Job ID = 6459043 SRX = SRX6386724 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:54:07 prefetch.2.10.7: 1) Downloading 'SRR9624456'... 2020-06-21T12:54:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:58:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:58:20 prefetch.2.10.7: 1) 'SRR9624456' was downloaded successfully Read 19811807 spots for SRR9624456/SRR9624456.sra Written 19811807 spots for SRR9624456/SRR9624456.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: 00:02:10 19811807 reads; of these: 19811807 (100.00%) were unpaired; of these: 18624818 (94.01%) aligned 0 times 843373 (4.26%) aligned exactly 1 time 343616 (1.73%) aligned >1 times 5.99% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 590341 / 1186989 = 0.4973 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 22:02:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.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 22:02:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:02:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:02:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:02:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:02:20: #1 total tags in treatment: 596648 INFO @ Sun, 21 Jun 2020 22:02:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:20: #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 22:02:20: #1 tags after filtering in treatment: 596122 INFO @ Sun, 21 Jun 2020 22:02:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:20: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:20: #2 number of paired peaks: 2145 INFO @ Sun, 21 Jun 2020 22:02:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:20: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 22:02:20: #2 alternative fragment length(s) may be 53,147,162 bps INFO @ Sun, 21 Jun 2020 22:02:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.05_model.r INFO @ Sun, 21 Jun 2020 22:02:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.05_summits.bed INFO @ Sun, 21 Jun 2020 22:02:23: Done! pass1 - making usageList (256 chroms): 0 millis pass2 - checking and writing primary data (456 records, 4 fields): 9 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 22:02:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.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 22:02:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:02:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:02:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:02:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:02:50: #1 total tags in treatment: 596648 INFO @ Sun, 21 Jun 2020 22:02:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:50: #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 22:02:50: #1 tags after filtering in treatment: 596122 INFO @ Sun, 21 Jun 2020 22:02:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:50: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:50: #2 number of paired peaks: 2145 INFO @ Sun, 21 Jun 2020 22:02:50: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:50: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:50: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:50: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:50: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 22:02:50: #2 alternative fragment length(s) may be 53,147,162 bps INFO @ Sun, 21 Jun 2020 22:02:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.10_model.r INFO @ Sun, 21 Jun 2020 22:02:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.10_summits.bed INFO @ Sun, 21 Jun 2020 22:02:53: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 5 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 22:03:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.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 22:03:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:15: #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 22:03:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:03:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:03:20: #1 total tags in treatment: 596648 INFO @ Sun, 21 Jun 2020 22:03:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:03:20: #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 22:03:20: #1 tags after filtering in treatment: 596122 INFO @ Sun, 21 Jun 2020 22:03:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:03:20: #1 finished! INFO @ Sun, 21 Jun 2020 22:03:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:03:20: #2 number of paired peaks: 2145 INFO @ Sun, 21 Jun 2020 22:03:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:03:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:03:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:03:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:03:20: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 22:03:20: #2 alternative fragment length(s) may be 53,147,162 bps INFO @ Sun, 21 Jun 2020 22:03:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.20_model.r INFO @ Sun, 21 Jun 2020 22:03:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:03:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:03:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:03:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:03:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386724/SRX6386724.20_summits.bed INFO @ Sun, 21 Jun 2020 22:03:23: Done! pass1 - making usageList (47 chroms): 0 millis pass2 - checking and writing primary data (81 records, 4 fields): 3 millis CompletedMACS2peakCalling