Job ID = 6457818 SRX = SRX4798861 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:12:07 prefetch.2.10.7: 1) Downloading 'SRR7965208'... 2020-06-21T12:12:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:13:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:13:17 prefetch.2.10.7: 'SRR7965208' is valid 2020-06-21T12:13:17 prefetch.2.10.7: 1) 'SRR7965208' was downloaded successfully Read 7009007 spots for SRR7965208/SRR7965208.sra Written 7009007 spots for SRR7965208/SRR7965208.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:44 7009007 reads; of these: 7009007 (100.00%) were unpaired; of these: 5425732 (77.41%) aligned 0 times 1430585 (20.41%) aligned exactly 1 time 152690 (2.18%) aligned >1 times 22.59% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 230540 / 1583275 = 0.1456 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 21:15:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.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 21:15:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:15:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:15:39: 1000000 INFO @ Sun, 21 Jun 2020 21:15:42: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:15:42: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:15:42: #1 total tags in treatment: 1352735 INFO @ Sun, 21 Jun 2020 21:15:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:15:42: #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 21:15:42: #1 tags after filtering in treatment: 1352210 INFO @ Sun, 21 Jun 2020 21:15:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:15:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:15:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:15:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:15:42: #2 number of paired peaks: 1630 INFO @ Sun, 21 Jun 2020 21:15:42: start model_add_line... INFO @ Sun, 21 Jun 2020 21:15:42: start X-correlation... INFO @ Sun, 21 Jun 2020 21:15:42: end of X-cor INFO @ Sun, 21 Jun 2020 21:15:42: #2 finished! INFO @ Sun, 21 Jun 2020 21:15:42: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 21:15:42: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 21:15:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.05_model.r INFO @ Sun, 21 Jun 2020 21:15:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:15:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:15:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:15:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:15:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.05_summits.bed INFO @ Sun, 21 Jun 2020 21:15:48: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (928 records, 4 fields): 8 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 21:16:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.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 21:16:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:16:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:16:09: 1000000 INFO @ Sun, 21 Jun 2020 21:16:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:16:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:16:12: #1 total tags in treatment: 1352735 INFO @ Sun, 21 Jun 2020 21:16:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:12: #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 21:16:12: #1 tags after filtering in treatment: 1352210 INFO @ Sun, 21 Jun 2020 21:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:12: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:12: #2 number of paired peaks: 1630 INFO @ Sun, 21 Jun 2020 21:16:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:12: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 21:16:12: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 21:16:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.10_model.r INFO @ Sun, 21 Jun 2020 21:16:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:16:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:16:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:16:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.10_summits.bed INFO @ Sun, 21 Jun 2020 21:16:18: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 4 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 21:16:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.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 21:16:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:16:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:16:39: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:16:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:16:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:16:41: #1 total tags in treatment: 1352735 INFO @ Sun, 21 Jun 2020 21:16:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:41: #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 21:16:42: #1 tags after filtering in treatment: 1352210 INFO @ Sun, 21 Jun 2020 21:16:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:42: #2 number of paired peaks: 1630 INFO @ Sun, 21 Jun 2020 21:16:42: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:42: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:42: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:42: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:42: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 21:16:42: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 21:16:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.20_model.r INFO @ Sun, 21 Jun 2020 21:16:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:16:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:16:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798861/SRX4798861.20_summits.bed INFO @ Sun, 21 Jun 2020 21:16:47: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 3 millis CompletedMACS2peakCalling