Job ID = 6458655 SRX = SRX5360584 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:34:07 prefetch.2.10.7: 1) Downloading 'SRR8559090'... 2020-06-21T12:34:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:35:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:35:08 prefetch.2.10.7: 'SRR8559090' is valid 2020-06-21T12:35:08 prefetch.2.10.7: 1) 'SRR8559090' was downloaded successfully Read 4158394 spots for SRR8559090/SRR8559090.sra Written 4158394 spots for SRR8559090/SRR8559090.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: 00:00:34 4158394 reads; of these: 4158394 (100.00%) were unpaired; of these: 3097291 (74.48%) aligned 0 times 928141 (22.32%) aligned exactly 1 time 132962 (3.20%) aligned >1 times 25.52% overall alignment rate Time searching: 00:00:35 Overall time: 00:00:35 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] 655770 / 1061103 = 0.6180 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 21:36:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.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 21:36:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:36:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:36:38: #1 total tags in treatment: 405333 INFO @ Sun, 21 Jun 2020 21:36:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:38: #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 21:36:38: #1 tags after filtering in treatment: 404728 INFO @ Sun, 21 Jun 2020 21:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:38: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:38: #2 number of paired peaks: 1777 INFO @ Sun, 21 Jun 2020 21:36:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:38: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:38: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:38: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 21:36:38: #2 alternative fragment length(s) may be 168,212,229 bps INFO @ Sun, 21 Jun 2020 21:36:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.05_model.r INFO @ Sun, 21 Jun 2020 21:36:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.05_summits.bed INFO @ Sun, 21 Jun 2020 21:36:40: Done! pass1 - making usageList (59 chroms): 1 millis pass2 - checking and writing primary data (123 records, 4 fields): 2 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 21:37:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.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 21:37:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:37:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:37:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:37:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:37:09: #1 total tags in treatment: 405333 INFO @ Sun, 21 Jun 2020 21:37:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:09: #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 21:37:09: #1 tags after filtering in treatment: 404728 INFO @ Sun, 21 Jun 2020 21:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:09: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:09: #2 number of paired peaks: 1777 INFO @ Sun, 21 Jun 2020 21:37:09: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:09: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:09: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:09: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:09: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 21:37:09: #2 alternative fragment length(s) may be 168,212,229 bps INFO @ Sun, 21 Jun 2020 21:37:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.10_model.r INFO @ Sun, 21 Jun 2020 21:37:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:37:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.10_summits.bed INFO @ Sun, 21 Jun 2020 21:37:11: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (57 records, 4 fields): 2 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 21:37:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.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 21:37:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:37:35: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:37:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:37:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:37:38: #1 total tags in treatment: 405333 INFO @ Sun, 21 Jun 2020 21:37:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:38: #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 21:37:38: #1 tags after filtering in treatment: 404728 INFO @ Sun, 21 Jun 2020 21:37:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:38: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:38: #2 number of paired peaks: 1777 INFO @ Sun, 21 Jun 2020 21:37:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:38: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:38: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:38: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 21:37:38: #2 alternative fragment length(s) may be 168,212,229 bps INFO @ Sun, 21 Jun 2020 21:37:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.20_model.r INFO @ Sun, 21 Jun 2020 21:37:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:37:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360584/SRX5360584.20_summits.bed INFO @ Sun, 21 Jun 2020 21:37:40: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (23 records, 4 fields): 29 millis CompletedMACS2peakCalling