Job ID = 2009761 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,916,279 reads read : 6,916,279 reads written : 6,916,279 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR497938.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: 00:02:10 6916279 reads; of these: 6916279 (100.00%) were unpaired; of these: 542053 (7.84%) aligned 0 times 5094406 (73.66%) aligned exactly 1 time 1279820 (18.50%) aligned >1 times 92.16% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 5156069 / 6374226 = 0.8089 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 19:50:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.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 19:50:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:50:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:50:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.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 19:50:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:50:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:50:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.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 19:50:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:50:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:50:40: 1000000 INFO @ Fri, 05 Jul 2019 19:50:42: 1000000 INFO @ Fri, 05 Jul 2019 19:50:42: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:50:42: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:50:42: #1 total tags in treatment: 1218157 INFO @ Fri, 05 Jul 2019 19:50:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:50:42: #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 19:50:42: #1 tags after filtering in treatment: 1218157 INFO @ Fri, 05 Jul 2019 19:50:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:50:42: #1 finished! INFO @ Fri, 05 Jul 2019 19:50:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:50:42: #2 number of paired peaks: 221 WARNING @ Fri, 05 Jul 2019 19:50:42: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Fri, 05 Jul 2019 19:50:42: start model_add_line... INFO @ Fri, 05 Jul 2019 19:50:42: start X-correlation... INFO @ Fri, 05 Jul 2019 19:50:42: end of X-cor INFO @ Fri, 05 Jul 2019 19:50:42: #2 finished! INFO @ Fri, 05 Jul 2019 19:50:42: #2 predicted fragment length is 253 bps INFO @ Fri, 05 Jul 2019 19:50:42: #2 alternative fragment length(s) may be 1,29,53,92,97,168,204,233,253,274,278,580 bps INFO @ Fri, 05 Jul 2019 19:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.05_model.r INFO @ Fri, 05 Jul 2019 19:50:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:50:43: 1000000 INFO @ Fri, 05 Jul 2019 19:50:44: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:50:44: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:50:44: #1 total tags in treatment: 1218157 INFO @ Fri, 05 Jul 2019 19:50:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:50:44: #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 19:50:44: #1 tags after filtering in treatment: 1218157 INFO @ Fri, 05 Jul 2019 19:50:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:50:44: #1 finished! INFO @ Fri, 05 Jul 2019 19:50:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:50:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:50:44: #2 number of paired peaks: 221 WARNING @ Fri, 05 Jul 2019 19:50:44: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Fri, 05 Jul 2019 19:50:44: start model_add_line... INFO @ Fri, 05 Jul 2019 19:50:44: start X-correlation... INFO @ Fri, 05 Jul 2019 19:50:44: end of X-cor INFO @ Fri, 05 Jul 2019 19:50:44: #2 finished! INFO @ Fri, 05 Jul 2019 19:50:44: #2 predicted fragment length is 253 bps INFO @ Fri, 05 Jul 2019 19:50:44: #2 alternative fragment length(s) may be 1,29,53,92,97,168,204,233,253,274,278,580 bps INFO @ Fri, 05 Jul 2019 19:50:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.10_model.r INFO @ Fri, 05 Jul 2019 19:50:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:50:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:50:45: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:50:45: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:50:45: #1 total tags in treatment: 1218157 INFO @ Fri, 05 Jul 2019 19:50:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:50:45: #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 19:50:45: #1 tags after filtering in treatment: 1218157 INFO @ Fri, 05 Jul 2019 19:50:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:50:45: #1 finished! INFO @ Fri, 05 Jul 2019 19:50:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:50:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:50:45: #2 number of paired peaks: 221 WARNING @ Fri, 05 Jul 2019 19:50:45: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Fri, 05 Jul 2019 19:50:45: start model_add_line... INFO @ Fri, 05 Jul 2019 19:50:45: start X-correlation... INFO @ Fri, 05 Jul 2019 19:50:45: end of X-cor INFO @ Fri, 05 Jul 2019 19:50:45: #2 finished! INFO @ Fri, 05 Jul 2019 19:50:45: #2 predicted fragment length is 253 bps INFO @ Fri, 05 Jul 2019 19:50:45: #2 alternative fragment length(s) may be 1,29,53,92,97,168,204,233,253,274,278,580 bps INFO @ Fri, 05 Jul 2019 19:50:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.20_model.r INFO @ Fri, 05 Jul 2019 19:50:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:50:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:50:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:50:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:50:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:50:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:50:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.05_summits.bed INFO @ Fri, 05 Jul 2019 19:50:51: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (442 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 19:50:51: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:50:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:50:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:50:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.10_summits.bed INFO @ Fri, 05 Jul 2019 19:50:52: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 19:50:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:50:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:50:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148617/SRX148617.20_summits.bed INFO @ Fri, 05 Jul 2019 19:50:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。