Job ID = 2641080 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,838,708 reads read : 17,677,416 reads written : 8,838,708 reads 0-length : 8,838,708 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: 00:01:51 8838708 reads; of these: 8838708 (100.00%) were unpaired; of these: 382449 (4.33%) aligned 0 times 7528844 (85.18%) aligned exactly 1 time 927415 (10.49%) aligned >1 times 95.67% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 5407377 / 8456259 = 0.6395 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:17:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.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 21:17:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:17:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:17:30: 1000000 INFO @ Sat, 24 Aug 2019 21:17:42: 2000000 INFO @ Sat, 24 Aug 2019 21:17:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.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 21:17:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:17:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:17:53: 3000000 INFO @ Sat, 24 Aug 2019 21:17:53: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:17:53: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:17:53: #1 total tags in treatment: 3048882 INFO @ Sat, 24 Aug 2019 21:17:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:17:53: #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 21:17:53: #1 tags after filtering in treatment: 3048882 INFO @ Sat, 24 Aug 2019 21:17:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:17:53: #1 finished! INFO @ Sat, 24 Aug 2019 21:17:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:17:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:17:53: #2 number of paired peaks: 232 WARNING @ Sat, 24 Aug 2019 21:17:53: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sat, 24 Aug 2019 21:17:53: start model_add_line... INFO @ Sat, 24 Aug 2019 21:17:53: start X-correlation... INFO @ Sat, 24 Aug 2019 21:17:54: end of X-cor INFO @ Sat, 24 Aug 2019 21:17:54: #2 finished! INFO @ Sat, 24 Aug 2019 21:17:54: #2 predicted fragment length is 270 bps INFO @ Sat, 24 Aug 2019 21:17:54: #2 alternative fragment length(s) may be 270 bps INFO @ Sat, 24 Aug 2019 21:17:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.05_model.r INFO @ Sat, 24 Aug 2019 21:17:54: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:17:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:18:01: 1000000 INFO @ Sat, 24 Aug 2019 21:18:09: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:18:12: 2000000 INFO @ Sat, 24 Aug 2019 21:18:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.05_peaks.xls INFO @ Sat, 24 Aug 2019 21:18:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:18:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.05_summits.bed INFO @ Sat, 24 Aug 2019 21:18:12: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1024 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:18:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.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 21:18:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:18:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:18:22: 3000000 INFO @ Sat, 24 Aug 2019 21:18:23: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:18:23: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:18:23: #1 total tags in treatment: 3048882 INFO @ Sat, 24 Aug 2019 21:18:23: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:18:23: #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 21:18:23: #1 tags after filtering in treatment: 3048882 INFO @ Sat, 24 Aug 2019 21:18:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:18:23: #1 finished! INFO @ Sat, 24 Aug 2019 21:18:23: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:18:23: #2 number of paired peaks: 232 WARNING @ Sat, 24 Aug 2019 21:18:23: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sat, 24 Aug 2019 21:18:23: start model_add_line... INFO @ Sat, 24 Aug 2019 21:18:23: start X-correlation... INFO @ Sat, 24 Aug 2019 21:18:23: end of X-cor INFO @ Sat, 24 Aug 2019 21:18:23: #2 finished! INFO @ Sat, 24 Aug 2019 21:18:23: #2 predicted fragment length is 270 bps INFO @ Sat, 24 Aug 2019 21:18:23: #2 alternative fragment length(s) may be 270 bps INFO @ Sat, 24 Aug 2019 21:18:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.10_model.r INFO @ Sat, 24 Aug 2019 21:18:23: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:18:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:18:29: 1000000 INFO @ Sat, 24 Aug 2019 21:18:38: 2000000 INFO @ Sat, 24 Aug 2019 21:18:38: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:18:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.10_peaks.xls INFO @ Sat, 24 Aug 2019 21:18:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:18:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.10_summits.bed INFO @ Sat, 24 Aug 2019 21:18:42: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (649 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:18:47: 3000000 INFO @ Sat, 24 Aug 2019 21:18:48: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:18:48: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:18:48: #1 total tags in treatment: 3048882 INFO @ Sat, 24 Aug 2019 21:18:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:18:48: #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 21:18:48: #1 tags after filtering in treatment: 3048882 INFO @ Sat, 24 Aug 2019 21:18:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:18:48: #1 finished! INFO @ Sat, 24 Aug 2019 21:18:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:18:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:18:48: #2 number of paired peaks: 232 WARNING @ Sat, 24 Aug 2019 21:18:48: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sat, 24 Aug 2019 21:18:48: start model_add_line... INFO @ Sat, 24 Aug 2019 21:18:48: start X-correlation... INFO @ Sat, 24 Aug 2019 21:18:48: end of X-cor INFO @ Sat, 24 Aug 2019 21:18:48: #2 finished! INFO @ Sat, 24 Aug 2019 21:18:48: #2 predicted fragment length is 270 bps INFO @ Sat, 24 Aug 2019 21:18:48: #2 alternative fragment length(s) may be 270 bps INFO @ Sat, 24 Aug 2019 21:18:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.20_model.r INFO @ Sat, 24 Aug 2019 21:18:48: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:18:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:19:03: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:19:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.20_peaks.xls INFO @ Sat, 24 Aug 2019 21:19:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:19:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5257274/SRX5257274.20_summits.bed INFO @ Sat, 24 Aug 2019 21:19:06: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (440 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。