFO @ Sun, 21 Jun 2020 21:32:14: 4000000 INFO @ Sun, 21 Jun 2020 21:32:20: 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 @ Sun, 21 Jun 2020 21:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.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 21:32:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:26: 6000000 INFO @ Sun, 21 Jun 2020 21:32:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:32:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:32:28: #1 total tags in treatment: 6329797 INFO @ Sun, 21 Jun 2020 21:32:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:28: #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 21:32:28: #1 tags after filtering in treatment: 6329697 INFO @ Sun, 21 Jun 2020 21:32:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:29: #2 number of paired peaks: 2403 INFO @ Sun, 21 Jun 2020 21:32:29: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:29: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:29: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:29: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:29: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:32:29: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:32:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.05_model.r INFO @ Sun, 21 Jun 2020 21:32:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:29: 1000000 INFO @ Sun, 21 Jun 2020 21:32:36: 2000000 INFO @ Sun, 21 Jun 2020 21:32:43: 3000000 INFO @ Sun, 21 Jun 2020 21:32:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:32:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:32:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:32:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.05_summits.bed INFO @ Sun, 21 Jun 2020 21:32:50: 4000000 INFO @ Sun, 21 Jun 2020 21:32:50: Done! 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 pass1 - making usageList (708 chroms): 1 millis pass2 - checking and writing primary data (3010 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.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 21:32:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:57: 5000000 INFO @ Sun, 21 Jun 2020 21:32:58: 1000000 INFO @ Sun, 21 Jun 2020 21:33:05: 6000000 INFO @ Sun, 21 Jun 2020 21:33:05: 2000000 INFO @ Sun, 21 Jun 2020 21:33:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:33:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:33:07: #1 total tags in treatment: 6329797 INFO @ Sun, 21 Jun 2020 21:33:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:07: #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 21:33:07: #1 tags after filtering in treatment: 6329697 INFO @ Sun, 21 Jun 2020 21:33:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:08: #2 number of paired peaks: 2403 INFO @ Sun, 21 Jun 2020 21:33:08: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:08: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:08: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:08: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:08: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:33:08: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:33:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.10_model.r INFO @ Sun, 21 Jun 2020 21:33:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:33:11: 3000000 INFO @ Sun, 21 Jun 2020 21:33:16: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:33:22: 5000000 INFO @ Sun, 21 Jun 2020 21:33:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:27: 6000000 INFO @ Sun, 21 Jun 2020 21:33:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:33:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:33:29: #1 total tags in treatment: 6329797 INFO @ Sun, 21 Jun 2020 21:33:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:29: #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 21:33:29: #1 tags after filtering in treatment: 6329697 INFO @ Sun, 21 Jun 2020 21:33:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:29: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:30: #2 number of paired peaks: 2403 INFO @ Sun, 21 Jun 2020 21:33:30: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:30: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:30: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:30: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:30: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:33:30: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:33:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.20_model.r INFO @ Sun, 21 Jun 2020 21:33:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:33:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.10_summits.bed INFO @ Sun, 21 Jun 2020 21:33:30: Done! pass1 - making usageList (560 chroms): 1 millis pass2 - checking and writing primary data (1825 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:33:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011074/SRX5011074.20_summits.bed INFO @ Sun, 21 Jun 2020 21:33:52: Done! pass1 - making usageList (265 chroms): 1 millis pass2 - checking and writing primary data (623 records, 4 fields): 9 millis CompletedMACS2peakCalling