Job ID = 2640954 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,962,301 reads read : 4,962,301 reads written : 4,962,301 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: 00:01:10 4962301 reads; of these: 4962301 (100.00%) were unpaired; of these: 2592229 (52.24%) aligned 0 times 1924086 (38.77%) aligned exactly 1 time 445986 (8.99%) aligned >1 times 47.76% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 2102247 / 2370072 = 0.8870 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:08:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.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 20:08:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:08:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:08:48: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:08:48: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:08:48: #1 total tags in treatment: 267825 INFO @ Sat, 24 Aug 2019 20:08:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:08:48: #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 20:08:48: #1 tags after filtering in treatment: 267825 INFO @ Sat, 24 Aug 2019 20:08:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:08:48: #1 finished! INFO @ Sat, 24 Aug 2019 20:08:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:08:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:08:48: #2 number of paired peaks: 347 WARNING @ Sat, 24 Aug 2019 20:08:48: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Sat, 24 Aug 2019 20:08:48: start model_add_line... INFO @ Sat, 24 Aug 2019 20:08:48: start X-correlation... INFO @ Sat, 24 Aug 2019 20:08:48: end of X-cor INFO @ Sat, 24 Aug 2019 20:08:48: #2 finished! INFO @ Sat, 24 Aug 2019 20:08:48: #2 predicted fragment length is 186 bps INFO @ Sat, 24 Aug 2019 20:08:48: #2 alternative fragment length(s) may be 186 bps INFO @ Sat, 24 Aug 2019 20:08:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.05_model.r INFO @ Sat, 24 Aug 2019 20:08:48: #3 Call peaks... INFO @ Sat, 24 Aug 2019 20:08:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 20:08:49: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 20:08:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.05_peaks.xls INFO @ Sat, 24 Aug 2019 20:08:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 20:08:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.05_summits.bed INFO @ Sat, 24 Aug 2019 20:08:49: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (706 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.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 20:09:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:09:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:09:18: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:09:18: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:09:18: #1 total tags in treatment: 267825 INFO @ Sat, 24 Aug 2019 20:09:18: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:09:18: #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 20:09:18: #1 tags after filtering in treatment: 267825 INFO @ Sat, 24 Aug 2019 20:09:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:09:18: #1 finished! INFO @ Sat, 24 Aug 2019 20:09:18: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:09:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:09:18: #2 number of paired peaks: 347 WARNING @ Sat, 24 Aug 2019 20:09:18: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Sat, 24 Aug 2019 20:09:18: start model_add_line... INFO @ Sat, 24 Aug 2019 20:09:18: start X-correlation... INFO @ Sat, 24 Aug 2019 20:09:18: end of X-cor INFO @ Sat, 24 Aug 2019 20:09:18: #2 finished! INFO @ Sat, 24 Aug 2019 20:09:18: #2 predicted fragment length is 186 bps INFO @ Sat, 24 Aug 2019 20:09:18: #2 alternative fragment length(s) may be 186 bps INFO @ Sat, 24 Aug 2019 20:09:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.10_model.r INFO @ Sat, 24 Aug 2019 20:09:18: #3 Call peaks... INFO @ Sat, 24 Aug 2019 20:09:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 20:09:19: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 20:09:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.10_peaks.xls INFO @ Sat, 24 Aug 2019 20:09:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 20:09:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.10_summits.bed INFO @ Sat, 24 Aug 2019 20:09:19: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (358 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.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 20:09:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:09:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:09:47: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:09:47: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:09:47: #1 total tags in treatment: 267825 INFO @ Sat, 24 Aug 2019 20:09:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:09:47: #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 20:09:47: #1 tags after filtering in treatment: 267825 INFO @ Sat, 24 Aug 2019 20:09:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:09:47: #1 finished! INFO @ Sat, 24 Aug 2019 20:09:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:09:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:09:47: #2 number of paired peaks: 347 WARNING @ Sat, 24 Aug 2019 20:09:47: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Sat, 24 Aug 2019 20:09:47: start model_add_line... INFO @ Sat, 24 Aug 2019 20:09:47: start X-correlation... INFO @ Sat, 24 Aug 2019 20:09:47: end of X-cor INFO @ Sat, 24 Aug 2019 20:09:47: #2 finished! INFO @ Sat, 24 Aug 2019 20:09:47: #2 predicted fragment length is 186 bps INFO @ Sat, 24 Aug 2019 20:09:47: #2 alternative fragment length(s) may be 186 bps INFO @ Sat, 24 Aug 2019 20:09:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.20_model.r INFO @ Sat, 24 Aug 2019 20:09:47: #3 Call peaks... INFO @ Sat, 24 Aug 2019 20:09:47: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 20:09:48: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 20:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.20_peaks.xls INFO @ Sat, 24 Aug 2019 20:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 20:09:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX472139/SRX472139.20_summits.bed INFO @ Sat, 24 Aug 2019 20:09:48: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (113 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。