Job ID = 2010019 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 96,030 reads read : 96,030 reads written : 96,030 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR716609.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: 00:00:01 96030 reads; of these: 96030 (100.00%) were unpaired; of these: 16389 (17.07%) aligned 0 times 67257 (70.04%) aligned exactly 1 time 12384 (12.90%) aligned >1 times 82.93% overall alignment rate Time searching: 00:00:01 Overall time: 00:00:01 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] 64696 / 79641 = 0.8123 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... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 20:53:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.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 20:53:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:53:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:53:15: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 20:53:15: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 20:53:15: #1 total tags in treatment: 14945 INFO @ Fri, 05 Jul 2019 20:53:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:53:15: #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 20:53:15: #1 tags after filtering in treatment: 14945 INFO @ Fri, 05 Jul 2019 20:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:53:15: #1 finished! INFO @ Fri, 05 Jul 2019 20:53:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:53:15: #2 number of paired peaks: 273 WARNING @ Fri, 05 Jul 2019 20:53:15: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Fri, 05 Jul 2019 20:53:15: start model_add_line... INFO @ Fri, 05 Jul 2019 20:53:15: start X-correlation... INFO @ Fri, 05 Jul 2019 20:53:15: end of X-cor INFO @ Fri, 05 Jul 2019 20:53:15: #2 finished! INFO @ Fri, 05 Jul 2019 20:53:15: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 20:53:15: #2 alternative fragment length(s) may be 46,66,87,137,214,239,279,359,520 bps INFO @ Fri, 05 Jul 2019 20:53:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.05_model.r INFO @ Fri, 05 Jul 2019 20:53:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:53:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:53:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:53:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.05_peaks.xls INFO @ Fri, 05 Jul 2019 20:53:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:53:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.05_summits.bed INFO @ Fri, 05 Jul 2019 20:53:15: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 20:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.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 20:53:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:53:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:53:16: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 20:53:16: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 20:53:16: #1 total tags in treatment: 14945 INFO @ Fri, 05 Jul 2019 20:53:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:53:16: #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 20:53:16: #1 tags after filtering in treatment: 14945 INFO @ Fri, 05 Jul 2019 20:53:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:53:16: #1 finished! INFO @ Fri, 05 Jul 2019 20:53:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:53:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:53:16: #2 number of paired peaks: 273 WARNING @ Fri, 05 Jul 2019 20:53:16: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Fri, 05 Jul 2019 20:53:16: start model_add_line... INFO @ Fri, 05 Jul 2019 20:53:16: start X-correlation... INFO @ Fri, 05 Jul 2019 20:53:16: end of X-cor INFO @ Fri, 05 Jul 2019 20:53:16: #2 finished! INFO @ Fri, 05 Jul 2019 20:53:16: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 20:53:16: #2 alternative fragment length(s) may be 46,66,87,137,214,239,279,359,520 bps INFO @ Fri, 05 Jul 2019 20:53:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.10_model.r INFO @ Fri, 05 Jul 2019 20:53:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:53:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:53:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:53:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.10_peaks.xls INFO @ Fri, 05 Jul 2019 20:53:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:53:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.10_summits.bed INFO @ Fri, 05 Jul 2019 20:53:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:53:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.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 20:53:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:53:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:53:17: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 20:53:17: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 20:53:17: #1 total tags in treatment: 14945 INFO @ Fri, 05 Jul 2019 20:53:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:53:17: #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 20:53:17: #1 tags after filtering in treatment: 14945 INFO @ Fri, 05 Jul 2019 20:53:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:53:17: #1 finished! INFO @ Fri, 05 Jul 2019 20:53:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:53:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:53:17: #2 number of paired peaks: 273 WARNING @ Fri, 05 Jul 2019 20:53:17: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Fri, 05 Jul 2019 20:53:17: start model_add_line... INFO @ Fri, 05 Jul 2019 20:53:17: start X-correlation... INFO @ Fri, 05 Jul 2019 20:53:17: end of X-cor INFO @ Fri, 05 Jul 2019 20:53:17: #2 finished! INFO @ Fri, 05 Jul 2019 20:53:17: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 20:53:17: #2 alternative fragment length(s) may be 46,66,87,137,214,239,279,359,520 bps INFO @ Fri, 05 Jul 2019 20:53:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.20_model.r INFO @ Fri, 05 Jul 2019 20:53:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:53:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:53:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.20_peaks.xls INFO @ Fri, 05 Jul 2019 20:53:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX237128/SRX237128.20_summits.bed INFO @ Fri, 05 Jul 2019 20:53:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling