Job ID = 1293156 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,092,384 reads read : 10,184,768 reads written : 5,092,384 reads 0-length : 5,092,384 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:23 5092384 reads; of these: 5092384 (100.00%) were unpaired; of these: 51742 (1.02%) aligned 0 times 4503274 (88.43%) aligned exactly 1 time 537368 (10.55%) aligned >1 times 98.98% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 1269589 / 5040642 = 0.2519 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 22:03:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.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 22:03:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:03:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:03:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.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 22:03:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:03:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:03:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.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 22:03:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:03:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:03:53: 1000000 INFO @ Sun, 02 Jun 2019 22:03:53: 1000000 INFO @ Sun, 02 Jun 2019 22:03:54: 1000000 INFO @ Sun, 02 Jun 2019 22:04:00: 2000000 INFO @ Sun, 02 Jun 2019 22:04:00: 2000000 INFO @ Sun, 02 Jun 2019 22:04:02: 2000000 INFO @ Sun, 02 Jun 2019 22:04:07: 3000000 INFO @ Sun, 02 Jun 2019 22:04:08: 3000000 INFO @ Sun, 02 Jun 2019 22:04:11: 3000000 INFO @ Sun, 02 Jun 2019 22:04:13: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:04:13: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:04:13: #1 total tags in treatment: 3771053 INFO @ Sun, 02 Jun 2019 22:04:13: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:13: #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 22:04:13: #1 tags after filtering in treatment: 3771053 INFO @ Sun, 02 Jun 2019 22:04:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:13: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:13: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:04:13: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:04:13: #1 total tags in treatment: 3771053 INFO @ Sun, 02 Jun 2019 22:04:13: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:13: #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 22:04:13: #1 tags after filtering in treatment: 3771053 INFO @ Sun, 02 Jun 2019 22:04:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:13: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:14: #2 number of paired peaks: 4310 INFO @ Sun, 02 Jun 2019 22:04:14: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:14: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:14: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:14: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:14: #2 predicted fragment length is 167 bps INFO @ Sun, 02 Jun 2019 22:04:14: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 02 Jun 2019 22:04:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.05_model.r INFO @ Sun, 02 Jun 2019 22:04:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:04:14: #2 number of paired peaks: 4310 INFO @ Sun, 02 Jun 2019 22:04:14: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:14: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:14: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:14: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:14: #2 predicted fragment length is 167 bps INFO @ Sun, 02 Jun 2019 22:04:14: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 02 Jun 2019 22:04:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.20_model.r INFO @ Sun, 02 Jun 2019 22:04:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:04:17: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:04:17: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:04:17: #1 total tags in treatment: 3771053 INFO @ Sun, 02 Jun 2019 22:04:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:17: #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 22:04:17: #1 tags after filtering in treatment: 3771053 INFO @ Sun, 02 Jun 2019 22:04:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:17: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:18: #2 number of paired peaks: 4310 INFO @ Sun, 02 Jun 2019 22:04:18: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:18: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:18: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:18: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:18: #2 predicted fragment length is 167 bps INFO @ Sun, 02 Jun 2019 22:04:18: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 02 Jun 2019 22:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.10_model.r INFO @ Sun, 02 Jun 2019 22:04:18: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:04:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:04:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:04:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:04:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:04:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:04:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.05_summits.bed INFO @ Sun, 02 Jun 2019 22:04:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4829 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:04:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:04:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:04:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.20_summits.bed INFO @ Sun, 02 Jun 2019 22:04:34: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3217 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:04:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:04:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:04:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402723/SRX5402723.10_summits.bed INFO @ Sun, 02 Jun 2019 22:04:38: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (4014 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。