Job ID = 2006011 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,171,482 reads read : 2,171,482 reads written : 2,171,482 spots read : 2,099,303 reads read : 2,099,303 reads written : 2,099,303 spots read : 2,146,587 reads read : 2,146,587 reads written : 2,146,587 spots read : 2,189,632 reads read : 2,189,632 reads written : 2,189,632 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529290.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529291.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529292.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529293.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: 00:06:22 8607004 reads; of these: 8607004 (100.00%) were unpaired; of these: 276105 (3.21%) aligned 0 times 6914165 (80.33%) aligned exactly 1 time 1416734 (16.46%) aligned >1 times 96.79% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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 8 files... [bam_rmdupse_core] 8216524 / 8330899 = 0.9863 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 15:07:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.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 15:07:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:07:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:07:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.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 15:07:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:07:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:07:17: #1 tag size is determined as 147 bps INFO @ Fri, 05 Jul 2019 15:07:17: #1 tag size = 147 INFO @ Fri, 05 Jul 2019 15:07:17: #1 total tags in treatment: 114375 INFO @ Fri, 05 Jul 2019 15:07:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:07:17: #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 15:07:17: #1 tags after filtering in treatment: 114375 INFO @ Fri, 05 Jul 2019 15:07:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:07:17: #1 finished! INFO @ Fri, 05 Jul 2019 15:07:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:07:17: #2 number of paired peaks: 290 WARNING @ Fri, 05 Jul 2019 15:07:17: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Fri, 05 Jul 2019 15:07:17: start model_add_line... INFO @ Fri, 05 Jul 2019 15:07:17: start X-correlation... INFO @ Fri, 05 Jul 2019 15:07:17: end of X-cor INFO @ Fri, 05 Jul 2019 15:07:17: #2 finished! INFO @ Fri, 05 Jul 2019 15:07:17: #2 predicted fragment length is 147 bps INFO @ Fri, 05 Jul 2019 15:07:17: #2 alternative fragment length(s) may be 147,177,550,568 bps INFO @ Fri, 05 Jul 2019 15:07:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.05_model.r WARNING @ Fri, 05 Jul 2019 15:07:18: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:07:18: #2 You may need to consider one of the other alternative d(s): 147,177,550,568 WARNING @ Fri, 05 Jul 2019 15:07:18: #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 15:07:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.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 15:07:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:07:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:07:18: #1 tag size is determined as 147 bps INFO @ Fri, 05 Jul 2019 15:07:18: #1 tag size = 147 INFO @ Fri, 05 Jul 2019 15:07:18: #1 total tags in treatment: 114375 INFO @ Fri, 05 Jul 2019 15:07:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:07:18: #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 15:07:18: #1 tags after filtering in treatment: 114375 INFO @ Fri, 05 Jul 2019 15:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:07:18: #1 finished! INFO @ Fri, 05 Jul 2019 15:07:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:07:18: #2 number of paired peaks: 290 WARNING @ Fri, 05 Jul 2019 15:07:18: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Fri, 05 Jul 2019 15:07:18: start model_add_line... INFO @ Fri, 05 Jul 2019 15:07:18: start X-correlation... INFO @ Fri, 05 Jul 2019 15:07:18: end of X-cor INFO @ Fri, 05 Jul 2019 15:07:18: #2 finished! INFO @ Fri, 05 Jul 2019 15:07:18: #2 predicted fragment length is 147 bps INFO @ Fri, 05 Jul 2019 15:07:18: #2 alternative fragment length(s) may be 147,177,550,568 bps INFO @ Fri, 05 Jul 2019 15:07:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.10_model.r INFO @ Fri, 05 Jul 2019 15:07:18: #3 Call peaks for each chromosome... WARNING @ Fri, 05 Jul 2019 15:07:18: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:07:18: #2 You may need to consider one of the other alternative d(s): 147,177,550,568 WARNING @ Fri, 05 Jul 2019 15:07:18: #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 15:07:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:07:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:07:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:07:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.05_summits.bed INFO @ Fri, 05 Jul 2019 15:07:18: Done! INFO @ Fri, 05 Jul 2019 15:07:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.10_summits.bed INFO @ Fri, 05 Jul 2019 15:07:19: Done! INFO @ Fri, 05 Jul 2019 15:07:19: #1 tag size is determined as 147 bps INFO @ Fri, 05 Jul 2019 15:07:19: #1 tag size = 147 INFO @ Fri, 05 Jul 2019 15:07:19: #1 total tags in treatment: 114375 INFO @ Fri, 05 Jul 2019 15:07:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:07:19: #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 15:07:19: #1 tags after filtering in treatment: 114375 INFO @ Fri, 05 Jul 2019 15:07:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:07:19: #1 finished! INFO @ Fri, 05 Jul 2019 15:07:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:07:19: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:07:19: #2 number of paired peaks: 290 WARNING @ Fri, 05 Jul 2019 15:07:19: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Fri, 05 Jul 2019 15:07:19: start model_add_line... INFO @ Fri, 05 Jul 2019 15:07:19: start X-correlation... INFO @ Fri, 05 Jul 2019 15:07:19: end of X-cor INFO @ Fri, 05 Jul 2019 15:07:19: #2 finished! INFO @ Fri, 05 Jul 2019 15:07:19: #2 predicted fragment length is 147 bps INFO @ Fri, 05 Jul 2019 15:07:19: #2 alternative fragment length(s) may be 147,177,550,568 bps INFO @ Fri, 05 Jul 2019 15:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.20_model.r WARNING @ Fri, 05 Jul 2019 15:07:19: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:07:19: #2 You may need to consider one of the other alternative d(s): 147,177,550,568 WARNING @ Fri, 05 Jul 2019 15:07:19: #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 15:07:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:07:19: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (57 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:07:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:07:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:07:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548094/ERX2548094.20_summits.bed INFO @ Fri, 05 Jul 2019 15:07:20: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (29 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。