Job ID = 2006631 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,670,942 reads read : 1,670,942 reads written : 1,670,942 spots read : 1,584,629 reads read : 1,584,629 reads written : 1,584,629 spots read : 1,630,721 reads read : 1,630,721 reads written : 1,630,721 spots read : 1,611,162 reads read : 1,611,162 reads written : 1,611,162 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529558.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529560.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529561.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: 00:02:47 6497454 reads; of these: 6497454 (100.00%) were unpaired; of these: 303285 (4.67%) aligned 0 times 5287124 (81.37%) aligned exactly 1 time 907045 (13.96%) aligned >1 times 95.33% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 5609985 / 6194169 = 0.9057 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 15:42:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.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 15:42:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:42:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:42:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.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 15:42:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:42:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:42:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.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 15:42:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:42:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:42:15: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:42:15: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:42:15: #1 total tags in treatment: 584184 INFO @ Fri, 05 Jul 2019 15:42:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:42:15: #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 15:42:15: #1 tags after filtering in treatment: 584184 INFO @ Fri, 05 Jul 2019 15:42:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:42:15: #1 finished! INFO @ Fri, 05 Jul 2019 15:42:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:42:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:42:16: #2 number of paired peaks: 260 WARNING @ Fri, 05 Jul 2019 15:42:16: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Fri, 05 Jul 2019 15:42:16: start model_add_line... INFO @ Fri, 05 Jul 2019 15:42:16: start X-correlation... INFO @ Fri, 05 Jul 2019 15:42:16: end of X-cor INFO @ Fri, 05 Jul 2019 15:42:16: #2 finished! INFO @ Fri, 05 Jul 2019 15:42:16: #2 predicted fragment length is 161 bps INFO @ Fri, 05 Jul 2019 15:42:16: #2 alternative fragment length(s) may be 2,75,96,123,161,212,219,268,299,480,504,528,578 bps INFO @ Fri, 05 Jul 2019 15:42:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.05_model.r INFO @ Fri, 05 Jul 2019 15:42:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:42:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:42:16: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:42:16: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:42:16: #1 total tags in treatment: 584184 INFO @ Fri, 05 Jul 2019 15:42:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:42:16: #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 15:42:16: #1 tags after filtering in treatment: 584184 INFO @ Fri, 05 Jul 2019 15:42:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:42:16: #1 finished! INFO @ Fri, 05 Jul 2019 15:42:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:42:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:42:16: #2 number of paired peaks: 260 WARNING @ Fri, 05 Jul 2019 15:42:16: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Fri, 05 Jul 2019 15:42:16: start model_add_line... INFO @ Fri, 05 Jul 2019 15:42:16: start X-correlation... INFO @ Fri, 05 Jul 2019 15:42:16: end of X-cor INFO @ Fri, 05 Jul 2019 15:42:16: #2 finished! INFO @ Fri, 05 Jul 2019 15:42:16: #2 predicted fragment length is 161 bps INFO @ Fri, 05 Jul 2019 15:42:16: #2 alternative fragment length(s) may be 2,75,96,123,161,212,219,268,299,480,504,528,578 bps INFO @ Fri, 05 Jul 2019 15:42:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.10_model.r INFO @ Fri, 05 Jul 2019 15:42:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:42:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:42:16: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:42:16: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:42:16: #1 total tags in treatment: 584184 INFO @ Fri, 05 Jul 2019 15:42:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:42:16: #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 15:42:16: #1 tags after filtering in treatment: 584184 INFO @ Fri, 05 Jul 2019 15:42:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:42:16: #1 finished! INFO @ Fri, 05 Jul 2019 15:42:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:42:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:42:16: #2 number of paired peaks: 260 WARNING @ Fri, 05 Jul 2019 15:42:16: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Fri, 05 Jul 2019 15:42:16: start model_add_line... INFO @ Fri, 05 Jul 2019 15:42:16: start X-correlation... INFO @ Fri, 05 Jul 2019 15:42:16: end of X-cor INFO @ Fri, 05 Jul 2019 15:42:16: #2 finished! INFO @ Fri, 05 Jul 2019 15:42:16: #2 predicted fragment length is 161 bps INFO @ Fri, 05 Jul 2019 15:42:16: #2 alternative fragment length(s) may be 2,75,96,123,161,212,219,268,299,480,504,528,578 bps INFO @ Fri, 05 Jul 2019 15:42:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.20_model.r INFO @ Fri, 05 Jul 2019 15:42:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:42:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:42:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:42:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:42:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:42:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:42:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:42:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.05_summits.bed INFO @ Fri, 05 Jul 2019 15:42:19: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (112 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:42:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:42:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:42:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.10_summits.bed INFO @ Fri, 05 Jul 2019 15:42:19: Done! INFO @ Fri, 05 Jul 2019 15:42:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:42:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:42:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548173/ERX2548173.20_summits.bed INFO @ Fri, 05 Jul 2019 15:42:19: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling