Job ID = 5791220 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,846,463 reads read : 11,692,926 reads written : 5,846,463 reads 0-length : 5,846,463 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:49 5846463 reads; of these: 5846463 (100.00%) were unpaired; of these: 1040012 (17.79%) aligned 0 times 4081384 (69.81%) aligned exactly 1 time 725067 (12.40%) aligned >1 times 82.21% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 3955571 / 4806451 = 0.8230 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 @ Wed, 22 Apr 2020 09:06:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 09:06:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:06:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:06:13: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 09:06:13: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 09:06:13: #1 total tags in treatment: 850880 INFO @ Wed, 22 Apr 2020 09:06:13: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:06:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:06:13: #1 tags after filtering in treatment: 850880 INFO @ Wed, 22 Apr 2020 09:06:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:06:13: #1 finished! INFO @ Wed, 22 Apr 2020 09:06:13: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:06:13: #2 number of paired peaks: 1059 INFO @ Wed, 22 Apr 2020 09:06:13: start model_add_line... INFO @ Wed, 22 Apr 2020 09:06:13: start X-correlation... INFO @ Wed, 22 Apr 2020 09:06:13: end of X-cor INFO @ Wed, 22 Apr 2020 09:06:13: #2 finished! INFO @ Wed, 22 Apr 2020 09:06:13: #2 predicted fragment length is 283 bps INFO @ Wed, 22 Apr 2020 09:06:13: #2 alternative fragment length(s) may be 4,283 bps INFO @ Wed, 22 Apr 2020 09:06:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.05_model.r INFO @ Wed, 22 Apr 2020 09:06:13: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:06:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:06:17: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:06:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:06:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:06:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.05_summits.bed INFO @ Wed, 22 Apr 2020 09:06:18: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (498 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 @ Wed, 22 Apr 2020 09:06:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 09:06:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:06:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:06:43: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 09:06:43: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 09:06:43: #1 total tags in treatment: 850880 INFO @ Wed, 22 Apr 2020 09:06:43: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:06:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:06:43: #1 tags after filtering in treatment: 850880 INFO @ Wed, 22 Apr 2020 09:06:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:06:43: #1 finished! INFO @ Wed, 22 Apr 2020 09:06:43: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:06:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:06:43: #2 number of paired peaks: 1059 INFO @ Wed, 22 Apr 2020 09:06:43: start model_add_line... INFO @ Wed, 22 Apr 2020 09:06:43: start X-correlation... INFO @ Wed, 22 Apr 2020 09:06:43: end of X-cor INFO @ Wed, 22 Apr 2020 09:06:43: #2 finished! INFO @ Wed, 22 Apr 2020 09:06:43: #2 predicted fragment length is 283 bps INFO @ Wed, 22 Apr 2020 09:06:43: #2 alternative fragment length(s) may be 4,283 bps INFO @ Wed, 22 Apr 2020 09:06:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.10_model.r INFO @ Wed, 22 Apr 2020 09:06:43: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:06:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:06:47: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:06:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:06:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:06:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.10_summits.bed INFO @ Wed, 22 Apr 2020 09:06:48: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (443 records, 4 fields): 3 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 @ Wed, 22 Apr 2020 09:07:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 09:07:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:07:08: #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 @ Wed, 22 Apr 2020 09:07:14: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 09:07:14: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 09:07:14: #1 total tags in treatment: 850880 INFO @ Wed, 22 Apr 2020 09:07:14: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:07:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:07:14: #1 tags after filtering in treatment: 850880 INFO @ Wed, 22 Apr 2020 09:07:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:07:14: #1 finished! INFO @ Wed, 22 Apr 2020 09:07:14: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:07:14: #2 number of paired peaks: 1059 INFO @ Wed, 22 Apr 2020 09:07:14: start model_add_line... INFO @ Wed, 22 Apr 2020 09:07:14: start X-correlation... INFO @ Wed, 22 Apr 2020 09:07:14: end of X-cor INFO @ Wed, 22 Apr 2020 09:07:14: #2 finished! INFO @ Wed, 22 Apr 2020 09:07:14: #2 predicted fragment length is 283 bps INFO @ Wed, 22 Apr 2020 09:07:14: #2 alternative fragment length(s) may be 4,283 bps INFO @ Wed, 22 Apr 2020 09:07:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.20_model.r INFO @ Wed, 22 Apr 2020 09:07:14: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:07:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:07:18: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7107357/SRX7107357.20_summits.bed INFO @ Wed, 22 Apr 2020 09:07:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (399 records, 4 fields): 2 millis CompletedMACS2peakCalling