Job ID = 9163646 sra ファイルのダウンロード中... Completed: 57457K bytes transferred in 3 seconds (128383K bits/sec), in 1 file, 2 directories. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 2366287 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977462/SRR1951308.sra Written 2366287 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:00:19 2366287 reads; of these: 2366287 (100.00%) were unpaired; of these: 386460 (16.33%) aligned 0 times 1782292 (75.32%) aligned exactly 1 time 197535 (8.35%) aligned >1 times 83.67% overall alignment rate Time searching: 00:00:19 Overall time: 00:00:19 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] 1880178 / 1979827 = 0.9497 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 @ Wed, 28 Jun 2017 11:11:06: # Command line: callpeak -t SRX977462.bam -f BAM -g 12100000 -n SRX977462.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977462.10 # format = BAM # ChIP-seq file = ['SRX977462.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 @ Wed, 28 Jun 2017 11:11:06: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:11:06: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:11:06: # Command line: callpeak -t SRX977462.bam -f BAM -g 12100000 -n SRX977462.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977462.05 # format = BAM # ChIP-seq file = ['SRX977462.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 @ Wed, 28 Jun 2017 11:11:06: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:11:06: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:11:06: # Command line: callpeak -t SRX977462.bam -f BAM -g 12100000 -n SRX977462.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977462.20 # format = BAM # ChIP-seq file = ['SRX977462.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 @ Wed, 28 Jun 2017 11:11:06: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:11:06: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:11:06: #1 tag size is determined as 40 bps INFO @ Wed, 28 Jun 2017 11:11:06: #1 tag size = 40 INFO @ Wed, 28 Jun 2017 11:11:06: #1 total tags in treatment: 99649 INFO @ Wed, 28 Jun 2017 11:11:06: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:11:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 11:11:06: #1 tag size is determined as 40 bps INFO @ Wed, 28 Jun 2017 11:11:06: #1 tag size = 40 INFO @ Wed, 28 Jun 2017 11:11:06: #1 total tags in treatment: 99649 INFO @ Wed, 28 Jun 2017 11:11:06: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:11:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 11:11:06: #1 tags after filtering in treatment: 99648 INFO @ Wed, 28 Jun 2017 11:11:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 11:11:06: #1 finished! INFO @ Wed, 28 Jun 2017 11:11:06: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:11:06: #1 tags after filtering in treatment: 99648 INFO @ Wed, 28 Jun 2017 11:11:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 11:11:06: #1 finished! INFO @ Wed, 28 Jun 2017 11:11:06: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:11:06: #1 tag size is determined as 40 bps INFO @ Wed, 28 Jun 2017 11:11:06: #1 tag size = 40 INFO @ Wed, 28 Jun 2017 11:11:06: #1 total tags in treatment: 99649 INFO @ Wed, 28 Jun 2017 11:11:06: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:11:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 11:11:06: #1 tags after filtering in treatment: 99648 INFO @ Wed, 28 Jun 2017 11:11:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 11:11:06: #1 finished! INFO @ Wed, 28 Jun 2017 11:11:06: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:11:06: #2 number of paired peaks: 490 WARNING @ Wed, 28 Jun 2017 11:11:06: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Wed, 28 Jun 2017 11:11:06: start model_add_line... INFO @ Wed, 28 Jun 2017 11:11:06: start X-correlation... INFO @ Wed, 28 Jun 2017 11:11:06: #2 number of paired peaks: 490 WARNING @ Wed, 28 Jun 2017 11:11:06: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Wed, 28 Jun 2017 11:11:06: start model_add_line... INFO @ Wed, 28 Jun 2017 11:11:06: start X-correlation... INFO @ Wed, 28 Jun 2017 11:11:06: #2 number of paired peaks: 490 WARNING @ Wed, 28 Jun 2017 11:11:06: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Wed, 28 Jun 2017 11:11:06: start model_add_line... INFO @ Wed, 28 Jun 2017 11:11:06: start X-correlation... INFO @ Wed, 28 Jun 2017 11:11:07: end of X-cor INFO @ Wed, 28 Jun 2017 11:11:07: #2 finished! INFO @ Wed, 28 Jun 2017 11:11:07: #2 predicted fragment length is 35 bps INFO @ Wed, 28 Jun 2017 11:11:07: end of X-cor INFO @ Wed, 28 Jun 2017 11:11:07: #2 alternative fragment length(s) may be 4,35,88,120,140,164,192,238,259,300,331,350,381,434,510,541,581 bps INFO @ Wed, 28 Jun 2017 11:11:07: #2 finished! INFO @ Wed, 28 Jun 2017 11:11:07: #2.2 Generate R script for model : SRX977462.20_model.r INFO @ Wed, 28 Jun 2017 11:11:07: #2 predicted fragment length is 35 bps INFO @ Wed, 28 Jun 2017 11:11:07: #2 alternative fragment length(s) may be 4,35,88,120,140,164,192,238,259,300,331,350,381,434,510,541,581 bps INFO @ Wed, 28 Jun 2017 11:11:07: #2.2 Generate R script for model : SRX977462.05_model.r INFO @ Wed, 28 Jun 2017 11:11:07: end of X-cor INFO @ Wed, 28 Jun 2017 11:11:07: #2 finished! INFO @ Wed, 28 Jun 2017 11:11:07: #2 predicted fragment length is 35 bps INFO @ Wed, 28 Jun 2017 11:11:07: #2 alternative fragment length(s) may be 4,35,88,120,140,164,192,238,259,300,331,350,381,434,510,541,581 bps INFO @ Wed, 28 Jun 2017 11:11:07: #2.2 Generate R script for model : SRX977462.10_model.r WARNING @ Wed, 28 Jun 2017 11:11:07: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 11:11:07: #2 You may need to consider one of the other alternative d(s): 4,35,88,120,140,164,192,238,259,300,331,350,381,434,510,541,581 WARNING @ Wed, 28 Jun 2017 11:11:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 11:11:07: #3 Call peaks... WARNING @ Wed, 28 Jun 2017 11:11:07: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 11:11:07: #2 You may need to consider one of the other alternative d(s): 4,35,88,120,140,164,192,238,259,300,331,350,381,434,510,541,581 WARNING @ Wed, 28 Jun 2017 11:11:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 11:11:07: #3 Call peaks... WARNING @ Wed, 28 Jun 2017 11:11:07: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 11:11:07: #2 You may need to consider one of the other alternative d(s): 4,35,88,120,140,164,192,238,259,300,331,350,381,434,510,541,581 WARNING @ Wed, 28 Jun 2017 11:11:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 11:11:07: #3 Call peaks... INFO @ Wed, 28 Jun 2017 11:11:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 11:11:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 11:11:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 11:11:07: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 11:11:07: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 11:11:07: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 11:11:07: #4 Write output xls file... SRX977462.20_peaks.xls INFO @ Wed, 28 Jun 2017 11:11:07: #4 Write peak in narrowPeak format file... SRX977462.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 11:11:07: #4 Write summits bed file... SRX977462.20_summits.bed INFO @ Wed, 28 Jun 2017 11:11:07: Done! INFO @ Wed, 28 Jun 2017 11:11:07: #4 Write output xls file... SRX977462.10_peaks.xls INFO @ Wed, 28 Jun 2017 11:11:07: #4 Write peak in narrowPeak format file... SRX977462.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 11:11:07: #4 Write summits bed file... SRX977462.10_summits.bed INFO @ Wed, 28 Jun 2017 11:11:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 11:11:07: #4 Write output xls file... SRX977462.05_peaks.xls INFO @ Wed, 28 Jun 2017 11:11:07: #4 Write peak in narrowPeak format file... SRX977462.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 11:11:07: #4 Write summits bed file... SRX977462.05_summits.bed INFO @ Wed, 28 Jun 2017 11:11:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。