Job ID = 2008401 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,037,516 reads read : 6,037,516 reads written : 6,037,516 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637596.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: 00:00:45 6037516 reads; of these: 6037516 (100.00%) were unpaired; of these: 4071009 (67.43%) aligned 0 times 1513732 (25.07%) aligned exactly 1 time 452775 (7.50%) aligned >1 times 32.57% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 751702 / 1966507 = 0.3823 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 19:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.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 19:00:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:00:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.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 19:00:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:00:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:00:52: 1000000 INFO @ Fri, 05 Jul 2019 19:00:53: 1000000 INFO @ Fri, 05 Jul 2019 19:00:53: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:00:53: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:00:53: #1 total tags in treatment: 1214805 INFO @ Fri, 05 Jul 2019 19:00:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:00:53: #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 19:00:53: #1 tags after filtering in treatment: 1214805 INFO @ Fri, 05 Jul 2019 19:00:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:00:53: #1 finished! INFO @ Fri, 05 Jul 2019 19:00:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:00:54: #2 number of paired peaks: 448 WARNING @ Fri, 05 Jul 2019 19:00:54: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Fri, 05 Jul 2019 19:00:54: start model_add_line... INFO @ Fri, 05 Jul 2019 19:00:54: start X-correlation... INFO @ Fri, 05 Jul 2019 19:00:54: end of X-cor INFO @ Fri, 05 Jul 2019 19:00:54: #2 finished! INFO @ Fri, 05 Jul 2019 19:00:54: #2 predicted fragment length is 157 bps INFO @ Fri, 05 Jul 2019 19:00:54: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 05 Jul 2019 19:00:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.05_model.r INFO @ Fri, 05 Jul 2019 19:00:55: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:00:55: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:00:55: #1 total tags in treatment: 1214805 INFO @ Fri, 05 Jul 2019 19:00:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:00:55: #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 19:00:55: #1 tags after filtering in treatment: 1214805 INFO @ Fri, 05 Jul 2019 19:00:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:00:55: #1 finished! INFO @ Fri, 05 Jul 2019 19:00:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:00:55: #2 number of paired peaks: 448 WARNING @ Fri, 05 Jul 2019 19:00:55: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Fri, 05 Jul 2019 19:00:55: start model_add_line... INFO @ Fri, 05 Jul 2019 19:00:55: start X-correlation... INFO @ Fri, 05 Jul 2019 19:00:55: end of X-cor INFO @ Fri, 05 Jul 2019 19:00:55: #2 finished! INFO @ Fri, 05 Jul 2019 19:00:55: #2 predicted fragment length is 157 bps INFO @ Fri, 05 Jul 2019 19:00:55: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 05 Jul 2019 19:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.10_model.r INFO @ Fri, 05 Jul 2019 19:01:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:01:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:01:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:01:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:01:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.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 19:01:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:01:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:01:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:01:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:01:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:01:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:01:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.05_summits.bed INFO @ Fri, 05 Jul 2019 19:01:26: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (2572 records, 4 fields): 8 millis INFO @ Fri, 05 Jul 2019 19:01:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:01:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:01:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.10_summits.bed INFO @ Fri, 05 Jul 2019 19:01:26: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1822 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 19:01:28: 1000000 INFO @ Fri, 05 Jul 2019 19:01:30: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:01:30: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:01:30: #1 total tags in treatment: 1214805 INFO @ Fri, 05 Jul 2019 19:01:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:01:30: #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 19:01:30: #1 tags after filtering in treatment: 1214805 INFO @ Fri, 05 Jul 2019 19:01:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:01:30: #1 finished! INFO @ Fri, 05 Jul 2019 19:01:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:01:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:01:30: #2 number of paired peaks: 448 WARNING @ Fri, 05 Jul 2019 19:01:30: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Fri, 05 Jul 2019 19:01:30: start model_add_line... INFO @ Fri, 05 Jul 2019 19:01:30: start X-correlation... INFO @ Fri, 05 Jul 2019 19:01:30: end of X-cor INFO @ Fri, 05 Jul 2019 19:01:30: #2 finished! INFO @ Fri, 05 Jul 2019 19:01:30: #2 predicted fragment length is 157 bps INFO @ Fri, 05 Jul 2019 19:01:30: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 05 Jul 2019 19:01:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.20_model.r INFO @ Fri, 05 Jul 2019 19:01:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:01:30: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:01:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:01:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:01:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:01:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594009/ERX594009.20_summits.bed INFO @ Fri, 05 Jul 2019 19:01:36: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1140 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。