Job ID = 2010505 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,259,763 reads read : 7,259,763 reads written : 7,259,763 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1029341.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: 00:00:52 7259763 reads; of these: 7259763 (100.00%) were unpaired; of these: 5148826 (70.92%) aligned 0 times 1631262 (22.47%) aligned exactly 1 time 479675 (6.61%) aligned >1 times 29.08% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 925513 / 2110937 = 0.4384 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 22:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.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 22:49:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:49:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.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 22:49:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:49:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:49:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.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 22:49:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:49:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:49:53: 1000000 INFO @ Fri, 05 Jul 2019 22:49:53: 1000000 INFO @ Fri, 05 Jul 2019 22:49:54: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:49:54: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:49:54: #1 total tags in treatment: 1185424 INFO @ Fri, 05 Jul 2019 22:49:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:49:54: #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 22:49:54: 1000000 INFO @ Fri, 05 Jul 2019 22:49:54: #1 tags after filtering in treatment: 1185424 INFO @ Fri, 05 Jul 2019 22:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:49:54: #1 finished! INFO @ Fri, 05 Jul 2019 22:49:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:49:54: #2 number of paired peaks: 111 WARNING @ Fri, 05 Jul 2019 22:49:54: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Fri, 05 Jul 2019 22:49:54: start model_add_line... INFO @ Fri, 05 Jul 2019 22:49:54: start X-correlation... INFO @ Fri, 05 Jul 2019 22:49:54: end of X-cor INFO @ Fri, 05 Jul 2019 22:49:54: #2 finished! INFO @ Fri, 05 Jul 2019 22:49:54: #2 predicted fragment length is 158 bps INFO @ Fri, 05 Jul 2019 22:49:54: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 05 Jul 2019 22:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.10_model.r INFO @ Fri, 05 Jul 2019 22:49:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:49:55: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:49:55: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:49:55: #1 total tags in treatment: 1185424 INFO @ Fri, 05 Jul 2019 22:49:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:49:55: #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 22:49:55: #1 tags after filtering in treatment: 1185424 INFO @ Fri, 05 Jul 2019 22:49:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:49:55: #1 finished! INFO @ Fri, 05 Jul 2019 22:49:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:49:55: #2 number of paired peaks: 111 WARNING @ Fri, 05 Jul 2019 22:49:55: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Fri, 05 Jul 2019 22:49:55: start model_add_line... INFO @ Fri, 05 Jul 2019 22:49:55: start X-correlation... INFO @ Fri, 05 Jul 2019 22:49:55: end of X-cor INFO @ Fri, 05 Jul 2019 22:49:55: #2 finished! INFO @ Fri, 05 Jul 2019 22:49:55: #2 predicted fragment length is 158 bps INFO @ Fri, 05 Jul 2019 22:49:55: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 05 Jul 2019 22:49:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.05_model.r INFO @ Fri, 05 Jul 2019 22:49:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:49:56: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:49:56: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:49:56: #1 total tags in treatment: 1185424 INFO @ Fri, 05 Jul 2019 22:49:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:49:56: #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 22:49:56: #1 tags after filtering in treatment: 1185424 INFO @ Fri, 05 Jul 2019 22:49:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:49:56: #1 finished! INFO @ Fri, 05 Jul 2019 22:49:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:49:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:49:56: #2 number of paired peaks: 111 WARNING @ Fri, 05 Jul 2019 22:49:56: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Fri, 05 Jul 2019 22:49:56: start model_add_line... INFO @ Fri, 05 Jul 2019 22:49:56: start X-correlation... INFO @ Fri, 05 Jul 2019 22:49:56: end of X-cor INFO @ Fri, 05 Jul 2019 22:49:56: #2 finished! INFO @ Fri, 05 Jul 2019 22:49:56: #2 predicted fragment length is 158 bps INFO @ Fri, 05 Jul 2019 22:49:56: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 05 Jul 2019 22:49:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.20_model.r INFO @ Fri, 05 Jul 2019 22:49:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:49:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:49:58: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:49:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:50:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:50:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.10_peaks.xls INFO @ Fri, 05 Jul 2019 22:50:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:50:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.10_summits.bed INFO @ Fri, 05 Jul 2019 22:50:00: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (470 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.05_peaks.xls INFO @ Fri, 05 Jul 2019 22:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.05_summits.bed INFO @ Fri, 05 Jul 2019 22:50:01: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (728 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 22:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.20_peaks.xls INFO @ Fri, 05 Jul 2019 22:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX377184/SRX377184.20_summits.bed INFO @ Fri, 05 Jul 2019 22:50:01: Done! CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。