Job ID = 6452361 SRX = SRX013009 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:23:03 prefetch.2.10.7: 1) Downloading 'SRR030275'... 2020-06-21T07:23:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:24:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:24:13 prefetch.2.10.7: 'SRR030275' is valid 2020-06-21T07:24:13 prefetch.2.10.7: 1) 'SRR030275' was downloaded successfully Read 4682572 spots for SRR030275/SRR030275.sra Written 4682572 spots for SRR030275/SRR030275.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: 00:00:55 4682572 reads; of these: 4682572 (100.00%) were unpaired; of these: 603863 (12.90%) aligned 0 times 3423637 (73.11%) aligned exactly 1 time 655072 (13.99%) aligned >1 times 87.10% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 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] 187071 / 4078709 = 0.0459 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 16:26:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.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 16:26:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:26:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:26:54: 1000000 INFO @ Sun, 21 Jun 2020 16:27:00: 2000000 INFO @ Sun, 21 Jun 2020 16:27:06: 3000000 INFO @ Sun, 21 Jun 2020 16:27:11: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:27:11: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:27:11: #1 total tags in treatment: 3891638 INFO @ Sun, 21 Jun 2020 16:27:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:27:11: #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 16:27:12: #1 tags after filtering in treatment: 3891517 INFO @ Sun, 21 Jun 2020 16:27:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:27:12: #1 finished! INFO @ Sun, 21 Jun 2020 16:27:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:27:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:27:12: #2 number of paired peaks: 1007 INFO @ Sun, 21 Jun 2020 16:27:12: start model_add_line... INFO @ Sun, 21 Jun 2020 16:27:12: start X-correlation... INFO @ Sun, 21 Jun 2020 16:27:12: end of X-cor INFO @ Sun, 21 Jun 2020 16:27:12: #2 finished! INFO @ Sun, 21 Jun 2020 16:27:12: #2 predicted fragment length is 144 bps INFO @ Sun, 21 Jun 2020 16:27:12: #2 alternative fragment length(s) may be 144 bps INFO @ Sun, 21 Jun 2020 16:27:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.05_model.r INFO @ Sun, 21 Jun 2020 16:27:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:27:12: #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 16:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.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 16:27:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:27:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:27:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:27:24: 1000000 INFO @ Sun, 21 Jun 2020 16:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.05_summits.bed INFO @ Sun, 21 Jun 2020 16:27:26: Done! pass1 - making usageList (154 chroms): 1 millis pass2 - checking and writing primary data (2725 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:27:30: 2000000 INFO @ Sun, 21 Jun 2020 16:27:36: 3000000 INFO @ Sun, 21 Jun 2020 16:27:41: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:27:41: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:27:41: #1 total tags in treatment: 3891638 INFO @ Sun, 21 Jun 2020 16:27:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:27:41: #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 16:27:41: #1 tags after filtering in treatment: 3891517 INFO @ Sun, 21 Jun 2020 16:27:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:27:41: #1 finished! INFO @ Sun, 21 Jun 2020 16:27:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:27:42: #2 number of paired peaks: 1007 INFO @ Sun, 21 Jun 2020 16:27:42: start model_add_line... INFO @ Sun, 21 Jun 2020 16:27:42: start X-correlation... INFO @ Sun, 21 Jun 2020 16:27:42: end of X-cor INFO @ Sun, 21 Jun 2020 16:27:42: #2 finished! INFO @ Sun, 21 Jun 2020 16:27:42: #2 predicted fragment length is 144 bps INFO @ Sun, 21 Jun 2020 16:27:42: #2 alternative fragment length(s) may be 144 bps INFO @ Sun, 21 Jun 2020 16:27:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.10_model.r INFO @ Sun, 21 Jun 2020 16:27:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:27:42: #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 16:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.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 16:27:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:27:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:27:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:27:53: 1000000 INFO @ Sun, 21 Jun 2020 16:27:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:27:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:27:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.10_summits.bed INFO @ Sun, 21 Jun 2020 16:27:55: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (693 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:27:58: 2000000 INFO @ Sun, 21 Jun 2020 16:28:03: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:28:08: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:28:08: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:28:08: #1 total tags in treatment: 3891638 INFO @ Sun, 21 Jun 2020 16:28:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:28:08: #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 16:28:08: #1 tags after filtering in treatment: 3891517 INFO @ Sun, 21 Jun 2020 16:28:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:28:08: #1 finished! INFO @ Sun, 21 Jun 2020 16:28:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:28:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:28:09: #2 number of paired peaks: 1007 INFO @ Sun, 21 Jun 2020 16:28:09: start model_add_line... INFO @ Sun, 21 Jun 2020 16:28:09: start X-correlation... INFO @ Sun, 21 Jun 2020 16:28:09: end of X-cor INFO @ Sun, 21 Jun 2020 16:28:09: #2 finished! INFO @ Sun, 21 Jun 2020 16:28:09: #2 predicted fragment length is 144 bps INFO @ Sun, 21 Jun 2020 16:28:09: #2 alternative fragment length(s) may be 144 bps INFO @ Sun, 21 Jun 2020 16:28:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.20_model.r INFO @ Sun, 21 Jun 2020 16:28:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:28:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:28:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:28:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:28:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:28:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013009/SRX013009.20_summits.bed INFO @ Sun, 21 Jun 2020 16:28:22: Done! pass1 - making usageList (59 chroms): 0 millis pass2 - checking and writing primary data (118 records, 4 fields): 4 millis CompletedMACS2peakCalling