Job ID = 2010909 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,384,619 reads read : 13,384,619 reads written : 13,384,619 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1103926.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: 00:01:48 13384619 reads; of these: 13384619 (100.00%) were unpaired; of these: 2444834 (18.27%) aligned 0 times 5764904 (43.07%) aligned exactly 1 time 5174881 (38.66%) aligned >1 times 81.73% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 9953890 / 10939785 = 0.9099 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 @ Sat, 06 Jul 2019 01:17:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.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 @ Sat, 06 Jul 2019 01:17:17: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:17:17: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:17:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.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 @ Sat, 06 Jul 2019 01:17:18: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:17:18: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:17:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.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 @ Sat, 06 Jul 2019 01:17:19: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:17:19: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:17:24: #1 tag size is determined as 43 bps INFO @ Sat, 06 Jul 2019 01:17:24: #1 tag size = 43 INFO @ Sat, 06 Jul 2019 01:17:24: #1 total tags in treatment: 985895 INFO @ Sat, 06 Jul 2019 01:17:24: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:17:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:17:24: #1 tags after filtering in treatment: 985895 INFO @ Sat, 06 Jul 2019 01:17:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:17:24: #1 finished! INFO @ Sat, 06 Jul 2019 01:17:24: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:17:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:17:24: #2 number of paired peaks: 210 WARNING @ Sat, 06 Jul 2019 01:17:24: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Sat, 06 Jul 2019 01:17:24: start model_add_line... INFO @ Sat, 06 Jul 2019 01:17:24: start X-correlation... INFO @ Sat, 06 Jul 2019 01:17:24: end of X-cor INFO @ Sat, 06 Jul 2019 01:17:24: #2 finished! INFO @ Sat, 06 Jul 2019 01:17:24: #2 predicted fragment length is 135 bps INFO @ Sat, 06 Jul 2019 01:17:24: #2 alternative fragment length(s) may be 3,68,104,135 bps INFO @ Sat, 06 Jul 2019 01:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.05_model.r INFO @ Sat, 06 Jul 2019 01:17:24: #3 Call peaks... INFO @ Sat, 06 Jul 2019 01:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 01:17:26: #1 tag size is determined as 43 bps INFO @ Sat, 06 Jul 2019 01:17:26: #1 tag size = 43 INFO @ Sat, 06 Jul 2019 01:17:26: #1 total tags in treatment: 985895 INFO @ Sat, 06 Jul 2019 01:17:26: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:17:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:17:26: #1 tags after filtering in treatment: 985895 INFO @ Sat, 06 Jul 2019 01:17:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:17:26: #1 finished! INFO @ Sat, 06 Jul 2019 01:17:26: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:17:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:17:26: #2 number of paired peaks: 210 WARNING @ Sat, 06 Jul 2019 01:17:26: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Sat, 06 Jul 2019 01:17:26: start model_add_line... INFO @ Sat, 06 Jul 2019 01:17:26: start X-correlation... INFO @ Sat, 06 Jul 2019 01:17:26: end of X-cor INFO @ Sat, 06 Jul 2019 01:17:26: #2 finished! INFO @ Sat, 06 Jul 2019 01:17:26: #2 predicted fragment length is 135 bps INFO @ Sat, 06 Jul 2019 01:17:26: #2 alternative fragment length(s) may be 3,68,104,135 bps INFO @ Sat, 06 Jul 2019 01:17:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.10_model.r INFO @ Sat, 06 Jul 2019 01:17:26: #3 Call peaks... INFO @ Sat, 06 Jul 2019 01:17:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 01:17:28: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 01:17:29: #1 tag size is determined as 43 bps INFO @ Sat, 06 Jul 2019 01:17:29: #1 tag size = 43 INFO @ Sat, 06 Jul 2019 01:17:29: #1 total tags in treatment: 985895 INFO @ Sat, 06 Jul 2019 01:17:29: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:17:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:17:29: #1 tags after filtering in treatment: 985895 INFO @ Sat, 06 Jul 2019 01:17:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:17:29: #1 finished! INFO @ Sat, 06 Jul 2019 01:17:29: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:17:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:17:29: #2 number of paired peaks: 210 WARNING @ Sat, 06 Jul 2019 01:17:29: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Sat, 06 Jul 2019 01:17:29: start model_add_line... INFO @ Sat, 06 Jul 2019 01:17:29: start X-correlation... INFO @ Sat, 06 Jul 2019 01:17:29: end of X-cor INFO @ Sat, 06 Jul 2019 01:17:29: #2 finished! INFO @ Sat, 06 Jul 2019 01:17:29: #2 predicted fragment length is 135 bps INFO @ Sat, 06 Jul 2019 01:17:29: #2 alternative fragment length(s) may be 3,68,104,135 bps INFO @ Sat, 06 Jul 2019 01:17:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.20_model.r INFO @ Sat, 06 Jul 2019 01:17:29: #3 Call peaks... INFO @ Sat, 06 Jul 2019 01:17:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 01:17:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.05_peaks.xls INFO @ Sat, 06 Jul 2019 01:17:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 01:17:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.05_summits.bed INFO @ Sat, 06 Jul 2019 01:17:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:17:30: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 01:17:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.10_peaks.xls INFO @ Sat, 06 Jul 2019 01:17:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 01:17:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.10_summits.bed INFO @ Sat, 06 Jul 2019 01:17:31: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (96 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:17:33: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 01:17:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.20_peaks.xls BedGraph に変換しました。 INFO @ Sat, 06 Jul 2019 01:17:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.20_peaks.narrowPeak BigWig に変換中... INFO @ Sat, 06 Jul 2019 01:17:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX423151/SRX423151.20_summits.bed INFO @ Sat, 06 Jul 2019 01:17:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。