Job ID = 2009009 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,485,691 reads read : 8,485,691 reads written : 8,485,691 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637569.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: 00:01:03 8485691 reads; of these: 8485691 (100.00%) were unpaired; of these: 1347707 (15.88%) aligned 0 times 5727142 (67.49%) aligned exactly 1 time 1410842 (16.63%) aligned >1 times 84.12% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 3463523 / 7137984 = 0.4852 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 05 Jul 2019 19:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.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 19:08:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:08:23: #1 read treatment tags... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 19:08:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.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 19:08:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:08:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:08:28: 1000000 INFO @ Fri, 05 Jul 2019 19:08:33: 2000000 INFO @ Fri, 05 Jul 2019 19:08:37: 3000000 INFO @ Fri, 05 Jul 2019 19:08:40: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:08:40: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:08:40: #1 total tags in treatment: 3674461 INFO @ Fri, 05 Jul 2019 19:08:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:08:40: #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 19:08:40: #1 tags after filtering in treatment: 3674461 INFO @ Fri, 05 Jul 2019 19:08:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:08:40: #1 finished! INFO @ Fri, 05 Jul 2019 19:08:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:08:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:08:41: #2 number of paired peaks: 158 WARNING @ Fri, 05 Jul 2019 19:08:41: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 05 Jul 2019 19:08:41: start model_add_line... INFO @ Fri, 05 Jul 2019 19:08:41: start X-correlation... INFO @ Fri, 05 Jul 2019 19:08:41: end of X-cor INFO @ Fri, 05 Jul 2019 19:08:41: #2 finished! INFO @ Fri, 05 Jul 2019 19:08:41: #2 predicted fragment length is 101 bps INFO @ Fri, 05 Jul 2019 19:08:41: #2 alternative fragment length(s) may be 4,87,101 bps INFO @ Fri, 05 Jul 2019 19:08:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.05_model.r INFO @ Fri, 05 Jul 2019 19:08:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:08:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.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 19:08:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:08:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:08:47: 1000000 INFO @ Fri, 05 Jul 2019 19:08:49: 1000000 INFO @ Fri, 05 Jul 2019 19:08:51: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:08:51: 2000000 INFO @ Fri, 05 Jul 2019 19:08:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:08:53: 2000000 INFO @ Fri, 05 Jul 2019 19:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.05_summits.bed INFO @ Fri, 05 Jul 2019 19:08:56: Done! INFO @ Fri, 05 Jul 2019 19:08:56: 3000000 pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (5086 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 19:08:58: 3000000 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:08:59: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:08:59: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:08:59: #1 total tags in treatment: 3674461 INFO @ Fri, 05 Jul 2019 19:08:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:08:59: #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 19:08:59: #1 tags after filtering in treatment: 3674461 INFO @ Fri, 05 Jul 2019 19:08:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:08:59: #1 finished! INFO @ Fri, 05 Jul 2019 19:08:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:08:59: #2 number of paired peaks: 158 WARNING @ Fri, 05 Jul 2019 19:08:59: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 05 Jul 2019 19:08:59: start model_add_line... INFO @ Fri, 05 Jul 2019 19:08:59: start X-correlation... INFO @ Fri, 05 Jul 2019 19:08:59: end of X-cor INFO @ Fri, 05 Jul 2019 19:08:59: #2 finished! INFO @ Fri, 05 Jul 2019 19:08:59: #2 predicted fragment length is 101 bps INFO @ Fri, 05 Jul 2019 19:08:59: #2 alternative fragment length(s) may be 4,87,101 bps INFO @ Fri, 05 Jul 2019 19:08:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.10_model.r INFO @ Fri, 05 Jul 2019 19:08:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:08:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:09:01: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:09:01: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:09:01: #1 total tags in treatment: 3674461 INFO @ Fri, 05 Jul 2019 19:09:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:09:01: #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 19:09:01: #1 tags after filtering in treatment: 3674461 INFO @ Fri, 05 Jul 2019 19:09:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:09:01: #1 finished! INFO @ Fri, 05 Jul 2019 19:09:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:09:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:09:01: #2 number of paired peaks: 158 WARNING @ Fri, 05 Jul 2019 19:09:01: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 05 Jul 2019 19:09:01: start model_add_line... INFO @ Fri, 05 Jul 2019 19:09:01: start X-correlation... INFO @ Fri, 05 Jul 2019 19:09:01: end of X-cor INFO @ Fri, 05 Jul 2019 19:09:01: #2 finished! INFO @ Fri, 05 Jul 2019 19:09:01: #2 predicted fragment length is 101 bps INFO @ Fri, 05 Jul 2019 19:09:01: #2 alternative fragment length(s) may be 4,87,101 bps INFO @ Fri, 05 Jul 2019 19:09:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.20_model.r INFO @ Fri, 05 Jul 2019 19:09:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:09:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:09:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:09:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:09:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:09:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:09:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.10_summits.bed INFO @ Fri, 05 Jul 2019 19:09:10: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (3599 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:09:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:09:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:09:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594027/ERX594027.20_summits.bed INFO @ Fri, 05 Jul 2019 19:09:12: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1913 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。