Job ID = 2009427 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,619,711 reads read : 21,619,711 reads written : 21,619,711 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR718797.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: 00:04:24 21619711 reads; of these: 21619711 (100.00%) were unpaired; of these: 1649789 (7.63%) aligned 0 times 16487949 (76.26%) aligned exactly 1 time 3481973 (16.11%) aligned >1 times 92.37% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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_sort_core] merging from 12 files... [bam_rmdupse_core] 18772646 / 19969922 = 0.9400 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 19:24:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.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 19:24:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:24:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:24:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.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 19:24:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:24:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.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 19:24:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:24:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:24:41: 1000000 INFO @ Fri, 05 Jul 2019 19:24:41: 1000000 INFO @ Fri, 05 Jul 2019 19:24:42: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:24:42: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:24:42: #1 total tags in treatment: 1197276 INFO @ Fri, 05 Jul 2019 19:24:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:24:42: #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 19:24:42: #1 tags after filtering in treatment: 1197276 INFO @ Fri, 05 Jul 2019 19:24:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:24:42: #1 finished! INFO @ Fri, 05 Jul 2019 19:24:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:24:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:24:42: #2 number of paired peaks: 636 WARNING @ Fri, 05 Jul 2019 19:24:42: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Fri, 05 Jul 2019 19:24:42: start model_add_line... INFO @ Fri, 05 Jul 2019 19:24:42: start X-correlation... INFO @ Fri, 05 Jul 2019 19:24:42: end of X-cor INFO @ Fri, 05 Jul 2019 19:24:42: #2 finished! INFO @ Fri, 05 Jul 2019 19:24:42: #2 predicted fragment length is 181 bps INFO @ Fri, 05 Jul 2019 19:24:42: #2 alternative fragment length(s) may be 181 bps INFO @ Fri, 05 Jul 2019 19:24:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.10_model.r INFO @ Fri, 05 Jul 2019 19:24:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:24:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:24:43: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:24:43: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:24:43: #1 total tags in treatment: 1197276 INFO @ Fri, 05 Jul 2019 19:24:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:24:43: #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 19:24:43: #1 tags after filtering in treatment: 1197276 INFO @ Fri, 05 Jul 2019 19:24:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:24:43: #1 finished! INFO @ Fri, 05 Jul 2019 19:24:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:24:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:24:43: #2 number of paired peaks: 636 WARNING @ Fri, 05 Jul 2019 19:24:43: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Fri, 05 Jul 2019 19:24:43: start model_add_line... INFO @ Fri, 05 Jul 2019 19:24:43: start X-correlation... INFO @ Fri, 05 Jul 2019 19:24:43: end of X-cor INFO @ Fri, 05 Jul 2019 19:24:43: #2 finished! INFO @ Fri, 05 Jul 2019 19:24:43: #2 predicted fragment length is 181 bps INFO @ Fri, 05 Jul 2019 19:24:43: #2 alternative fragment length(s) may be 181 bps INFO @ Fri, 05 Jul 2019 19:24:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.05_model.r INFO @ Fri, 05 Jul 2019 19:24:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:24:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:24:45: 1000000 INFO @ Fri, 05 Jul 2019 19:24:47: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:24:47: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:24:47: #1 total tags in treatment: 1197276 INFO @ Fri, 05 Jul 2019 19:24:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:24:47: #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 19:24:47: #1 tags after filtering in treatment: 1197276 INFO @ Fri, 05 Jul 2019 19:24:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:24:47: #1 finished! INFO @ Fri, 05 Jul 2019 19:24:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:24:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:24:47: #2 number of paired peaks: 636 WARNING @ Fri, 05 Jul 2019 19:24:47: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Fri, 05 Jul 2019 19:24:47: start model_add_line... INFO @ Fri, 05 Jul 2019 19:24:47: start X-correlation... INFO @ Fri, 05 Jul 2019 19:24:47: end of X-cor INFO @ Fri, 05 Jul 2019 19:24:47: #2 finished! INFO @ Fri, 05 Jul 2019 19:24:47: #2 predicted fragment length is 181 bps INFO @ Fri, 05 Jul 2019 19:24:47: #2 alternative fragment length(s) may be 181 bps INFO @ Fri, 05 Jul 2019 19:24:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.20_model.r INFO @ Fri, 05 Jul 2019 19:24:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:24:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:24:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:24:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:24:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:24:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:24:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.20_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.20_summits.bed INFO @ Fri, 05 Jul 2019 19:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:25:12: Done! INFO @ Fri, 05 Jul 2019 19:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.10_summits.bed INFO @ Fri, 05 Jul 2019 19:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX662721/ERX662721.05_summits.bed INFO @ Fri, 05 Jul 2019 19:25:12: Done! INFO @ Fri, 05 Jul 2019 19:25:12: Done! pass1 - making usageList (16 chroms): 1 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (656 records, 4 fields): 6 millis pass2 - checking and writing primary data (483 records, 4 fields): 4 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (828 records, 4 fields): 6 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling