Job ID = 2009015 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,239,151 reads read : 7,239,151 reads written : 7,239,151 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637541.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: 00:01:19 7239151 reads; of these: 7239151 (100.00%) were unpaired; of these: 1392084 (19.23%) aligned 0 times 4674170 (64.57%) aligned exactly 1 time 1172897 (16.20%) aligned >1 times 80.77% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 2429541 / 5847067 = 0.4155 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 @ Fri, 05 Jul 2019 19:09:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 19:09:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:09:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:09:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 19:09:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:09:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:09:52: 1000000 INFO @ Fri, 05 Jul 2019 19:09:53: 1000000 INFO @ Fri, 05 Jul 2019 19:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 19:09:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:09:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:10:01: 2000000 INFO @ Fri, 05 Jul 2019 19:10:02: 2000000 INFO @ Fri, 05 Jul 2019 19:10:05: 1000000 INFO @ Fri, 05 Jul 2019 19:10:10: 3000000 INFO @ Fri, 05 Jul 2019 19:10:10: 3000000 INFO @ Fri, 05 Jul 2019 19:10:13: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:10:13: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:10:13: #1 total tags in treatment: 3417526 INFO @ Fri, 05 Jul 2019 19:10:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:10:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:10:13: #1 tags after filtering in treatment: 3417526 INFO @ Fri, 05 Jul 2019 19:10:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:10:13: #1 finished! INFO @ Fri, 05 Jul 2019 19:10:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:10:13: #2 number of paired peaks: 182 WARNING @ Fri, 05 Jul 2019 19:10:13: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Fri, 05 Jul 2019 19:10:13: start model_add_line... INFO @ Fri, 05 Jul 2019 19:10:14: start X-correlation... INFO @ Fri, 05 Jul 2019 19:10:14: end of X-cor INFO @ Fri, 05 Jul 2019 19:10:14: #2 finished! INFO @ Fri, 05 Jul 2019 19:10:14: #2 predicted fragment length is 117 bps INFO @ Fri, 05 Jul 2019 19:10:14: #2 alternative fragment length(s) may be 4,88,117 bps INFO @ Fri, 05 Jul 2019 19:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.05_model.r INFO @ Fri, 05 Jul 2019 19:10:14: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:10:14: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:10:14: #1 total tags in treatment: 3417526 INFO @ Fri, 05 Jul 2019 19:10:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:10:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:10:14: #1 tags after filtering in treatment: 3417526 INFO @ Fri, 05 Jul 2019 19:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:10:14: #1 finished! INFO @ Fri, 05 Jul 2019 19:10:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:10:14: 2000000 INFO @ Fri, 05 Jul 2019 19:10:14: #2 number of paired peaks: 182 WARNING @ Fri, 05 Jul 2019 19:10:14: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Fri, 05 Jul 2019 19:10:14: start model_add_line... INFO @ Fri, 05 Jul 2019 19:10:14: start X-correlation... INFO @ Fri, 05 Jul 2019 19:10:14: end of X-cor INFO @ Fri, 05 Jul 2019 19:10:14: #2 finished! INFO @ Fri, 05 Jul 2019 19:10:14: #2 predicted fragment length is 117 bps INFO @ Fri, 05 Jul 2019 19:10:14: #2 alternative fragment length(s) may be 4,88,117 bps INFO @ Fri, 05 Jul 2019 19:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.10_model.r INFO @ Fri, 05 Jul 2019 19:10:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:10:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:10:23: 3000000 INFO @ Fri, 05 Jul 2019 19:10:26: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:10:26: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:10:26: #1 total tags in treatment: 3417526 INFO @ Fri, 05 Jul 2019 19:10:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:10:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:10:26: #1 tags after filtering in treatment: 3417526 INFO @ Fri, 05 Jul 2019 19:10:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:10:26: #1 finished! INFO @ Fri, 05 Jul 2019 19:10:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:10:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:10:26: #2 number of paired peaks: 182 WARNING @ Fri, 05 Jul 2019 19:10:26: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Fri, 05 Jul 2019 19:10:26: start model_add_line... INFO @ Fri, 05 Jul 2019 19:10:26: start X-correlation... INFO @ Fri, 05 Jul 2019 19:10:26: end of X-cor INFO @ Fri, 05 Jul 2019 19:10:26: #2 finished! INFO @ Fri, 05 Jul 2019 19:10:26: #2 predicted fragment length is 117 bps INFO @ Fri, 05 Jul 2019 19:10:26: #2 alternative fragment length(s) may be 4,88,117 bps INFO @ Fri, 05 Jul 2019 19:10:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.20_model.r INFO @ Fri, 05 Jul 2019 19:10:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:10:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:10:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:10:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:10:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:10:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:10:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.05_summits.bed INFO @ Fri, 05 Jul 2019 19:10:31: Done! INFO @ Fri, 05 Jul 2019 19:10:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:10:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.10_summits.bed INFO @ Fri, 05 Jul 2019 19:10:31: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (4308 records, 4 fields): 11 millis pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (2975 records, 4 fields): 9 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:10:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:10:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594031/ERX594031.20_summits.bed INFO @ Fri, 05 Jul 2019 19:10:51: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1604 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。