Job ID = 2006625 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,098,579 reads read : 2,098,579 reads written : 2,098,579 spots read : 2,081,816 reads read : 2,081,816 reads written : 2,081,816 spots read : 2,053,260 reads read : 2,053,260 reads written : 2,053,260 spots read : 2,019,599 reads read : 2,019,599 reads written : 2,019,599 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529543.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529544.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529545.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: 00:02:14 8253254 reads; of these: 8253254 (100.00%) were unpaired; of these: 305482 (3.70%) aligned 0 times 7161473 (86.77%) aligned exactly 1 time 786299 (9.53%) aligned >1 times 96.30% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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] 7440201 / 7947772 = 0.9361 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 15:43:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.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 15:43:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:43:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:43:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.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 15:43:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:43:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:43:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.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 15:43:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:43:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:43:50: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:43:50: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:43:50: #1 total tags in treatment: 507571 INFO @ Fri, 05 Jul 2019 15:43:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:43:50: #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 15:43:50: #1 tags after filtering in treatment: 507571 INFO @ Fri, 05 Jul 2019 15:43:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:43:50: #1 finished! INFO @ Fri, 05 Jul 2019 15:43:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:43:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:43:50: #2 number of paired peaks: 397 WARNING @ Fri, 05 Jul 2019 15:43:50: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Fri, 05 Jul 2019 15:43:50: start model_add_line... INFO @ Fri, 05 Jul 2019 15:43:50: start X-correlation... INFO @ Fri, 05 Jul 2019 15:43:50: end of X-cor INFO @ Fri, 05 Jul 2019 15:43:50: #2 finished! INFO @ Fri, 05 Jul 2019 15:43:50: #2 predicted fragment length is 230 bps INFO @ Fri, 05 Jul 2019 15:43:50: #2 alternative fragment length(s) may be 230 bps INFO @ Fri, 05 Jul 2019 15:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.05_model.r INFO @ Fri, 05 Jul 2019 15:43:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:43:51: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:43:51: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:43:51: #1 total tags in treatment: 507571 INFO @ Fri, 05 Jul 2019 15:43:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:43:51: #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 15:43:52: #1 tags after filtering in treatment: 507571 INFO @ Fri, 05 Jul 2019 15:43:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:43:52: #1 finished! INFO @ Fri, 05 Jul 2019 15:43:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:43:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:43:52: #2 number of paired peaks: 397 WARNING @ Fri, 05 Jul 2019 15:43:52: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Fri, 05 Jul 2019 15:43:52: start model_add_line... INFO @ Fri, 05 Jul 2019 15:43:52: start X-correlation... INFO @ Fri, 05 Jul 2019 15:43:52: end of X-cor INFO @ Fri, 05 Jul 2019 15:43:52: #2 finished! INFO @ Fri, 05 Jul 2019 15:43:52: #2 predicted fragment length is 230 bps INFO @ Fri, 05 Jul 2019 15:43:52: #2 alternative fragment length(s) may be 230 bps INFO @ Fri, 05 Jul 2019 15:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.10_model.r INFO @ Fri, 05 Jul 2019 15:43:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:43:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:43:52: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:43:52: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:43:52: #1 total tags in treatment: 507571 INFO @ Fri, 05 Jul 2019 15:43:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:43:52: #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 15:43:52: #1 tags after filtering in treatment: 507571 INFO @ Fri, 05 Jul 2019 15:43:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:43:52: #1 finished! INFO @ Fri, 05 Jul 2019 15:43:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:43:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:43:52: #2 number of paired peaks: 397 WARNING @ Fri, 05 Jul 2019 15:43:52: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Fri, 05 Jul 2019 15:43:52: start model_add_line... INFO @ Fri, 05 Jul 2019 15:43:52: start X-correlation... INFO @ Fri, 05 Jul 2019 15:43:52: end of X-cor INFO @ Fri, 05 Jul 2019 15:43:52: #2 finished! INFO @ Fri, 05 Jul 2019 15:43:52: #2 predicted fragment length is 230 bps INFO @ Fri, 05 Jul 2019 15:43:52: #2 alternative fragment length(s) may be 230 bps INFO @ Fri, 05 Jul 2019 15:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.20_model.r INFO @ Fri, 05 Jul 2019 15:43:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:43:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:43:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:43:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:43:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:43:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.05_summits.bed INFO @ Fri, 05 Jul 2019 15:43:54: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (409 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:43:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:43:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:43:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:43:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:43:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.10_summits.bed INFO @ Fri, 05 Jul 2019 15:43:55: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (285 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:43:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:43:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:43:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548169/ERX2548169.20_summits.bed INFO @ Fri, 05 Jul 2019 15:43:55: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (222 records, 4 fields): 3 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。