Job ID = 2009752 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,864,384 reads read : 2,864,384 reads written : 2,864,384 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR497929.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:25 2864384 reads; of these: 2864384 (100.00%) were unpaired; of these: 278188 (9.71%) aligned 0 times 1908264 (66.62%) aligned exactly 1 time 677932 (23.67%) aligned >1 times 90.29% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 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] 1483396 / 2586196 = 0.5736 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 19:46:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.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 19:46:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:46:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:46:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.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 19:46:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:46:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:46:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.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 19:46:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:46:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:47:05: 1000000 INFO @ Fri, 05 Jul 2019 19:47:06: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:47:06: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:47:06: #1 total tags in treatment: 1102800 INFO @ Fri, 05 Jul 2019 19:47:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:47:06: #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 19:47:06: #1 tags after filtering in treatment: 1102800 INFO @ Fri, 05 Jul 2019 19:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:47:06: #1 finished! INFO @ Fri, 05 Jul 2019 19:47:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:47:06: 1000000 INFO @ Fri, 05 Jul 2019 19:47:06: #2 number of paired peaks: 768 WARNING @ Fri, 05 Jul 2019 19:47:06: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Fri, 05 Jul 2019 19:47:06: start model_add_line... INFO @ Fri, 05 Jul 2019 19:47:06: start X-correlation... INFO @ Fri, 05 Jul 2019 19:47:07: end of X-cor INFO @ Fri, 05 Jul 2019 19:47:07: #2 finished! INFO @ Fri, 05 Jul 2019 19:47:07: #2 predicted fragment length is 203 bps INFO @ Fri, 05 Jul 2019 19:47:07: #2 alternative fragment length(s) may be 4,203 bps INFO @ Fri, 05 Jul 2019 19:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.10_model.r INFO @ Fri, 05 Jul 2019 19:47:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:47:07: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:47:07: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:47:07: #1 total tags in treatment: 1102800 INFO @ Fri, 05 Jul 2019 19:47:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:47:07: #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 19:47:07: #1 tags after filtering in treatment: 1102800 INFO @ Fri, 05 Jul 2019 19:47:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:47:07: #1 finished! INFO @ Fri, 05 Jul 2019 19:47:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:47:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:47:07: #2 number of paired peaks: 768 WARNING @ Fri, 05 Jul 2019 19:47:07: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Fri, 05 Jul 2019 19:47:07: start model_add_line... INFO @ Fri, 05 Jul 2019 19:47:07: start X-correlation... INFO @ Fri, 05 Jul 2019 19:47:07: end of X-cor INFO @ Fri, 05 Jul 2019 19:47:07: #2 finished! INFO @ Fri, 05 Jul 2019 19:47:07: #2 predicted fragment length is 203 bps INFO @ Fri, 05 Jul 2019 19:47:07: #2 alternative fragment length(s) may be 4,203 bps INFO @ Fri, 05 Jul 2019 19:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.05_model.r INFO @ Fri, 05 Jul 2019 19:47:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:47:07: 1000000 INFO @ Fri, 05 Jul 2019 19:47:08: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:47:08: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:47:08: #1 total tags in treatment: 1102800 INFO @ Fri, 05 Jul 2019 19:47:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:47:08: #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 19:47:08: #1 tags after filtering in treatment: 1102800 INFO @ Fri, 05 Jul 2019 19:47:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:47:08: #1 finished! INFO @ Fri, 05 Jul 2019 19:47:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:47:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:47:09: #2 number of paired peaks: 768 WARNING @ Fri, 05 Jul 2019 19:47:09: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Fri, 05 Jul 2019 19:47:09: start model_add_line... INFO @ Fri, 05 Jul 2019 19:47:09: start X-correlation... INFO @ Fri, 05 Jul 2019 19:47:09: end of X-cor INFO @ Fri, 05 Jul 2019 19:47:09: #2 finished! INFO @ Fri, 05 Jul 2019 19:47:09: #2 predicted fragment length is 203 bps INFO @ Fri, 05 Jul 2019 19:47:09: #2 alternative fragment length(s) may be 4,203 bps INFO @ Fri, 05 Jul 2019 19:47:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.20_model.r INFO @ Fri, 05 Jul 2019 19:47:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:47:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:47:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:47:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 19:47:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:47:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:47:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.10_summits.bed INFO @ Fri, 05 Jul 2019 19:47:16: Done! INFO @ Fri, 05 Jul 2019 19:47:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:47:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:47:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:47:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.05_summits.bed INFO @ Fri, 05 Jul 2019 19:47:17: Done! INFO @ Fri, 05 Jul 2019 19:47:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:47:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:47:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148608/SRX148608.20_summits.bed INFO @ Fri, 05 Jul 2019 19:47:18: Done! pass1 - making usageList (17 chroms)pass1 - making usageList (17 chroms): 1 millis : 1 millis pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (63 records, 4 fields): 11 millis pass2 - checking and writing primary data (316 records, 4 fields): 12 millis pass2 - checking and writing primary data (756 records, 4 fields): 15 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling