Job ID = 1291638 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,883,662 reads read : 9,883,662 reads written : 9,883,662 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:02:38 9883662 reads; of these: 9883662 (100.00%) were unpaired; of these: 1370338 (13.86%) aligned 0 times 5935766 (60.06%) aligned exactly 1 time 2577558 (26.08%) aligned >1 times 86.14% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 4997263 / 8513324 = 0.5870 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 @ Sun, 02 Jun 2019 16:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.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 @ Sun, 02 Jun 2019 16:15:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:15:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.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 @ Sun, 02 Jun 2019 16:15:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:15:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.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 @ Sun, 02 Jun 2019 16:15:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:15:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:15:58: 1000000 INFO @ Sun, 02 Jun 2019 16:15:59: 1000000 INFO @ Sun, 02 Jun 2019 16:16:01: 1000000 INFO @ Sun, 02 Jun 2019 16:16:07: 2000000 INFO @ Sun, 02 Jun 2019 16:16:07: 2000000 INFO @ Sun, 02 Jun 2019 16:16:12: 2000000 INFO @ Sun, 02 Jun 2019 16:16:15: 3000000 INFO @ Sun, 02 Jun 2019 16:16:15: 3000000 INFO @ Sun, 02 Jun 2019 16:16:20: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:16:20: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:16:20: #1 total tags in treatment: 3516061 INFO @ Sun, 02 Jun 2019 16:16:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:16:20: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:16:20: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:16:20: #1 total tags in treatment: 3516061 INFO @ Sun, 02 Jun 2019 16:16:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:16:20: #1 tags after filtering in treatment: 3516061 INFO @ Sun, 02 Jun 2019 16:16:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:20: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:20: #1 tags after filtering in treatment: 3516061 INFO @ Sun, 02 Jun 2019 16:16:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:20: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:20: #2 number of paired peaks: 2919 INFO @ Sun, 02 Jun 2019 16:16:20: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:20: #2 number of paired peaks: 2919 INFO @ Sun, 02 Jun 2019 16:16:20: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:20: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:20: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:20: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:20: #2 predicted fragment length is 158 bps INFO @ Sun, 02 Jun 2019 16:16:20: #2 alternative fragment length(s) may be 2,158 bps INFO @ Sun, 02 Jun 2019 16:16:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.20_model.r INFO @ Sun, 02 Jun 2019 16:16:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:16:20: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:20: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:20: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:20: #2 predicted fragment length is 158 bps INFO @ Sun, 02 Jun 2019 16:16:20: #2 alternative fragment length(s) may be 2,158 bps INFO @ Sun, 02 Jun 2019 16:16:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.05_model.r INFO @ Sun, 02 Jun 2019 16:16:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:16:23: 3000000 INFO @ Sun, 02 Jun 2019 16:16:28: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:16:28: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:16:28: #1 total tags in treatment: 3516061 INFO @ Sun, 02 Jun 2019 16:16:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:16:28: #1 tags after filtering in treatment: 3516061 INFO @ Sun, 02 Jun 2019 16:16:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:28: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:29: #2 number of paired peaks: 2919 INFO @ Sun, 02 Jun 2019 16:16:29: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:29: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:29: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:29: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:29: #2 predicted fragment length is 158 bps INFO @ Sun, 02 Jun 2019 16:16:29: #2 alternative fragment length(s) may be 2,158 bps INFO @ Sun, 02 Jun 2019 16:16:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.10_model.r INFO @ Sun, 02 Jun 2019 16:16:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:16:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:16:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:16:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:16:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:16:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.20_summits.bed INFO @ Sun, 02 Jun 2019 16:16:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (107 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:16:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:16:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:16:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.05_summits.bed INFO @ Sun, 02 Jun 2019 16:16:38: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1345 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:16:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:16:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:16:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:16:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX148638/SRX148638.10_summits.bed INFO @ Sun, 02 Jun 2019 16:16:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (395 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。