Job ID = 10608994 sra ファイルのダウンロード中... Completed: 422207K bytes transferred in 46 seconds (74104K bits/sec), in 1 file. 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 7323407 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2745396/SRR5457327.sra Written 7323407 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:01:49 7323407 reads; of these: 7323407 (100.00%) were unpaired; of these: 1961858 (26.79%) aligned 0 times 2785011 (38.03%) aligned exactly 1 time 2576538 (35.18%) aligned >1 times 73.21% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 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] 3044663 / 5361549 = 0.5679 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 @ Thu, 03 May 2018 22:59:55: # Command line: callpeak -t SRX2745396.bam -f BAM -g 12100000 -n SRX2745396.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2745396.20 # format = BAM # ChIP-seq file = ['SRX2745396.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 @ Thu, 03 May 2018 22:59:55: #1 read tag files... INFO @ Thu, 03 May 2018 22:59:55: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:59:55: # Command line: callpeak -t SRX2745396.bam -f BAM -g 12100000 -n SRX2745396.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2745396.10 # format = BAM # ChIP-seq file = ['SRX2745396.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 @ Thu, 03 May 2018 22:59:55: #1 read tag files... INFO @ Thu, 03 May 2018 22:59:55: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:59:55: # Command line: callpeak -t SRX2745396.bam -f BAM -g 12100000 -n SRX2745396.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2745396.05 # format = BAM # ChIP-seq file = ['SRX2745396.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 @ Thu, 03 May 2018 22:59:55: #1 read tag files... INFO @ Thu, 03 May 2018 22:59:55: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:00:03: 1000000 INFO @ Thu, 03 May 2018 23:00:03: 1000000 INFO @ Thu, 03 May 2018 23:00:03: 1000000 INFO @ Thu, 03 May 2018 23:00:11: 2000000 INFO @ Thu, 03 May 2018 23:00:11: 2000000 INFO @ Thu, 03 May 2018 23:00:11: 2000000 INFO @ Thu, 03 May 2018 23:00:13: #1 tag size is determined as 101 bps INFO @ Thu, 03 May 2018 23:00:13: #1 tag size = 101 INFO @ Thu, 03 May 2018 23:00:13: #1 total tags in treatment: 2316886 INFO @ Thu, 03 May 2018 23:00:13: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:00:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:00:14: #1 tags after filtering in treatment: 2316886 INFO @ Thu, 03 May 2018 23:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:00:14: #1 finished! INFO @ Thu, 03 May 2018 23:00:14: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:00:14: #1 tag size is determined as 101 bps INFO @ Thu, 03 May 2018 23:00:14: #1 tag size = 101 INFO @ Thu, 03 May 2018 23:00:14: #1 total tags in treatment: 2316886 INFO @ Thu, 03 May 2018 23:00:14: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:00:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:00:14: #1 tags after filtering in treatment: 2316886 INFO @ Thu, 03 May 2018 23:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:00:14: #1 finished! INFO @ Thu, 03 May 2018 23:00:14: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:00:14: #1 tag size is determined as 101 bps INFO @ Thu, 03 May 2018 23:00:14: #1 tag size = 101 INFO @ Thu, 03 May 2018 23:00:14: #1 total tags in treatment: 2316886 INFO @ Thu, 03 May 2018 23:00:14: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:00:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:00:14: #2 number of paired peaks: 139 WARNING @ Thu, 03 May 2018 23:00:14: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Thu, 03 May 2018 23:00:14: start model_add_line... INFO @ Thu, 03 May 2018 23:00:14: #1 tags after filtering in treatment: 2316886 INFO @ Thu, 03 May 2018 23:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:00:14: #1 finished! INFO @ Thu, 03 May 2018 23:00:14: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:00:14: start X-correlation... INFO @ Thu, 03 May 2018 23:00:14: end of X-cor INFO @ Thu, 03 May 2018 23:00:14: #2 finished! INFO @ Thu, 03 May 2018 23:00:14: #2 predicted fragment length is 330 bps INFO @ Thu, 03 May 2018 23:00:14: #2 alternative fragment length(s) may be 330 bps INFO @ Thu, 03 May 2018 23:00:14: #2.2 Generate R script for model : SRX2745396.05_model.r INFO @ Thu, 03 May 2018 23:00:14: #3 Call peaks... INFO @ Thu, 03 May 2018 23:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:00:14: #2 number of paired peaks: 139 WARNING @ Thu, 03 May 2018 23:00:14: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Thu, 03 May 2018 23:00:14: start model_add_line... INFO @ Thu, 03 May 2018 23:00:14: start X-correlation... INFO @ Thu, 03 May 2018 23:00:14: end of X-cor INFO @ Thu, 03 May 2018 23:00:14: #2 finished! INFO @ Thu, 03 May 2018 23:00:14: #2 predicted fragment length is 330 bps INFO @ Thu, 03 May 2018 23:00:14: #2 alternative fragment length(s) may be 330 bps INFO @ Thu, 03 May 2018 23:00:14: #2.2 Generate R script for model : SRX2745396.20_model.r INFO @ Thu, 03 May 2018 23:00:14: #3 Call peaks... INFO @ Thu, 03 May 2018 23:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:00:14: #2 number of paired peaks: 139 WARNING @ Thu, 03 May 2018 23:00:14: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Thu, 03 May 2018 23:00:14: start model_add_line... INFO @ Thu, 03 May 2018 23:00:14: start X-correlation... INFO @ Thu, 03 May 2018 23:00:14: end of X-cor INFO @ Thu, 03 May 2018 23:00:14: #2 finished! INFO @ Thu, 03 May 2018 23:00:14: #2 predicted fragment length is 330 bps INFO @ Thu, 03 May 2018 23:00:14: #2 alternative fragment length(s) may be 330 bps INFO @ Thu, 03 May 2018 23:00:14: #2.2 Generate R script for model : SRX2745396.10_model.r INFO @ Thu, 03 May 2018 23:00:14: #3 Call peaks... INFO @ Thu, 03 May 2018 23:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:00:25: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:00:25: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:00:25: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:00:27: #4 Write output xls file... SRX2745396.05_peaks.xls INFO @ Thu, 03 May 2018 23:00:27: #4 Write peak in narrowPeak format file... SRX2745396.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:00:27: #4 Write summits bed file... SRX2745396.05_summits.bed INFO @ Thu, 03 May 2018 23:00:27: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (504 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 23:00:28: #4 Write output xls file... SRX2745396.10_peaks.xls INFO @ Thu, 03 May 2018 23:00:28: #4 Write peak in narrowPeak format file... SRX2745396.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:00:28: #4 Write summits bed file... SRX2745396.10_summits.bed INFO @ Thu, 03 May 2018 23:00:28: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (396 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 23:00:28: #4 Write output xls file... SRX2745396.20_peaks.xls INFO @ Thu, 03 May 2018 23:00:28: #4 Write peak in narrowPeak format file... SRX2745396.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:00:28: #4 Write summits bed file... SRX2745396.20_summits.bed INFO @ Thu, 03 May 2018 23:00:28: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (350 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。