Job ID = 6454189 SRX = SRX186110 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:08:54 prefetch.2.10.7: 1) Downloading 'SRR567587'... 2020-06-21T09:08:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:10:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:10:34 prefetch.2.10.7: 'SRR567587' is valid 2020-06-21T09:10:34 prefetch.2.10.7: 1) 'SRR567587' was downloaded successfully Read 9768492 spots for SRR567587/SRR567587.sra Written 9768492 spots for SRR567587/SRR567587.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: 00:01:45 9768492 reads; of these: 9768492 (100.00%) were unpaired; of these: 3633407 (37.20%) aligned 0 times 4471805 (45.78%) aligned exactly 1 time 1663280 (17.03%) aligned >1 times 62.80% overall alignment rate Time searching: 00:01:45 Overall time: 00:01:45 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] 2759926 / 6135085 = 0.4499 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 18:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.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 18:14:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:25: 1000000 INFO @ Sun, 21 Jun 2020 18:14:30: 2000000 INFO @ Sun, 21 Jun 2020 18:14:36: 3000000 INFO @ Sun, 21 Jun 2020 18:14:38: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:14:38: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:14:38: #1 total tags in treatment: 3375159 INFO @ Sun, 21 Jun 2020 18:14:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:38: #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 18:14:38: #1 tags after filtering in treatment: 3375151 INFO @ Sun, 21 Jun 2020 18:14:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:38: #2 number of paired peaks: 2005 INFO @ Sun, 21 Jun 2020 18:14:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:38: #2 predicted fragment length is 87 bps INFO @ Sun, 21 Jun 2020 18:14:38: #2 alternative fragment length(s) may be 87,562 bps INFO @ Sun, 21 Jun 2020 18:14:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.05_model.r INFO @ Sun, 21 Jun 2020 18:14:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:14:46: #3 Call peaks for each chromosome... 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 18:14:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.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 18:14:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:14:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:14:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.05_summits.bed INFO @ Sun, 21 Jun 2020 18:14:50: Done! pass1 - making usageList (614 chroms): 2 millis pass2 - checking and writing primary data (4597 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:14:55: 1000000 INFO @ Sun, 21 Jun 2020 18:15:00: 2000000 INFO @ Sun, 21 Jun 2020 18:15:05: 3000000 INFO @ Sun, 21 Jun 2020 18:15:07: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:15:07: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:15:07: #1 total tags in treatment: 3375159 INFO @ Sun, 21 Jun 2020 18:15:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:07: #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 18:15:08: #1 tags after filtering in treatment: 3375151 INFO @ Sun, 21 Jun 2020 18:15:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:08: #2 number of paired peaks: 2005 INFO @ Sun, 21 Jun 2020 18:15:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:08: #2 predicted fragment length is 87 bps INFO @ Sun, 21 Jun 2020 18:15:08: #2 alternative fragment length(s) may be 87,562 bps INFO @ Sun, 21 Jun 2020 18:15:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.10_model.r INFO @ Sun, 21 Jun 2020 18:15:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:15:16: #3 Call peaks for each chromosome... 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 18:15:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.10_summits.bed INFO @ Sun, 21 Jun 2020 18:15:19: Done! INFO @ Sun, 21 Jun 2020 18:15:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.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 18:15:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:20: #1 read treatment tags... pass1 - making usageList (507 chroms): 2 millis pass2 - checking and writing primary data (2520 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:15:25: 1000000 INFO @ Sun, 21 Jun 2020 18:15:30: 2000000 INFO @ Sun, 21 Jun 2020 18:15:36: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:15:38: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:15:38: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:15:38: #1 total tags in treatment: 3375159 INFO @ Sun, 21 Jun 2020 18:15:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:38: #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 18:15:38: #1 tags after filtering in treatment: 3375151 INFO @ Sun, 21 Jun 2020 18:15:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:38: #2 number of paired peaks: 2005 INFO @ Sun, 21 Jun 2020 18:15:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:38: #2 predicted fragment length is 87 bps INFO @ Sun, 21 Jun 2020 18:15:38: #2 alternative fragment length(s) may be 87,562 bps INFO @ Sun, 21 Jun 2020 18:15:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.20_model.r INFO @ Sun, 21 Jun 2020 18:15:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:15:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX186110/SRX186110.20_summits.bed INFO @ Sun, 21 Jun 2020 18:15:50: Done! pass1 - making usageList (279 chroms): 1 millis pass2 - checking and writing primary data (686 records, 4 fields): 9 millis CompletedMACS2peakCalling