Job ID = 2006097 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,111,040 reads read : 3,111,040 reads written : 3,111,040 spots read : 2,961,060 reads read : 2,961,060 reads written : 2,961,060 spots read : 2,928,915 reads read : 2,928,915 reads written : 2,928,915 spots read : 3,094,695 reads read : 3,094,695 reads written : 3,094,695 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529322.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529323.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529325.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: 00:08:44 12095710 reads; of these: 12095710 (100.00%) were unpaired; of these: 366636 (3.03%) aligned 0 times 9759935 (80.69%) aligned exactly 1 time 1969139 (16.28%) aligned >1 times 96.97% overall alignment rate Time searching: 00:08:44 Overall time: 00:08:44 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] 11579658 / 11729074 = 0.9873 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 15:21:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.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 15:21:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:21:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:21:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.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 15:21:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:21:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:21:48: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 15:21:48: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 15:21:48: #1 total tags in treatment: 149416 INFO @ Fri, 05 Jul 2019 15:21:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:21:48: #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 15:21:48: #1 tags after filtering in treatment: 149416 INFO @ Fri, 05 Jul 2019 15:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:21:48: #1 finished! INFO @ Fri, 05 Jul 2019 15:21:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:21:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:21:48: #2 number of paired peaks: 325 WARNING @ Fri, 05 Jul 2019 15:21:48: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 05 Jul 2019 15:21:48: start model_add_line... INFO @ Fri, 05 Jul 2019 15:21:48: start X-correlation... INFO @ Fri, 05 Jul 2019 15:21:48: end of X-cor INFO @ Fri, 05 Jul 2019 15:21:48: #2 finished! INFO @ Fri, 05 Jul 2019 15:21:48: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 15:21:48: #2 alternative fragment length(s) may be 16,105,151,191,220,251,272,338,554,584,598 bps INFO @ Fri, 05 Jul 2019 15:21:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.05_model.r WARNING @ Fri, 05 Jul 2019 15:21:48: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:21:48: #2 You may need to consider one of the other alternative d(s): 16,105,151,191,220,251,272,338,554,584,598 WARNING @ Fri, 05 Jul 2019 15:21:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:21:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:21:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:21:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.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 15:21:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:21:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:21:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:21:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:21:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:21:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.05_summits.bed INFO @ Fri, 05 Jul 2019 15:21:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (42 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:21:49: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 15:21:49: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 15:21:49: #1 total tags in treatment: 149416 INFO @ Fri, 05 Jul 2019 15:21:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:21:49: #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 15:21:49: #1 tags after filtering in treatment: 149416 INFO @ Fri, 05 Jul 2019 15:21:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:21:49: #1 finished! INFO @ Fri, 05 Jul 2019 15:21:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:21:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:21:49: #2 number of paired peaks: 325 WARNING @ Fri, 05 Jul 2019 15:21:49: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 05 Jul 2019 15:21:49: start model_add_line... INFO @ Fri, 05 Jul 2019 15:21:49: start X-correlation... INFO @ Fri, 05 Jul 2019 15:21:49: end of X-cor INFO @ Fri, 05 Jul 2019 15:21:49: #2 finished! INFO @ Fri, 05 Jul 2019 15:21:49: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 15:21:49: #2 alternative fragment length(s) may be 16,105,151,191,220,251,272,338,554,584,598 bps INFO @ Fri, 05 Jul 2019 15:21:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.10_model.r WARNING @ Fri, 05 Jul 2019 15:21:49: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:21:49: #2 You may need to consider one of the other alternative d(s): 16,105,151,191,220,251,272,338,554,584,598 WARNING @ Fri, 05 Jul 2019 15:21:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:21:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:21:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:21:50: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 15:21:50: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 15:21:50: #1 total tags in treatment: 149416 INFO @ Fri, 05 Jul 2019 15:21:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:21:50: #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 15:21:50: #1 tags after filtering in treatment: 149416 INFO @ Fri, 05 Jul 2019 15:21:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:21:50: #1 finished! INFO @ Fri, 05 Jul 2019 15:21:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:21:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:21:50: #2 number of paired peaks: 325 WARNING @ Fri, 05 Jul 2019 15:21:50: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 05 Jul 2019 15:21:50: start model_add_line... INFO @ Fri, 05 Jul 2019 15:21:50: start X-correlation... INFO @ Fri, 05 Jul 2019 15:21:50: end of X-cor INFO @ Fri, 05 Jul 2019 15:21:50: #2 finished! INFO @ Fri, 05 Jul 2019 15:21:50: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 15:21:50: #2 alternative fragment length(s) may be 16,105,151,191,220,251,272,338,554,584,598 bps INFO @ Fri, 05 Jul 2019 15:21:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.20_model.r WARNING @ Fri, 05 Jul 2019 15:21:50: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:21:50: #2 You may need to consider one of the other alternative d(s): 16,105,151,191,220,251,272,338,554,584,598 WARNING @ Fri, 05 Jul 2019 15:21:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:21:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:21:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:21:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:21:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:21:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:21:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.10_summits.bed INFO @ Fri, 05 Jul 2019 15:21:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:21:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:21:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:21:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:21:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548108/ERX2548108.20_summits.bed INFO @ Fri, 05 Jul 2019 15:21:50: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。