Job ID = 1293291 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,615,763 reads read : 20,615,763 reads written : 20,615,763 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: 00:06:00 20615763 reads; of these: 20615763 (100.00%) were unpaired; of these: 5419512 (26.29%) aligned 0 times 10608011 (51.46%) aligned exactly 1 time 4588240 (22.26%) aligned >1 times 73.71% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 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] 8049593 / 15196251 = 0.5297 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 22:50:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.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 22:50:54: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:50:54: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:50:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.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 22:50:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:50:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:50:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.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 22:50:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:50:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:51:02: 1000000 INFO @ Sun, 02 Jun 2019 22:51:03: 1000000 INFO @ Sun, 02 Jun 2019 22:51:03: 1000000 INFO @ Sun, 02 Jun 2019 22:51:08: 2000000 INFO @ Sun, 02 Jun 2019 22:51:11: 2000000 INFO @ Sun, 02 Jun 2019 22:51:11: 2000000 INFO @ Sun, 02 Jun 2019 22:51:15: 3000000 INFO @ Sun, 02 Jun 2019 22:51:18: 3000000 INFO @ Sun, 02 Jun 2019 22:51:20: 3000000 INFO @ Sun, 02 Jun 2019 22:51:22: 4000000 INFO @ Sun, 02 Jun 2019 22:51:26: 4000000 INFO @ Sun, 02 Jun 2019 22:51:27: 4000000 INFO @ Sun, 02 Jun 2019 22:51:29: 5000000 INFO @ Sun, 02 Jun 2019 22:51:34: 5000000 INFO @ Sun, 02 Jun 2019 22:51:35: 5000000 INFO @ Sun, 02 Jun 2019 22:51:36: 6000000 INFO @ Sun, 02 Jun 2019 22:51:41: 6000000 INFO @ Sun, 02 Jun 2019 22:51:43: 7000000 INFO @ Sun, 02 Jun 2019 22:51:44: 6000000 INFO @ Sun, 02 Jun 2019 22:51:44: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:51:44: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:51:44: #1 total tags in treatment: 7146658 INFO @ Sun, 02 Jun 2019 22:51:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:51:44: #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 22:51:44: #1 tags after filtering in treatment: 7146658 INFO @ Sun, 02 Jun 2019 22:51:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:51:44: #1 finished! INFO @ Sun, 02 Jun 2019 22:51:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:51:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:51:45: #2 number of paired peaks: 2969 INFO @ Sun, 02 Jun 2019 22:51:45: start model_add_line... INFO @ Sun, 02 Jun 2019 22:51:45: start X-correlation... INFO @ Sun, 02 Jun 2019 22:51:45: end of X-cor INFO @ Sun, 02 Jun 2019 22:51:45: #2 finished! INFO @ Sun, 02 Jun 2019 22:51:45: #2 predicted fragment length is 136 bps INFO @ Sun, 02 Jun 2019 22:51:45: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 02 Jun 2019 22:51:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.05_model.r INFO @ Sun, 02 Jun 2019 22:51:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:51:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:51:49: 7000000 INFO @ Sun, 02 Jun 2019 22:51:50: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:51:50: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:51:50: #1 total tags in treatment: 7146658 INFO @ Sun, 02 Jun 2019 22:51:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:51:50: #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 22:51:50: #1 tags after filtering in treatment: 7146658 INFO @ Sun, 02 Jun 2019 22:51:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:51:50: #1 finished! INFO @ Sun, 02 Jun 2019 22:51:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:51:51: #2 number of paired peaks: 2969 INFO @ Sun, 02 Jun 2019 22:51:51: start model_add_line... INFO @ Sun, 02 Jun 2019 22:51:51: start X-correlation... INFO @ Sun, 02 Jun 2019 22:51:51: end of X-cor INFO @ Sun, 02 Jun 2019 22:51:51: #2 finished! INFO @ Sun, 02 Jun 2019 22:51:51: #2 predicted fragment length is 136 bps INFO @ Sun, 02 Jun 2019 22:51:51: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 02 Jun 2019 22:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.20_model.r INFO @ Sun, 02 Jun 2019 22:51:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:51:51: 7000000 INFO @ Sun, 02 Jun 2019 22:51:52: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:51:52: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:51:52: #1 total tags in treatment: 7146658 INFO @ Sun, 02 Jun 2019 22:51:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:51:52: #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 22:51:53: #1 tags after filtering in treatment: 7146658 INFO @ Sun, 02 Jun 2019 22:51:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:51:53: #1 finished! INFO @ Sun, 02 Jun 2019 22:51:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:51:54: #2 number of paired peaks: 2969 INFO @ Sun, 02 Jun 2019 22:51:54: start model_add_line... INFO @ Sun, 02 Jun 2019 22:51:54: start X-correlation... INFO @ Sun, 02 Jun 2019 22:51:54: end of X-cor INFO @ Sun, 02 Jun 2019 22:51:54: #2 finished! INFO @ Sun, 02 Jun 2019 22:51:54: #2 predicted fragment length is 136 bps INFO @ Sun, 02 Jun 2019 22:51:54: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 02 Jun 2019 22:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.10_model.r INFO @ Sun, 02 Jun 2019 22:51:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:52:08: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:52:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:52:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.05_summits.bed INFO @ Sun, 02 Jun 2019 22:52:19: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8743 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:52:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:52:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:52:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.20_summits.bed INFO @ Sun, 02 Jun 2019 22:52:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3100 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:52:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:52:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:52:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX032306/ERX032306.10_summits.bed INFO @ Sun, 02 Jun 2019 22:52:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5648 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。