Job ID = 2008388 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,783,624 reads read : 6,783,624 reads written : 6,783,624 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637598.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: 00:00:49 6783624 reads; of these: 6783624 (100.00%) were unpaired; of these: 4976188 (73.36%) aligned 0 times 1026581 (15.13%) aligned exactly 1 time 780855 (11.51%) aligned >1 times 26.64% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 963322 / 1807436 = 0.5330 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 18:56:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.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 18:56:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.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 18:56:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.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 18:56:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:17: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:56:17: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:56:17: #1 total tags in treatment: 844114 INFO @ Fri, 05 Jul 2019 18:56:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:17: #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 18:56:17: #1 tags after filtering in treatment: 844114 INFO @ Fri, 05 Jul 2019 18:56:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:56:17: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:17: #2 number of paired peaks: 289 WARNING @ Fri, 05 Jul 2019 18:56:17: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Fri, 05 Jul 2019 18:56:17: start model_add_line... INFO @ Fri, 05 Jul 2019 18:56:17: start X-correlation... INFO @ Fri, 05 Jul 2019 18:56:17: end of X-cor INFO @ Fri, 05 Jul 2019 18:56:17: #2 finished! INFO @ Fri, 05 Jul 2019 18:56:17: #2 predicted fragment length is 155 bps INFO @ Fri, 05 Jul 2019 18:56:17: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 05 Jul 2019 18:56:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.05_model.r INFO @ Fri, 05 Jul 2019 18:56:18: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:56:18: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:56:18: #1 total tags in treatment: 844114 INFO @ Fri, 05 Jul 2019 18:56:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:18: #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 18:56:18: #1 tags after filtering in treatment: 844114 INFO @ Fri, 05 Jul 2019 18:56:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:56:18: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:18: #2 number of paired peaks: 289 WARNING @ Fri, 05 Jul 2019 18:56:18: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Fri, 05 Jul 2019 18:56:18: start model_add_line... INFO @ Fri, 05 Jul 2019 18:56:18: start X-correlation... INFO @ Fri, 05 Jul 2019 18:56:18: end of X-cor INFO @ Fri, 05 Jul 2019 18:56:18: #2 finished! INFO @ Fri, 05 Jul 2019 18:56:18: #2 predicted fragment length is 155 bps INFO @ Fri, 05 Jul 2019 18:56:18: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 05 Jul 2019 18:56:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.10_model.r INFO @ Fri, 05 Jul 2019 18:56:18: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:56:18: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:56:18: #1 total tags in treatment: 844114 INFO @ Fri, 05 Jul 2019 18:56:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:18: #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 18:56:18: #1 tags after filtering in treatment: 844114 INFO @ Fri, 05 Jul 2019 18:56:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:56:18: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:18: #2 number of paired peaks: 289 WARNING @ Fri, 05 Jul 2019 18:56:18: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Fri, 05 Jul 2019 18:56:18: start model_add_line... INFO @ Fri, 05 Jul 2019 18:56:18: start X-correlation... INFO @ Fri, 05 Jul 2019 18:56:18: end of X-cor INFO @ Fri, 05 Jul 2019 18:56:18: #2 finished! INFO @ Fri, 05 Jul 2019 18:56:18: #2 predicted fragment length is 155 bps INFO @ Fri, 05 Jul 2019 18:56:18: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 05 Jul 2019 18:56:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.20_model.r BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:56:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:56:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:56:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:56:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:56:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:56:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:56:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:56:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:56:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:56:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:56:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:56:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.20_summits.bed INFO @ Fri, 05 Jul 2019 18:56:37: Done! INFO @ Fri, 05 Jul 2019 18:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.10_summits.bed INFO @ Fri, 05 Jul 2019 18:56:37: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (387 records, 4 fields): 3 millis pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (731 records, 4 fields): 7 millis BigWig に変換しました。 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:56:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594001/ERX594001.05_summits.bed INFO @ Fri, 05 Jul 2019 18:56:59: Done! CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1613 records, 4 fields): 8 millis CompletedMACS2peakCalling