Job ID = 6459441 SRX = SRX6780074 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:08:34 prefetch.2.10.7: 1) Downloading 'SRR10045475'... 2020-06-21T13:08:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:12:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:12:03 prefetch.2.10.7: 'SRR10045475' is valid 2020-06-21T13:12:03 prefetch.2.10.7: 1) 'SRR10045475' was downloaded successfully Read 9619103 spots for SRR10045475/SRR10045475.sra Written 9619103 spots for SRR10045475/SRR10045475.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: 00:02:34 9619103 reads; of these: 9619103 (100.00%) were unpaired; of these: 821612 (8.54%) aligned 0 times 6274927 (65.23%) aligned exactly 1 time 2522564 (26.22%) aligned >1 times 91.46% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 4613794 / 8797491 = 0.5244 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 22:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.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 22:17:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:48: 1000000 INFO @ Sun, 21 Jun 2020 22:17:53: 2000000 INFO @ Sun, 21 Jun 2020 22:17:59: 3000000 INFO @ Sun, 21 Jun 2020 22:18:05: 4000000 INFO @ Sun, 21 Jun 2020 22:18:06: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:18:06: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:18:06: #1 total tags in treatment: 4183697 INFO @ Sun, 21 Jun 2020 22:18:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:06: #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 22:18:06: #1 tags after filtering in treatment: 4183687 INFO @ Sun, 21 Jun 2020 22:18:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:06: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:07: #2 number of paired peaks: 1537 INFO @ Sun, 21 Jun 2020 22:18:07: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:07: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:07: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:07: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:07: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 22:18:07: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 22:18:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.05_model.r INFO @ Sun, 21 Jun 2020 22:18:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:07: #3 Pre-compute pvalue-qvalue table... 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 22:18:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.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 22:18:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:19: 1000000 INFO @ Sun, 21 Jun 2020 22:18:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.05_summits.bed INFO @ Sun, 21 Jun 2020 22:18:22: Done! pass1 - making usageList (644 chroms): 1 millis pass2 - checking and writing primary data (1820 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:18:24: 2000000 INFO @ Sun, 21 Jun 2020 22:18:30: 3000000 INFO @ Sun, 21 Jun 2020 22:18:36: 4000000 INFO @ Sun, 21 Jun 2020 22:18:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:18:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:18:37: #1 total tags in treatment: 4183697 INFO @ Sun, 21 Jun 2020 22:18:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:37: #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 22:18:38: #1 tags after filtering in treatment: 4183687 INFO @ Sun, 21 Jun 2020 22:18:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:38: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:38: #2 number of paired peaks: 1537 INFO @ Sun, 21 Jun 2020 22:18:38: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:38: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:38: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:38: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:38: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 22:18:38: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 22:18:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.10_model.r INFO @ Sun, 21 Jun 2020 22:18:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:38: #3 Pre-compute pvalue-qvalue table... 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 22:18:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.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 22:18:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:49: 1000000 INFO @ Sun, 21 Jun 2020 22:18:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.10_summits.bed INFO @ Sun, 21 Jun 2020 22:18:53: Done! pass1 - making usageList (555 chroms): 1 millis pass2 - checking and writing primary data (1489 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:18:55: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:19:02: 3000000 INFO @ Sun, 21 Jun 2020 22:19:09: 4000000 INFO @ Sun, 21 Jun 2020 22:19:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:19:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:19:10: #1 total tags in treatment: 4183697 INFO @ Sun, 21 Jun 2020 22:19:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:10: #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 22:19:11: #1 tags after filtering in treatment: 4183687 INFO @ Sun, 21 Jun 2020 22:19:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:19:11: #1 finished! INFO @ Sun, 21 Jun 2020 22:19:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:19:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:19:11: #2 number of paired peaks: 1537 INFO @ Sun, 21 Jun 2020 22:19:11: start model_add_line... INFO @ Sun, 21 Jun 2020 22:19:11: start X-correlation... INFO @ Sun, 21 Jun 2020 22:19:11: end of X-cor INFO @ Sun, 21 Jun 2020 22:19:11: #2 finished! INFO @ Sun, 21 Jun 2020 22:19:11: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 22:19:11: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 22:19:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.20_model.r BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:19:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:19:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:19:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:19:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:19:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:19:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6780074/SRX6780074.20_summits.bed INFO @ Sun, 21 Jun 2020 22:19:26: Done! pass1 - making usageList (394 chroms): 1 millis pass2 - checking and writing primary data (1018 records, 4 fields): 12 millis CompletedMACS2peakCalling