Job ID = 1293426 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 550,618 reads read : 550,618 reads written : 550,618 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: 00:00:08 550618 reads; of these: 550618 (100.00%) were unpaired; of these: 60268 (10.95%) aligned 0 times 379234 (68.87%) aligned exactly 1 time 111116 (20.18%) aligned >1 times 89.05% overall alignment rate Time searching: 00:00:08 Overall time: 00:00:08 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] 24650 / 490350 = 0.0503 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 23:45:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.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 @ Sun, 02 Jun 2019 23:45:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:45:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:45:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.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 @ Sun, 02 Jun 2019 23:45:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:45:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:45:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.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 @ Sun, 02 Jun 2019 23:45:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:45:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:45:42: #1 tag size is determined as 27 bps INFO @ Sun, 02 Jun 2019 23:45:42: #1 tag size = 27 INFO @ Sun, 02 Jun 2019 23:45:42: #1 total tags in treatment: 465700 INFO @ Sun, 02 Jun 2019 23:45:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:45:42: #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 23:45:42: #1 tags after filtering in treatment: 465700 INFO @ Sun, 02 Jun 2019 23:45:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:45:42: #1 finished! INFO @ Sun, 02 Jun 2019 23:45:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:45:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:45:42: #2 number of paired peaks: 3214 INFO @ Sun, 02 Jun 2019 23:45:42: start model_add_line... INFO @ Sun, 02 Jun 2019 23:45:42: start X-correlation... INFO @ Sun, 02 Jun 2019 23:45:42: end of X-cor INFO @ Sun, 02 Jun 2019 23:45:42: #2 finished! INFO @ Sun, 02 Jun 2019 23:45:42: #2 predicted fragment length is 167 bps INFO @ Sun, 02 Jun 2019 23:45:42: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 02 Jun 2019 23:45:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.20_model.r INFO @ Sun, 02 Jun 2019 23:45:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:45:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:45:42: #1 tag size is determined as 27 bps INFO @ Sun, 02 Jun 2019 23:45:42: #1 tag size = 27 INFO @ Sun, 02 Jun 2019 23:45:42: #1 total tags in treatment: 465700 INFO @ Sun, 02 Jun 2019 23:45:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:45:42: #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 23:45:42: #1 tags after filtering in treatment: 465700 INFO @ Sun, 02 Jun 2019 23:45:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:45:42: #1 finished! INFO @ Sun, 02 Jun 2019 23:45:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:45:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:45:42: #1 tag size is determined as 27 bps INFO @ Sun, 02 Jun 2019 23:45:42: #1 tag size = 27 INFO @ Sun, 02 Jun 2019 23:45:42: #1 total tags in treatment: 465700 INFO @ Sun, 02 Jun 2019 23:45:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:45:42: #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 23:45:42: #1 tags after filtering in treatment: 465700 INFO @ Sun, 02 Jun 2019 23:45:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:45:42: #1 finished! INFO @ Sun, 02 Jun 2019 23:45:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:45:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:45:42: #2 number of paired peaks: 3214 INFO @ Sun, 02 Jun 2019 23:45:42: start model_add_line... INFO @ Sun, 02 Jun 2019 23:45:42: start X-correlation... INFO @ Sun, 02 Jun 2019 23:45:42: end of X-cor INFO @ Sun, 02 Jun 2019 23:45:42: #2 finished! INFO @ Sun, 02 Jun 2019 23:45:42: #2 predicted fragment length is 167 bps INFO @ Sun, 02 Jun 2019 23:45:42: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 02 Jun 2019 23:45:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.10_model.r INFO @ Sun, 02 Jun 2019 23:45:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:45:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:45:42: #2 number of paired peaks: 3214 INFO @ Sun, 02 Jun 2019 23:45:42: start model_add_line... INFO @ Sun, 02 Jun 2019 23:45:42: start X-correlation... INFO @ Sun, 02 Jun 2019 23:45:42: end of X-cor INFO @ Sun, 02 Jun 2019 23:45:42: #2 finished! INFO @ Sun, 02 Jun 2019 23:45:42: #2 predicted fragment length is 167 bps INFO @ Sun, 02 Jun 2019 23:45:42: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 02 Jun 2019 23:45:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.05_model.r INFO @ Sun, 02 Jun 2019 23:45:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:45:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:45:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:45:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:45:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:45:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:45:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.20_peaks.narrowPeak BedGraph に変換しました。 INFO @ Sun, 02 Jun 2019 23:45:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.20_summits.bed INFO @ Sun, 02 Jun 2019 23:45:44: Done! BigWig に変換中... pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (36 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:45:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:45:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:45:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.10_summits.bed INFO @ Sun, 02 Jun 2019 23:45:45: Done! INFO @ Sun, 02 Jun 2019 23:45:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:45:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:45:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX242712/ERX242712.05_summits.bed pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (272 records, 4 fields): 2 millis INFO @ Sun, 02 Jun 2019 23:45:45: Done! CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (979 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。