Job ID = 5720528 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 126,212 reads read : 126,212 reads written : 126,212 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289693.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: 00:00:02 126212 reads; of these: 126212 (100.00%) were unpaired; of these: 22091 (17.50%) aligned 0 times 74622 (59.12%) aligned exactly 1 time 29499 (23.37%) aligned >1 times 82.50% overall alignment rate Time searching: 00:00:02 Overall time: 00:00:02 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] 46065 / 104121 = 0.4424 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 00:27:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.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 00:27:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:27:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:27:53: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:27:53: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:27:53: #1 total tags in treatment: 58056 INFO @ Thu, 16 Apr 2020 00:27:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:27:53: #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 00:27:53: #1 tags after filtering in treatment: 58056 INFO @ Thu, 16 Apr 2020 00:27:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:27:53: #1 finished! INFO @ Thu, 16 Apr 2020 00:27:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:27:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:27:53: #2 number of paired peaks: 1662 INFO @ Thu, 16 Apr 2020 00:27:53: start model_add_line... INFO @ Thu, 16 Apr 2020 00:27:53: start X-correlation... INFO @ Thu, 16 Apr 2020 00:27:53: end of X-cor INFO @ Thu, 16 Apr 2020 00:27:53: #2 finished! INFO @ Thu, 16 Apr 2020 00:27:53: #2 predicted fragment length is 293 bps INFO @ Thu, 16 Apr 2020 00:27:53: #2 alternative fragment length(s) may be 293 bps INFO @ Thu, 16 Apr 2020 00:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.05_model.r INFO @ Thu, 16 Apr 2020 00:27:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:27:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:27:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:27:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:27:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:27:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.05_summits.bed INFO @ Thu, 16 Apr 2020 00:27:53: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (39 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 00:28:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.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 00:28:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:28:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:28:23: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:28:23: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:28:23: #1 total tags in treatment: 58056 INFO @ Thu, 16 Apr 2020 00:28:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:28:23: #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 00:28:23: #1 tags after filtering in treatment: 58056 INFO @ Thu, 16 Apr 2020 00:28:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:28:23: #1 finished! INFO @ Thu, 16 Apr 2020 00:28:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:28:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:28:23: #2 number of paired peaks: 1662 INFO @ Thu, 16 Apr 2020 00:28:23: start model_add_line... INFO @ Thu, 16 Apr 2020 00:28:23: start X-correlation... INFO @ Thu, 16 Apr 2020 00:28:23: end of X-cor INFO @ Thu, 16 Apr 2020 00:28:23: #2 finished! INFO @ Thu, 16 Apr 2020 00:28:23: #2 predicted fragment length is 293 bps INFO @ Thu, 16 Apr 2020 00:28:23: #2 alternative fragment length(s) may be 293 bps INFO @ Thu, 16 Apr 2020 00:28:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.10_model.r INFO @ Thu, 16 Apr 2020 00:28:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:28:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:28:23: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:28:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:28:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.10_summits.bed INFO @ Thu, 16 Apr 2020 00:28:23: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (15 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 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 00:28:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.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 00:28:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:28:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:28:53: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:28:53: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:28:53: #1 total tags in treatment: 58056 INFO @ Thu, 16 Apr 2020 00:28:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:28:53: #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 00:28:53: #1 tags after filtering in treatment: 58056 INFO @ Thu, 16 Apr 2020 00:28:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:28:53: #1 finished! INFO @ Thu, 16 Apr 2020 00:28:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:28:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:28:53: #2 number of paired peaks: 1662 INFO @ Thu, 16 Apr 2020 00:28:53: start model_add_line... INFO @ Thu, 16 Apr 2020 00:28:53: start X-correlation... INFO @ Thu, 16 Apr 2020 00:28:53: end of X-cor INFO @ Thu, 16 Apr 2020 00:28:53: #2 finished! INFO @ Thu, 16 Apr 2020 00:28:53: #2 predicted fragment length is 293 bps INFO @ Thu, 16 Apr 2020 00:28:53: #2 alternative fragment length(s) may be 293 bps INFO @ Thu, 16 Apr 2020 00:28:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.20_model.r INFO @ Thu, 16 Apr 2020 00:28:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:28:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:28:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:28:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:28:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:28:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592416/SRX2592416.20_summits.bed INFO @ Thu, 16 Apr 2020 00:28:53: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling