Job ID = 2009033 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,977,708 reads read : 4,977,708 reads written : 4,977,708 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637563.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: 00:00:30 4977708 reads; of these: 4977708 (100.00%) were unpaired; of these: 3727201 (74.88%) aligned 0 times 935562 (18.80%) aligned exactly 1 time 314945 (6.33%) aligned >1 times 25.12% overall alignment rate Time searching: 00:00:30 Overall time: 00:00:30 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] 406138 / 1250507 = 0.3248 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 19:12:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.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 19:12:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:12:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:12:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.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 19:12:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:12:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:12:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.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 19:12:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:12:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:12:33: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:12:33: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:12:33: #1 total tags in treatment: 844369 INFO @ Fri, 05 Jul 2019 19:12:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:12:33: #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 19:12:33: #1 tags after filtering in treatment: 844369 INFO @ Fri, 05 Jul 2019 19:12:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:12:33: #1 finished! INFO @ Fri, 05 Jul 2019 19:12:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:12:33: #2 number of paired peaks: 407 WARNING @ Fri, 05 Jul 2019 19:12:33: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Fri, 05 Jul 2019 19:12:33: start model_add_line... INFO @ Fri, 05 Jul 2019 19:12:33: start X-correlation... INFO @ Fri, 05 Jul 2019 19:12:33: end of X-cor INFO @ Fri, 05 Jul 2019 19:12:33: #2 finished! INFO @ Fri, 05 Jul 2019 19:12:33: #2 predicted fragment length is 172 bps INFO @ Fri, 05 Jul 2019 19:12:33: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 05 Jul 2019 19:12:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.05_model.r INFO @ Fri, 05 Jul 2019 19:12:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:12:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:12:34: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:12:34: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:12:34: #1 total tags in treatment: 844369 INFO @ Fri, 05 Jul 2019 19:12:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:12:34: #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 19:12:34: #1 tags after filtering in treatment: 844369 INFO @ Fri, 05 Jul 2019 19:12:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:12:34: #1 finished! INFO @ Fri, 05 Jul 2019 19:12:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:12:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:12:34: #2 number of paired peaks: 407 WARNING @ Fri, 05 Jul 2019 19:12:34: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Fri, 05 Jul 2019 19:12:34: start model_add_line... INFO @ Fri, 05 Jul 2019 19:12:34: start X-correlation... INFO @ Fri, 05 Jul 2019 19:12:34: end of X-cor INFO @ Fri, 05 Jul 2019 19:12:34: #2 finished! INFO @ Fri, 05 Jul 2019 19:12:34: #2 predicted fragment length is 172 bps INFO @ Fri, 05 Jul 2019 19:12:34: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 05 Jul 2019 19:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.10_model.r INFO @ Fri, 05 Jul 2019 19:12:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:12:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:12:34: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:12:34: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:12:34: #1 total tags in treatment: 844369 INFO @ Fri, 05 Jul 2019 19:12:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:12:34: #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 19:12:34: #1 tags after filtering in treatment: 844369 INFO @ Fri, 05 Jul 2019 19:12:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:12:34: #1 finished! INFO @ Fri, 05 Jul 2019 19:12:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:12:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:12:34: #2 number of paired peaks: 407 WARNING @ Fri, 05 Jul 2019 19:12:34: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Fri, 05 Jul 2019 19:12:34: start model_add_line... INFO @ Fri, 05 Jul 2019 19:12:34: start X-correlation... INFO @ Fri, 05 Jul 2019 19:12:34: end of X-cor INFO @ Fri, 05 Jul 2019 19:12:34: #2 finished! INFO @ Fri, 05 Jul 2019 19:12:34: #2 predicted fragment length is 172 bps INFO @ Fri, 05 Jul 2019 19:12:34: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 05 Jul 2019 19:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.20_model.r INFO @ Fri, 05 Jul 2019 19:12:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:12:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:12:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:12:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:12:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:12:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:12:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:12:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.20_peaks.xls BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 19:12:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:12:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.05_peaks.narrowPeak BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:13:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:13:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.10_summits.bed INFO @ Fri, 05 Jul 2019 19:13:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.05_summits.bed INFO @ Fri, 05 Jul 2019 19:13:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594045/ERX594045.20_summits.bed INFO @ Fri, 05 Jul 2019 19:13:03: Done! INFO @ Fri, 05 Jul 2019 19:13:03: Done! INFO @ Fri, 05 Jul 2019 19:13:03: Done! pass1 - making usageList (16 chroms): 1 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (766 records, 4 fields): 5 millis pass2 - checking and writing primary data (1352 records, 4 fields): 5 millis pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1991 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling