Job ID = 2589242 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 858,599 reads read : 858,599 reads written : 858,599 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR164273.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: 00:00:06 858599 reads; of these: 858599 (100.00%) were unpaired; of these: 636916 (74.18%) aligned 0 times 191832 (22.34%) aligned exactly 1 time 29851 (3.48%) aligned >1 times 25.82% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 8474 / 221683 = 0.0382 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 17:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 17:13:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:13:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:13:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 17:13:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:13:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:13:04: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:13:04: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:13:04: #1 total tags in treatment: 213209 INFO @ Mon, 12 Aug 2019 17:13:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:13:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:13:04: #1 tags after filtering in treatment: 213209 INFO @ Mon, 12 Aug 2019 17:13:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:13:04: #1 finished! INFO @ Mon, 12 Aug 2019 17:13:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:13:04: #2 number of paired peaks: 1052 INFO @ Mon, 12 Aug 2019 17:13:04: start model_add_line... INFO @ Mon, 12 Aug 2019 17:13:04: start X-correlation... INFO @ Mon, 12 Aug 2019 17:13:04: end of X-cor INFO @ Mon, 12 Aug 2019 17:13:04: #2 finished! INFO @ Mon, 12 Aug 2019 17:13:04: #2 predicted fragment length is 165 bps INFO @ Mon, 12 Aug 2019 17:13:04: #2 alternative fragment length(s) may be 165 bps INFO @ Mon, 12 Aug 2019 17:13:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.05_model.r INFO @ Mon, 12 Aug 2019 17:13:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:13:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 17:13:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:13:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:13:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:13:05: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:13:05: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:13:05: #1 total tags in treatment: 213209 INFO @ Mon, 12 Aug 2019 17:13:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:13:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:13:05: #1 tags after filtering in treatment: 213209 INFO @ Mon, 12 Aug 2019 17:13:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:13:05: #1 finished! INFO @ Mon, 12 Aug 2019 17:13:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:13:05: #2 number of paired peaks: 1052 INFO @ Mon, 12 Aug 2019 17:13:05: start model_add_line... INFO @ Mon, 12 Aug 2019 17:13:05: start X-correlation... INFO @ Mon, 12 Aug 2019 17:13:05: end of X-cor INFO @ Mon, 12 Aug 2019 17:13:05: #2 finished! INFO @ Mon, 12 Aug 2019 17:13:05: #2 predicted fragment length is 165 bps INFO @ Mon, 12 Aug 2019 17:13:05: #2 alternative fragment length(s) may be 165 bps INFO @ Mon, 12 Aug 2019 17:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.10_model.r INFO @ Mon, 12 Aug 2019 17:13:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:13:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:13:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:13:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.05_summits.bed INFO @ Mon, 12 Aug 2019 17:13:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 17:13:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 12 Aug 2019 17:13:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:13:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:13:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.10_summits.bed INFO @ Mon, 12 Aug 2019 17:13:06: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:13:07: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:13:07: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:13:07: #1 total tags in treatment: 213209 INFO @ Mon, 12 Aug 2019 17:13:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:13:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:13:07: #1 tags after filtering in treatment: 213209 INFO @ Mon, 12 Aug 2019 17:13:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:13:07: #1 finished! INFO @ Mon, 12 Aug 2019 17:13:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:13:07: #2 number of paired peaks: 1052 INFO @ Mon, 12 Aug 2019 17:13:07: start model_add_line... INFO @ Mon, 12 Aug 2019 17:13:07: start X-correlation... INFO @ Mon, 12 Aug 2019 17:13:07: end of X-cor INFO @ Mon, 12 Aug 2019 17:13:07: #2 finished! INFO @ Mon, 12 Aug 2019 17:13:07: #2 predicted fragment length is 165 bps INFO @ Mon, 12 Aug 2019 17:13:07: #2 alternative fragment length(s) may be 165 bps INFO @ Mon, 12 Aug 2019 17:13:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.20_model.r INFO @ Mon, 12 Aug 2019 17:13:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:13:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:13:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:13:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:13:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:13:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX054266/SRX054266.20_summits.bed INFO @ Mon, 12 Aug 2019 17:13:08: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis CompletedMACS2peakCalling