Job ID = 6452505 SRX = SRX013105 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:30:41 prefetch.2.10.7: 1) Downloading 'SRR030371'... 2020-06-21T08:30:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:30:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:30:58 prefetch.2.10.7: 'SRR030371' is valid 2020-06-21T08:30:58 prefetch.2.10.7: 1) 'SRR030371' was downloaded successfully Read 445788 spots for SRR030371/SRR030371.sra Written 445788 spots for SRR030371/SRR030371.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: 00:00:05 445788 reads; of these: 445788 (100.00%) were unpaired; of these: 48765 (10.94%) aligned 0 times 359133 (80.56%) aligned exactly 1 time 37890 (8.50%) aligned >1 times 89.06% overall alignment rate Time searching: 00:00:05 Overall time: 00:00:05 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] 15946 / 397023 = 0.0402 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 17:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.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 17:31:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:48: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:31:48: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:31:48: #1 total tags in treatment: 381077 INFO @ Sun, 21 Jun 2020 17:31:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:48: #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 17:31:48: #1 tags after filtering in treatment: 380376 INFO @ Sun, 21 Jun 2020 17:31:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:48: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:48: #2 number of paired peaks: 3712 INFO @ Sun, 21 Jun 2020 17:31:48: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:48: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:48: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:48: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:48: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 17:31:48: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 17:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.05_model.r INFO @ Sun, 21 Jun 2020 17:31:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.05_summits.bed INFO @ Sun, 21 Jun 2020 17:31:50: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (135 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 17:32:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.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 17:32:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:32:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:32:18: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:32:18: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:32:18: #1 total tags in treatment: 381077 INFO @ Sun, 21 Jun 2020 17:32:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:32:18: #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 17:32:18: #1 tags after filtering in treatment: 380376 INFO @ Sun, 21 Jun 2020 17:32:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:32:18: #1 finished! INFO @ Sun, 21 Jun 2020 17:32:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:32:18: #2 number of paired peaks: 3712 INFO @ Sun, 21 Jun 2020 17:32:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:32:18: start X-correlation... INFO @ Sun, 21 Jun 2020 17:32:18: end of X-cor INFO @ Sun, 21 Jun 2020 17:32:18: #2 finished! INFO @ Sun, 21 Jun 2020 17:32:18: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 17:32:18: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 17:32:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.10_model.r INFO @ Sun, 21 Jun 2020 17:32:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:32:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:32:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:32:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.10_summits.bed INFO @ Sun, 21 Jun 2020 17:32:20: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 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 17:32:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.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 17:32:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:32:45: #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 17:32:48: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:32:48: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:32:48: #1 total tags in treatment: 381077 INFO @ Sun, 21 Jun 2020 17:32:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:32:48: #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 17:32:48: #1 tags after filtering in treatment: 380376 INFO @ Sun, 21 Jun 2020 17:32:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:32:48: #1 finished! INFO @ Sun, 21 Jun 2020 17:32:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:32:48: #2 number of paired peaks: 3712 INFO @ Sun, 21 Jun 2020 17:32:48: start model_add_line... INFO @ Sun, 21 Jun 2020 17:32:48: start X-correlation... INFO @ Sun, 21 Jun 2020 17:32:48: end of X-cor INFO @ Sun, 21 Jun 2020 17:32:48: #2 finished! INFO @ Sun, 21 Jun 2020 17:32:48: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 17:32:48: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 17:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.20_model.r INFO @ Sun, 21 Jun 2020 17:32:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:32:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:32:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:32:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013105/SRX013105.20_summits.bed INFO @ Sun, 21 Jun 2020 17:32:50: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling