Job ID = 2010290 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,163 reads read : 25,163 reads written : 25,163 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR948389.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: 00:00:00 25163 reads; of these: 25163 (100.00%) were unpaired; of these: 12241 (48.65%) aligned 0 times 10270 (40.81%) aligned exactly 1 time 2652 (10.54%) aligned >1 times 51.35% overall alignment rate Time searching: 00:00:00 Overall time: 00:00:00 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] 1058 / 12922 = 0.0819 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 22:00:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.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 22:00:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:00:36: #1 read treatment tags... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 22:00:36: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 22:00:36: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 22:00:36: #1 total tags in treatment: 11864 INFO @ Fri, 05 Jul 2019 22:00:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:00:36: #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 22:00:36: #1 tags after filtering in treatment: 11864 INFO @ Fri, 05 Jul 2019 22:00:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:00:36: #1 finished! INFO @ Fri, 05 Jul 2019 22:00:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:00:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:00:36: #2 number of paired peaks: 591 WARNING @ Fri, 05 Jul 2019 22:00:36: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Fri, 05 Jul 2019 22:00:36: start model_add_line... INFO @ Fri, 05 Jul 2019 22:00:36: start X-correlation... INFO @ Fri, 05 Jul 2019 22:00:36: end of X-cor INFO @ Fri, 05 Jul 2019 22:00:36: #2 finished! INFO @ Fri, 05 Jul 2019 22:00:36: #2 predicted fragment length is 302 bps INFO @ Fri, 05 Jul 2019 22:00:36: #2 alternative fragment length(s) may be 228,251,302 bps INFO @ Fri, 05 Jul 2019 22:00:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.05_model.r INFO @ Fri, 05 Jul 2019 22:00:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:00:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:00:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:00:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.05_peaks.xls INFO @ Fri, 05 Jul 2019 22:00:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:00:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.05_summits.bed INFO @ Fri, 05 Jul 2019 22:00:37: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:00:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.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 22:00:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:00:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:00:37: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 22:00:37: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 22:00:37: #1 total tags in treatment: 11864 INFO @ Fri, 05 Jul 2019 22:00:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:00:37: #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 22:00:37: #1 tags after filtering in treatment: 11864 INFO @ Fri, 05 Jul 2019 22:00:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:00:37: #1 finished! INFO @ Fri, 05 Jul 2019 22:00:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:00:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:00:37: #2 number of paired peaks: 591 WARNING @ Fri, 05 Jul 2019 22:00:37: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Fri, 05 Jul 2019 22:00:37: start model_add_line... INFO @ Fri, 05 Jul 2019 22:00:37: start X-correlation... INFO @ Fri, 05 Jul 2019 22:00:37: end of X-cor INFO @ Fri, 05 Jul 2019 22:00:37: #2 finished! INFO @ Fri, 05 Jul 2019 22:00:37: #2 predicted fragment length is 302 bps INFO @ Fri, 05 Jul 2019 22:00:37: #2 alternative fragment length(s) may be 228,251,302 bps INFO @ Fri, 05 Jul 2019 22:00:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.10_model.r INFO @ Fri, 05 Jul 2019 22:00:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:00:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:00:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:00:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.10_peaks.xls INFO @ Fri, 05 Jul 2019 22:00:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:00:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.10_summits.bed INFO @ Fri, 05 Jul 2019 22:00:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:00:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.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 22:00:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:00:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:00:38: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 22:00:38: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 22:00:38: #1 total tags in treatment: 11864 INFO @ Fri, 05 Jul 2019 22:00:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:00:38: #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 22:00:38: #1 tags after filtering in treatment: 11864 INFO @ Fri, 05 Jul 2019 22:00:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:00:38: #1 finished! INFO @ Fri, 05 Jul 2019 22:00:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:00:38: #2 number of paired peaks: 591 WARNING @ Fri, 05 Jul 2019 22:00:38: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Fri, 05 Jul 2019 22:00:38: start model_add_line... INFO @ Fri, 05 Jul 2019 22:00:38: start X-correlation... INFO @ Fri, 05 Jul 2019 22:00:38: end of X-cor INFO @ Fri, 05 Jul 2019 22:00:38: #2 finished! INFO @ Fri, 05 Jul 2019 22:00:38: #2 predicted fragment length is 302 bps INFO @ Fri, 05 Jul 2019 22:00:38: #2 alternative fragment length(s) may be 228,251,302 bps INFO @ Fri, 05 Jul 2019 22:00:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.20_model.r INFO @ Fri, 05 Jul 2019 22:00:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:00:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:00:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:00:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.20_peaks.xls INFO @ Fri, 05 Jul 2019 22:00:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:00:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX332089/SRX332089.20_summits.bed INFO @ Fri, 05 Jul 2019 22:00:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling