Job ID = 2006935 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,380,313 reads read : 1,380,313 reads written : 1,380,313 spots read : 1,314,012 reads read : 1,314,012 reads written : 1,314,012 spots read : 1,442,293 reads read : 1,442,293 reads written : 1,442,293 spots read : 1,305,325 reads read : 1,305,325 reads written : 1,305,325 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529601.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529602.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529603.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: 00:01:17 5441943 reads; of these: 5441943 (100.00%) were unpaired; of these: 309709 (5.69%) aligned 0 times 4343710 (79.82%) aligned exactly 1 time 788524 (14.49%) aligned >1 times 94.31% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 5019173 / 5132234 = 0.9780 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 15:51:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.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 15:51:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:51:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:51:40: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:51:40: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:51:40: #1 total tags in treatment: 113061 INFO @ Fri, 05 Jul 2019 15:51:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:51:40: #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 15:51:40: #1 tags after filtering in treatment: 113061 INFO @ Fri, 05 Jul 2019 15:51:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:51:40: #1 finished! INFO @ Fri, 05 Jul 2019 15:51:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:51:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:51:40: #2 number of paired peaks: 404 WARNING @ Fri, 05 Jul 2019 15:51:40: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Fri, 05 Jul 2019 15:51:40: start model_add_line... INFO @ Fri, 05 Jul 2019 15:51:40: start X-correlation... INFO @ Fri, 05 Jul 2019 15:51:40: end of X-cor INFO @ Fri, 05 Jul 2019 15:51:40: #2 finished! INFO @ Fri, 05 Jul 2019 15:51:40: #2 predicted fragment length is 214 bps INFO @ Fri, 05 Jul 2019 15:51:40: #2 alternative fragment length(s) may be 4,21,35,51,69,92,115,125,139,164,194,214,292,351,374,389,409,453,499,541,592 bps INFO @ Fri, 05 Jul 2019 15:51:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.05_model.r INFO @ Fri, 05 Jul 2019 15:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.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 15:51:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:51:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:51:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:51:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:51:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:51:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:51:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:51:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.05_summits.bed INFO @ Fri, 05 Jul 2019 15:51:40: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.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 15:51:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:51:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:51:41: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:51:41: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:51:41: #1 total tags in treatment: 113061 INFO @ Fri, 05 Jul 2019 15:51:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:51:41: #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 15:51:41: #1 tags after filtering in treatment: 113061 INFO @ Fri, 05 Jul 2019 15:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:51:41: #1 finished! INFO @ Fri, 05 Jul 2019 15:51:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:51:41: #2 number of paired peaks: 404 WARNING @ Fri, 05 Jul 2019 15:51:41: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Fri, 05 Jul 2019 15:51:41: start model_add_line... INFO @ Fri, 05 Jul 2019 15:51:41: start X-correlation... INFO @ Fri, 05 Jul 2019 15:51:41: end of X-cor INFO @ Fri, 05 Jul 2019 15:51:41: #2 finished! INFO @ Fri, 05 Jul 2019 15:51:41: #2 predicted fragment length is 214 bps INFO @ Fri, 05 Jul 2019 15:51:41: #2 alternative fragment length(s) may be 4,21,35,51,69,92,115,125,139,164,194,214,292,351,374,389,409,453,499,541,592 bps INFO @ Fri, 05 Jul 2019 15:51:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.10_model.r INFO @ Fri, 05 Jul 2019 15:51:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:51:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:51:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:51:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:51:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:51:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.10_summits.bed INFO @ Fri, 05 Jul 2019 15:51:41: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:51:42: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:51:42: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:51:42: #1 total tags in treatment: 113061 INFO @ Fri, 05 Jul 2019 15:51:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:51:42: #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 15:51:42: #1 tags after filtering in treatment: 113061 INFO @ Fri, 05 Jul 2019 15:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:51:42: #1 finished! INFO @ Fri, 05 Jul 2019 15:51:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:51:42: #2 number of paired peaks: 404 WARNING @ Fri, 05 Jul 2019 15:51:42: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Fri, 05 Jul 2019 15:51:42: start model_add_line... INFO @ Fri, 05 Jul 2019 15:51:42: start X-correlation... INFO @ Fri, 05 Jul 2019 15:51:42: end of X-cor INFO @ Fri, 05 Jul 2019 15:51:42: #2 finished! INFO @ Fri, 05 Jul 2019 15:51:42: #2 predicted fragment length is 214 bps INFO @ Fri, 05 Jul 2019 15:51:42: #2 alternative fragment length(s) may be 4,21,35,51,69,92,115,125,139,164,194,214,292,351,374,389,409,453,499,541,592 bps INFO @ Fri, 05 Jul 2019 15:51:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.20_model.r INFO @ Fri, 05 Jul 2019 15:51:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:51:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:51:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:51:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548188/ERX2548188.20_summits.bed INFO @ Fri, 05 Jul 2019 15:51:42: Done! CompletedMACS2peakCalling pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling