Job ID = 5720635 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,703,161 reads read : 6,703,161 reads written : 6,703,161 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289737.sra.cache’: No such file or directory 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: 00:00:43 6703161 reads; of these: 6703161 (100.00%) were unpaired; of these: 5094455 (76.00%) aligned 0 times 1320973 (19.71%) aligned exactly 1 time 287733 (4.29%) aligned >1 times 24.00% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 279726 / 1608706 = 0.1739 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 @ Thu, 16 Apr 2020 00:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.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 @ Thu, 16 Apr 2020 00:46:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:46:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:46:07: 1000000 INFO @ Thu, 16 Apr 2020 00:46:09: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:46:09: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:46:09: #1 total tags in treatment: 1328980 INFO @ Thu, 16 Apr 2020 00:46:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:46:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:46:09: #1 tags after filtering in treatment: 1328980 INFO @ Thu, 16 Apr 2020 00:46:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:46:09: #1 finished! INFO @ Thu, 16 Apr 2020 00:46:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:46:09: #2 number of paired peaks: 4499 INFO @ Thu, 16 Apr 2020 00:46:09: start model_add_line... INFO @ Thu, 16 Apr 2020 00:46:09: start X-correlation... INFO @ Thu, 16 Apr 2020 00:46:09: end of X-cor INFO @ Thu, 16 Apr 2020 00:46:09: #2 finished! INFO @ Thu, 16 Apr 2020 00:46:09: #2 predicted fragment length is 157 bps INFO @ Thu, 16 Apr 2020 00:46:09: #2 alternative fragment length(s) may be 157 bps INFO @ Thu, 16 Apr 2020 00:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.05_model.r INFO @ Thu, 16 Apr 2020 00:46:09: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:46:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:46:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:46:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:46:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.05_summits.bed INFO @ Thu, 16 Apr 2020 00:46:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4756 records, 4 fields): 5 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 @ Thu, 16 Apr 2020 00:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.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 @ Thu, 16 Apr 2020 00:46:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:46:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:46:37: 1000000 INFO @ Thu, 16 Apr 2020 00:46:38: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:46:38: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:46:38: #1 total tags in treatment: 1328980 INFO @ Thu, 16 Apr 2020 00:46:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:46:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:46:38: #1 tags after filtering in treatment: 1328980 INFO @ Thu, 16 Apr 2020 00:46:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:46:38: #1 finished! INFO @ Thu, 16 Apr 2020 00:46:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:46:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:46:39: #2 number of paired peaks: 4499 INFO @ Thu, 16 Apr 2020 00:46:39: start model_add_line... INFO @ Thu, 16 Apr 2020 00:46:39: start X-correlation... INFO @ Thu, 16 Apr 2020 00:46:39: end of X-cor INFO @ Thu, 16 Apr 2020 00:46:39: #2 finished! INFO @ Thu, 16 Apr 2020 00:46:39: #2 predicted fragment length is 157 bps INFO @ Thu, 16 Apr 2020 00:46:39: #2 alternative fragment length(s) may be 157 bps INFO @ Thu, 16 Apr 2020 00:46:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.10_model.r INFO @ Thu, 16 Apr 2020 00:46:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:46:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:46:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:46:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.10_summits.bed INFO @ Thu, 16 Apr 2020 00:46:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3498 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 @ Thu, 16 Apr 2020 00:47:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.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 @ Thu, 16 Apr 2020 00:47:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:47:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:47:07: 1000000 INFO @ Thu, 16 Apr 2020 00:47:09: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:47:09: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:47:09: #1 total tags in treatment: 1328980 INFO @ Thu, 16 Apr 2020 00:47:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:47:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:47:09: #1 tags after filtering in treatment: 1328980 INFO @ Thu, 16 Apr 2020 00:47:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:47:09: #1 finished! INFO @ Thu, 16 Apr 2020 00:47:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:47:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:47:09: #2 number of paired peaks: 4499 INFO @ Thu, 16 Apr 2020 00:47:09: start model_add_line... INFO @ Thu, 16 Apr 2020 00:47:09: start X-correlation... INFO @ Thu, 16 Apr 2020 00:47:09: end of X-cor INFO @ Thu, 16 Apr 2020 00:47:09: #2 finished! INFO @ Thu, 16 Apr 2020 00:47:09: #2 predicted fragment length is 157 bps INFO @ Thu, 16 Apr 2020 00:47:09: #2 alternative fragment length(s) may be 157 bps INFO @ Thu, 16 Apr 2020 00:47:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.20_model.r INFO @ Thu, 16 Apr 2020 00:47:09: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:47:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:47:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:47:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:47:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:47:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592460/SRX2592460.20_summits.bed INFO @ Thu, 16 Apr 2020 00:47:14: Done! BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (2326 records, 4 fields): 4 millis CompletedMACS2peakCalling