Job ID = 2009751 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,487,794 reads read : 5,487,794 reads written : 5,487,794 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR497928.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: 00:00:41 5487794 reads; of these: 5487794 (100.00%) were unpaired; of these: 736360 (13.42%) aligned 0 times 3264978 (59.50%) aligned exactly 1 time 1486456 (27.09%) aligned >1 times 86.58% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 2785123 / 4751434 = 0.5862 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 19:44:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.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 19:44:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:44:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.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 19:44:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:44:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:44:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.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 19:44:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:44:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:44:32: 1000000 INFO @ Fri, 05 Jul 2019 19:44:34: 1000000 INFO @ Fri, 05 Jul 2019 19:44:35: 1000000 INFO @ Fri, 05 Jul 2019 19:44:40: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:44:40: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:44:40: #1 total tags in treatment: 1966311 INFO @ Fri, 05 Jul 2019 19:44:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:44:40: #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 19:44:40: #1 tags after filtering in treatment: 1966311 INFO @ Fri, 05 Jul 2019 19:44:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:44:40: #1 finished! INFO @ Fri, 05 Jul 2019 19:44:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:44:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:44:40: #2 number of paired peaks: 411 WARNING @ Fri, 05 Jul 2019 19:44:40: Fewer paired peaks (411) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 411 pairs to build model! INFO @ Fri, 05 Jul 2019 19:44:40: start model_add_line... INFO @ Fri, 05 Jul 2019 19:44:40: start X-correlation... INFO @ Fri, 05 Jul 2019 19:44:40: end of X-cor INFO @ Fri, 05 Jul 2019 19:44:40: #2 finished! INFO @ Fri, 05 Jul 2019 19:44:40: #2 predicted fragment length is 170 bps INFO @ Fri, 05 Jul 2019 19:44:40: #2 alternative fragment length(s) may be 2,170,188 bps INFO @ Fri, 05 Jul 2019 19:44:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.05_model.r INFO @ Fri, 05 Jul 2019 19:44:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:44:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:44:42: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:44:42: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:44:42: #1 total tags in treatment: 1966311 INFO @ Fri, 05 Jul 2019 19:44:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:44:42: #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 19:44:42: #1 tags after filtering in treatment: 1966311 INFO @ Fri, 05 Jul 2019 19:44:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:44:42: #1 finished! INFO @ Fri, 05 Jul 2019 19:44:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:44:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:44:42: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:44:42: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:44:42: #1 total tags in treatment: 1966311 INFO @ Fri, 05 Jul 2019 19:44:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:44:42: #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 19:44:42: #1 tags after filtering in treatment: 1966311 INFO @ Fri, 05 Jul 2019 19:44:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:44:42: #1 finished! INFO @ Fri, 05 Jul 2019 19:44:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:44:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:44:42: #2 number of paired peaks: 411 WARNING @ Fri, 05 Jul 2019 19:44:42: Fewer paired peaks (411) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 411 pairs to build model! INFO @ Fri, 05 Jul 2019 19:44:42: start model_add_line... INFO @ Fri, 05 Jul 2019 19:44:43: start X-correlation... INFO @ Fri, 05 Jul 2019 19:44:43: end of X-cor INFO @ Fri, 05 Jul 2019 19:44:43: #2 finished! INFO @ Fri, 05 Jul 2019 19:44:43: #2 predicted fragment length is 170 bps INFO @ Fri, 05 Jul 2019 19:44:43: #2 alternative fragment length(s) may be 2,170,188 bps INFO @ Fri, 05 Jul 2019 19:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.10_model.r INFO @ Fri, 05 Jul 2019 19:44:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:44:43: #2 number of paired peaks: 411 WARNING @ Fri, 05 Jul 2019 19:44:43: Fewer paired peaks (411) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 411 pairs to build model! INFO @ Fri, 05 Jul 2019 19:44:43: start model_add_line... INFO @ Fri, 05 Jul 2019 19:44:43: start X-correlation... INFO @ Fri, 05 Jul 2019 19:44:43: end of X-cor INFO @ Fri, 05 Jul 2019 19:44:43: #2 finished! INFO @ Fri, 05 Jul 2019 19:44:43: #2 predicted fragment length is 170 bps INFO @ Fri, 05 Jul 2019 19:44:43: #2 alternative fragment length(s) may be 2,170,188 bps INFO @ Fri, 05 Jul 2019 19:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.20_model.r INFO @ Fri, 05 Jul 2019 19:44:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:44:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:44:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:44:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:44:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.05_summits.bed INFO @ Fri, 05 Jul 2019 19:44:52: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (778 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 19:44:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:44:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.20_summits.bed INFO @ Fri, 05 Jul 2019 19:44:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 19:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148607/SRX148607.10_summits.bed INFO @ Fri, 05 Jul 2019 19:44:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (336 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。