Job ID = 2640778 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,363,085 reads read : 3,363,085 reads written : 3,363,085 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:22 3363085 reads; of these: 3363085 (100.00%) were unpaired; of these: 2636646 (78.40%) aligned 0 times 552513 (16.43%) aligned exactly 1 time 173926 (5.17%) aligned >1 times 21.60% overall alignment rate Time searching: 00:00:22 Overall time: 00:00:22 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] 121274 / 726439 = 0.1669 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:10:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.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 @ Sat, 24 Aug 2019 19:10:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:10:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:10:42: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 19:10:42: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 19:10:42: #1 total tags in treatment: 605165 INFO @ Sat, 24 Aug 2019 19:10:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:10:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:10:42: #1 tags after filtering in treatment: 605165 INFO @ Sat, 24 Aug 2019 19:10:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:10:42: #1 finished! INFO @ Sat, 24 Aug 2019 19:10:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:10:42: #2 number of paired peaks: 263 WARNING @ Sat, 24 Aug 2019 19:10:42: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Sat, 24 Aug 2019 19:10:42: start model_add_line... INFO @ Sat, 24 Aug 2019 19:10:42: start X-correlation... INFO @ Sat, 24 Aug 2019 19:10:42: end of X-cor INFO @ Sat, 24 Aug 2019 19:10:42: #2 finished! INFO @ Sat, 24 Aug 2019 19:10:42: #2 predicted fragment length is 167 bps INFO @ Sat, 24 Aug 2019 19:10:42: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 24 Aug 2019 19:10:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.05_model.r INFO @ Sat, 24 Aug 2019 19:10:42: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:10:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:10:44: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:10:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:10:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:10:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.05_summits.bed INFO @ Sat, 24 Aug 2019 19:10:45: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (704 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.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 @ Sat, 24 Aug 2019 19:11:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:11:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:11:10: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 19:11:10: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 19:11:10: #1 total tags in treatment: 605165 INFO @ Sat, 24 Aug 2019 19:11:10: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:11:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:11:10: #1 tags after filtering in treatment: 605165 INFO @ Sat, 24 Aug 2019 19:11:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:11:10: #1 finished! INFO @ Sat, 24 Aug 2019 19:11:10: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:11:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:11:11: #2 number of paired peaks: 263 WARNING @ Sat, 24 Aug 2019 19:11:11: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Sat, 24 Aug 2019 19:11:11: start model_add_line... INFO @ Sat, 24 Aug 2019 19:11:11: start X-correlation... INFO @ Sat, 24 Aug 2019 19:11:11: end of X-cor INFO @ Sat, 24 Aug 2019 19:11:11: #2 finished! INFO @ Sat, 24 Aug 2019 19:11:11: #2 predicted fragment length is 167 bps INFO @ Sat, 24 Aug 2019 19:11:11: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 24 Aug 2019 19:11:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.10_model.r INFO @ Sat, 24 Aug 2019 19:11:11: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:11:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:11:13: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:11:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:11:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:11:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.10_summits.bed INFO @ Sat, 24 Aug 2019 19:11:14: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (391 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:11:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.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 @ Sat, 24 Aug 2019 19:11:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:11:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:11:41: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 19:11:41: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 19:11:41: #1 total tags in treatment: 605165 INFO @ Sat, 24 Aug 2019 19:11:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:11:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:11:41: #1 tags after filtering in treatment: 605165 INFO @ Sat, 24 Aug 2019 19:11:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:11:41: #1 finished! INFO @ Sat, 24 Aug 2019 19:11:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:11:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:11:41: #2 number of paired peaks: 263 WARNING @ Sat, 24 Aug 2019 19:11:41: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Sat, 24 Aug 2019 19:11:41: start model_add_line... INFO @ Sat, 24 Aug 2019 19:11:41: start X-correlation... INFO @ Sat, 24 Aug 2019 19:11:41: end of X-cor INFO @ Sat, 24 Aug 2019 19:11:41: #2 finished! INFO @ Sat, 24 Aug 2019 19:11:41: #2 predicted fragment length is 167 bps INFO @ Sat, 24 Aug 2019 19:11:41: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 24 Aug 2019 19:11:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.20_model.r INFO @ Sat, 24 Aug 2019 19:11:41: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:11:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:11:43: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:11:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:11:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:11:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX321078/ERX321078.20_summits.bed INFO @ Sat, 24 Aug 2019 19:11:44: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。