Job ID = 6452453 SRX = SRX013070 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:37:12 prefetch.2.10.7: 1) Downloading 'SRR030336'... 2020-06-21T07:37:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:38:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:38:17 prefetch.2.10.7: 'SRR030336' is valid 2020-06-21T07:38:17 prefetch.2.10.7: 1) 'SRR030336' was downloaded successfully Read 5088120 spots for SRR030336/SRR030336.sra Written 5088120 spots for SRR030336/SRR030336.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: 00:00:49 5088120 reads; of these: 5088120 (100.00%) were unpaired; of these: 374352 (7.36%) aligned 0 times 4300487 (84.52%) aligned exactly 1 time 413281 (8.12%) aligned >1 times 92.64% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 1656893 / 4713768 = 0.3515 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 16:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.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 16:40:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:40:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:40:55: 1000000 INFO @ Sun, 21 Jun 2020 16:41:00: 2000000 INFO @ Sun, 21 Jun 2020 16:41:06: 3000000 INFO @ Sun, 21 Jun 2020 16:41:06: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:41:06: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:41:06: #1 total tags in treatment: 3056875 INFO @ Sun, 21 Jun 2020 16:41:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:41:06: #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 16:41:07: #1 tags after filtering in treatment: 3056535 INFO @ Sun, 21 Jun 2020 16:41:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:41:07: #1 finished! INFO @ Sun, 21 Jun 2020 16:41:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:41:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:41:07: #2 number of paired peaks: 2286 INFO @ Sun, 21 Jun 2020 16:41:07: start model_add_line... INFO @ Sun, 21 Jun 2020 16:41:07: start X-correlation... INFO @ Sun, 21 Jun 2020 16:41:07: end of X-cor INFO @ Sun, 21 Jun 2020 16:41:07: #2 finished! INFO @ Sun, 21 Jun 2020 16:41:07: #2 predicted fragment length is 212 bps INFO @ Sun, 21 Jun 2020 16:41:07: #2 alternative fragment length(s) may be 212 bps INFO @ Sun, 21 Jun 2020 16:41:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.05_model.r INFO @ Sun, 21 Jun 2020 16:41:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:41:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:41:15: #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 16:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.05_summits.bed INFO @ Sun, 21 Jun 2020 16:41:18: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (2625 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:41:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.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 16:41:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:41:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:41:25: 1000000 INFO @ Sun, 21 Jun 2020 16:41:31: 2000000 INFO @ Sun, 21 Jun 2020 16:41:37: 3000000 INFO @ Sun, 21 Jun 2020 16:41:37: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:41:37: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:41:37: #1 total tags in treatment: 3056875 INFO @ Sun, 21 Jun 2020 16:41:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:41:37: #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 16:41:38: #1 tags after filtering in treatment: 3056535 INFO @ Sun, 21 Jun 2020 16:41:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:41:38: #1 finished! INFO @ Sun, 21 Jun 2020 16:41:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:41:38: #2 number of paired peaks: 2286 INFO @ Sun, 21 Jun 2020 16:41:38: start model_add_line... INFO @ Sun, 21 Jun 2020 16:41:38: start X-correlation... INFO @ Sun, 21 Jun 2020 16:41:38: end of X-cor INFO @ Sun, 21 Jun 2020 16:41:38: #2 finished! INFO @ Sun, 21 Jun 2020 16:41:38: #2 predicted fragment length is 212 bps INFO @ Sun, 21 Jun 2020 16:41:38: #2 alternative fragment length(s) may be 212 bps INFO @ Sun, 21 Jun 2020 16:41:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.10_model.r INFO @ Sun, 21 Jun 2020 16:41:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:41:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:41:46: #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 16:41:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.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 16:41:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:41:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:41:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:41:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:41:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.10_summits.bed INFO @ Sun, 21 Jun 2020 16:41:50: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (1106 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:41:55: 1000000 INFO @ Sun, 21 Jun 2020 16:42:00: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:42:06: 3000000 INFO @ Sun, 21 Jun 2020 16:42:07: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:42:07: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:42:07: #1 total tags in treatment: 3056875 INFO @ Sun, 21 Jun 2020 16:42:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:42:07: #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 16:42:07: #1 tags after filtering in treatment: 3056535 INFO @ Sun, 21 Jun 2020 16:42:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:42:07: #1 finished! INFO @ Sun, 21 Jun 2020 16:42:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:42:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:42:07: #2 number of paired peaks: 2286 INFO @ Sun, 21 Jun 2020 16:42:07: start model_add_line... INFO @ Sun, 21 Jun 2020 16:42:08: start X-correlation... INFO @ Sun, 21 Jun 2020 16:42:08: end of X-cor INFO @ Sun, 21 Jun 2020 16:42:08: #2 finished! INFO @ Sun, 21 Jun 2020 16:42:08: #2 predicted fragment length is 212 bps INFO @ Sun, 21 Jun 2020 16:42:08: #2 alternative fragment length(s) may be 212 bps INFO @ Sun, 21 Jun 2020 16:42:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.20_model.r INFO @ Sun, 21 Jun 2020 16:42:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:42:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:42:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:42:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:42:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:42:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013070/SRX013070.20_summits.bed INFO @ Sun, 21 Jun 2020 16:42:19: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 2 millis CompletedMACS2peakCalling