Job ID = 2011794 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,853,645 reads read : 11,707,290 reads written : 5,853,645 reads 0-length : 5,853,645 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: 00:01:08 5853645 reads; of these: 5853645 (100.00%) were unpaired; of these: 1911030 (32.65%) aligned 0 times 3602371 (61.54%) aligned exactly 1 time 340244 (5.81%) aligned >1 times 67.35% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 3263024 / 3942615 = 0.8276 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 @ Sat, 06 Jul 2019 02:44:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.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, 06 Jul 2019 02:44:07: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:44:07: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:44:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.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, 06 Jul 2019 02:44:08: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:44:08: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:44:12: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:44:12: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:44:12: #1 total tags in treatment: 679591 INFO @ Sat, 06 Jul 2019 02:44:12: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:44:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:44:12: #1 tags after filtering in treatment: 679591 INFO @ Sat, 06 Jul 2019 02:44:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:44:12: #1 finished! INFO @ Sat, 06 Jul 2019 02:44:12: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:44:12: #2 number of paired peaks: 176 WARNING @ Sat, 06 Jul 2019 02:44:12: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 06 Jul 2019 02:44:12: start model_add_line... INFO @ Sat, 06 Jul 2019 02:44:12: start X-correlation... INFO @ Sat, 06 Jul 2019 02:44:12: end of X-cor INFO @ Sat, 06 Jul 2019 02:44:12: #2 finished! INFO @ Sat, 06 Jul 2019 02:44:12: #2 predicted fragment length is 164 bps INFO @ Sat, 06 Jul 2019 02:44:12: #2 alternative fragment length(s) may be 4,76,108,137,164 bps INFO @ Sat, 06 Jul 2019 02:44:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.05_model.r INFO @ Sat, 06 Jul 2019 02:44:13: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:44:13: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:44:13: #1 total tags in treatment: 679591 INFO @ Sat, 06 Jul 2019 02:44:13: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:44:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:44:13: #1 tags after filtering in treatment: 679591 INFO @ Sat, 06 Jul 2019 02:44:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:44:13: #1 finished! INFO @ Sat, 06 Jul 2019 02:44:13: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:44:13: #2 number of paired peaks: 176 WARNING @ Sat, 06 Jul 2019 02:44:13: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 06 Jul 2019 02:44:13: start model_add_line... INFO @ Sat, 06 Jul 2019 02:44:13: start X-correlation... INFO @ Sat, 06 Jul 2019 02:44:13: end of X-cor INFO @ Sat, 06 Jul 2019 02:44:13: #2 finished! INFO @ Sat, 06 Jul 2019 02:44:13: #2 predicted fragment length is 164 bps INFO @ Sat, 06 Jul 2019 02:44:13: #2 alternative fragment length(s) may be 4,76,108,137,164 bps INFO @ Sat, 06 Jul 2019 02:44:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.10_model.r INFO @ Sat, 06 Jul 2019 02:44:18: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:44:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:44:18: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:44:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:44:20: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:44:20: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:44:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.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, 06 Jul 2019 02:44:20: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:44:20: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:44:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.10_peaks.xls INFO @ Sat, 06 Jul 2019 02:44:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:44:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.10_summits.bed INFO @ Sat, 06 Jul 2019 02:44:21: Done! INFO @ Sat, 06 Jul 2019 02:44:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.05_peaks.xls INFO @ Sat, 06 Jul 2019 02:44:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:44:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.05_summits.bed INFO @ Sat, 06 Jul 2019 02:44:21: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (265 records, 4 fields): 3 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (471 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:44:26: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:44:26: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:44:26: #1 total tags in treatment: 679591 INFO @ Sat, 06 Jul 2019 02:44:26: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:44:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:44:26: #1 tags after filtering in treatment: 679591 INFO @ Sat, 06 Jul 2019 02:44:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:44:26: #1 finished! INFO @ Sat, 06 Jul 2019 02:44:26: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:44:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:44:26: #2 number of paired peaks: 176 WARNING @ Sat, 06 Jul 2019 02:44:26: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 06 Jul 2019 02:44:26: start model_add_line... INFO @ Sat, 06 Jul 2019 02:44:26: start X-correlation... INFO @ Sat, 06 Jul 2019 02:44:26: end of X-cor INFO @ Sat, 06 Jul 2019 02:44:26: #2 finished! INFO @ Sat, 06 Jul 2019 02:44:26: #2 predicted fragment length is 164 bps INFO @ Sat, 06 Jul 2019 02:44:26: #2 alternative fragment length(s) may be 4,76,108,137,164 bps INFO @ Sat, 06 Jul 2019 02:44:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.20_model.r INFO @ Sat, 06 Jul 2019 02:44:26: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:44:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:44:29: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:44:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.20_peaks.xls INFO @ Sat, 06 Jul 2019 02:44:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:44:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028224/SRX5028224.20_summits.bed INFO @ Sat, 06 Jul 2019 02:44:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。