Job ID = 2007610 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,411,446 reads read : 1,411,446 reads written : 1,411,446 spots read : 1,374,684 reads read : 1,374,684 reads written : 1,374,684 spots read : 1,421,961 reads read : 1,421,961 reads written : 1,421,961 spots read : 1,324,913 reads read : 1,324,913 reads written : 1,324,913 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529732.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529733.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529734.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529735.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: 00:02:15 5533004 reads; of these: 5533004 (100.00%) were unpaired; of these: 305345 (5.52%) aligned 0 times 4290724 (77.55%) aligned exactly 1 time 936935 (16.93%) aligned >1 times 94.48% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 5019224 / 5227659 = 0.9601 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 16:04:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.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 16:04:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:04:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:04:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.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 16:04:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:04:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.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 16:04:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:04:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:04:14: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:04:14: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:04:14: #1 total tags in treatment: 208435 INFO @ Fri, 05 Jul 2019 16:04:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:04:14: #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 16:04:14: #1 tags after filtering in treatment: 208435 INFO @ Fri, 05 Jul 2019 16:04:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:04:14: #1 finished! INFO @ Fri, 05 Jul 2019 16:04:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:04:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:04:14: #2 number of paired peaks: 446 WARNING @ Fri, 05 Jul 2019 16:04:14: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Fri, 05 Jul 2019 16:04:14: start model_add_line... INFO @ Fri, 05 Jul 2019 16:04:14: start X-correlation... INFO @ Fri, 05 Jul 2019 16:04:14: end of X-cor INFO @ Fri, 05 Jul 2019 16:04:14: #2 finished! INFO @ Fri, 05 Jul 2019 16:04:14: #2 predicted fragment length is 187 bps INFO @ Fri, 05 Jul 2019 16:04:14: #2 alternative fragment length(s) may be 42,83,129,187,229,241,285,396,454 bps INFO @ Fri, 05 Jul 2019 16:04:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.05_model.r INFO @ Fri, 05 Jul 2019 16:04:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:04:15: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:04:15: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:04:15: #1 total tags in treatment: 208435 INFO @ Fri, 05 Jul 2019 16:04:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:04:15: #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 16:04:15: #1 tags after filtering in treatment: 208435 INFO @ Fri, 05 Jul 2019 16:04:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:04:15: #1 finished! INFO @ Fri, 05 Jul 2019 16:04:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:04:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:04:15: #2 number of paired peaks: 446 WARNING @ Fri, 05 Jul 2019 16:04:15: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Fri, 05 Jul 2019 16:04:15: start model_add_line... INFO @ Fri, 05 Jul 2019 16:04:15: start X-correlation... INFO @ Fri, 05 Jul 2019 16:04:15: end of X-cor INFO @ Fri, 05 Jul 2019 16:04:15: #2 finished! INFO @ Fri, 05 Jul 2019 16:04:15: #2 predicted fragment length is 187 bps INFO @ Fri, 05 Jul 2019 16:04:15: #2 alternative fragment length(s) may be 42,83,129,187,229,241,285,396,454 bps INFO @ Fri, 05 Jul 2019 16:04:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.10_model.r INFO @ Fri, 05 Jul 2019 16:04:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:04:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:04:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:04:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:04:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:04:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.05_summits.bed INFO @ Fri, 05 Jul 2019 16:04:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:04:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:04:16: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:04:16: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:04:16: #1 total tags in treatment: 208435 INFO @ Fri, 05 Jul 2019 16:04:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:04:16: #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 16:04:16: #1 tags after filtering in treatment: 208435 INFO @ Fri, 05 Jul 2019 16:04:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:04:16: #1 finished! INFO @ Fri, 05 Jul 2019 16:04:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:04:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:04:16: #2 number of paired peaks: 446 WARNING @ Fri, 05 Jul 2019 16:04:16: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Fri, 05 Jul 2019 16:04:16: start model_add_line... INFO @ Fri, 05 Jul 2019 16:04:16: start X-correlation... INFO @ Fri, 05 Jul 2019 16:04:16: end of X-cor INFO @ Fri, 05 Jul 2019 16:04:16: #2 finished! INFO @ Fri, 05 Jul 2019 16:04:16: #2 predicted fragment length is 187 bps INFO @ Fri, 05 Jul 2019 16:04:16: #2 alternative fragment length(s) may be 42,83,129,187,229,241,285,396,454 bps INFO @ Fri, 05 Jul 2019 16:04:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.20_model.r INFO @ Fri, 05 Jul 2019 16:04:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:04:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:04:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:04:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:04:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.10_summits.bed INFO @ Fri, 05 Jul 2019 16:04:16: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:04:17: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:04:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.20_peaks.xls BedGraph に変換しました。 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:04:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548224/ERX2548224.20_summits.bed BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:04:28: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis BigWig に変換しました。 CompletedMACS2peakCalling