Job ID = 5720679 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 314,487 reads read : 314,487 reads written : 314,487 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289771.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: 00:00:04 314487 reads; of these: 314487 (100.00%) were unpaired; of these: 139535 (44.37%) aligned 0 times 150561 (47.88%) aligned exactly 1 time 24391 (7.76%) aligned >1 times 55.63% overall alignment rate Time searching: 00:00:04 Overall time: 00:00:04 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] 2035 / 174952 = 0.0116 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 00:51:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.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 00:51:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:51:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:51:18: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:51:18: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:51:18: #1 total tags in treatment: 172917 INFO @ Thu, 16 Apr 2020 00:51:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:51:18: #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 00:51:18: #1 tags after filtering in treatment: 172915 INFO @ Thu, 16 Apr 2020 00:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:51:18: #1 finished! INFO @ Thu, 16 Apr 2020 00:51:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:51:18: #2 number of paired peaks: 5615 INFO @ Thu, 16 Apr 2020 00:51:18: start model_add_line... INFO @ Thu, 16 Apr 2020 00:51:18: start X-correlation... INFO @ Thu, 16 Apr 2020 00:51:18: end of X-cor INFO @ Thu, 16 Apr 2020 00:51:18: #2 finished! INFO @ Thu, 16 Apr 2020 00:51:18: #2 predicted fragment length is 160 bps INFO @ Thu, 16 Apr 2020 00:51:18: #2 alternative fragment length(s) may be 160 bps INFO @ Thu, 16 Apr 2020 00:51:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.05_model.r INFO @ Thu, 16 Apr 2020 00:51:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:51:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:51:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:51:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:51:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.05_summits.bed INFO @ Thu, 16 Apr 2020 00:51:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (353 records, 4 fields): 1 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 00:51:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.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 00:51:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:51:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:51:48: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:51:48: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:51:48: #1 total tags in treatment: 172917 INFO @ Thu, 16 Apr 2020 00:51:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:51:48: #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 00:51:48: #1 tags after filtering in treatment: 172915 INFO @ Thu, 16 Apr 2020 00:51:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:51:48: #1 finished! INFO @ Thu, 16 Apr 2020 00:51:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:51:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:51:48: #2 number of paired peaks: 5615 INFO @ Thu, 16 Apr 2020 00:51:48: start model_add_line... INFO @ Thu, 16 Apr 2020 00:51:48: start X-correlation... INFO @ Thu, 16 Apr 2020 00:51:48: end of X-cor INFO @ Thu, 16 Apr 2020 00:51:48: #2 finished! INFO @ Thu, 16 Apr 2020 00:51:48: #2 predicted fragment length is 160 bps INFO @ Thu, 16 Apr 2020 00:51:48: #2 alternative fragment length(s) may be 160 bps INFO @ Thu, 16 Apr 2020 00:51:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.10_model.r INFO @ Thu, 16 Apr 2020 00:51:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:51:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:51:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:51:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:51:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:51:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.10_summits.bed INFO @ Thu, 16 Apr 2020 00:51:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (95 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 @ Thu, 16 Apr 2020 00:52:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.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 00:52:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:52:17: #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 @ Thu, 16 Apr 2020 00:52:18: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:52:18: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:52:18: #1 total tags in treatment: 172917 INFO @ Thu, 16 Apr 2020 00:52:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:52:18: #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 00:52:18: #1 tags after filtering in treatment: 172915 INFO @ Thu, 16 Apr 2020 00:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:52:18: #1 finished! INFO @ Thu, 16 Apr 2020 00:52:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:52:18: #2 number of paired peaks: 5615 INFO @ Thu, 16 Apr 2020 00:52:18: start model_add_line... INFO @ Thu, 16 Apr 2020 00:52:18: start X-correlation... INFO @ Thu, 16 Apr 2020 00:52:18: end of X-cor INFO @ Thu, 16 Apr 2020 00:52:18: #2 finished! INFO @ Thu, 16 Apr 2020 00:52:18: #2 predicted fragment length is 160 bps INFO @ Thu, 16 Apr 2020 00:52:18: #2 alternative fragment length(s) may be 160 bps INFO @ Thu, 16 Apr 2020 00:52:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.20_model.r INFO @ Thu, 16 Apr 2020 00:52:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:52:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592494/SRX2592494.20_summits.bed INFO @ Thu, 16 Apr 2020 00:52:19: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 0 millis CompletedMACS2peakCalling