Job ID = 9302860 sra ファイルのダウンロード中... Completed: 447535K bytes transferred in 7 seconds (508491K 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 15677828 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1514715/SRR3082930.sra Written 15677828 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: 00:01:24 15677828 reads; of these: 15677828 (100.00%) were unpaired; of these: 13614684 (86.84%) aligned 0 times 1630613 (10.40%) aligned exactly 1 time 432531 (2.76%) aligned >1 times 13.16% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 1876295 / 2063144 = 0.9094 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, 28 Jul 2017 11:26:36: # Command line: callpeak -t SRX1514715.bam -f BAM -g 12100000 -n SRX1514715.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1514715.10 # format = BAM # ChIP-seq file = ['SRX1514715.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, 28 Jul 2017 11:26:36: # Command line: callpeak -t SRX1514715.bam -f BAM -g 12100000 -n SRX1514715.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1514715.05 # format = BAM # ChIP-seq file = ['SRX1514715.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, 28 Jul 2017 11:26:36: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:26:36: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:26:36: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:26:36: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:26:36: # Command line: callpeak -t SRX1514715.bam -f BAM -g 12100000 -n SRX1514715.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1514715.20 # format = BAM # ChIP-seq file = ['SRX1514715.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, 28 Jul 2017 11:26:36: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:26:36: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:26:37: #1 tag size is determined as 49 bps INFO @ Fri, 28 Jul 2017 11:26:37: #1 tag size = 49 INFO @ Fri, 28 Jul 2017 11:26:37: #1 total tags in treatment: 186849 INFO @ Fri, 28 Jul 2017 11:26:37: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:26:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:26:37: #1 tags after filtering in treatment: 186849 INFO @ Fri, 28 Jul 2017 11:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 28 Jul 2017 11:26:37: #1 finished! INFO @ Fri, 28 Jul 2017 11:26:37: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:26:37: #1 tag size is determined as 49 bps INFO @ Fri, 28 Jul 2017 11:26:37: #1 tag size = 49 INFO @ Fri, 28 Jul 2017 11:26:37: #1 tag size is determined as 49 bps INFO @ Fri, 28 Jul 2017 11:26:37: #1 total tags in treatment: 186849 INFO @ Fri, 28 Jul 2017 11:26:37: #1 tag size = 49 INFO @ Fri, 28 Jul 2017 11:26:37: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:26:37: #1 total tags in treatment: 186849 INFO @ Fri, 28 Jul 2017 11:26:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:26:37: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:26:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:26:37: #1 tags after filtering in treatment: 186849 INFO @ Fri, 28 Jul 2017 11:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 28 Jul 2017 11:26:37: #1 tags after filtering in treatment: 186849 INFO @ Fri, 28 Jul 2017 11:26:37: #1 finished! INFO @ Fri, 28 Jul 2017 11:26:37: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 28 Jul 2017 11:26:37: #1 finished! INFO @ Fri, 28 Jul 2017 11:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:26:37: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:26:37: #2 number of paired peaks: 378 WARNING @ Fri, 28 Jul 2017 11:26:37: Fewer paired peaks (378) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 378 pairs to build model! INFO @ Fri, 28 Jul 2017 11:26:37: start model_add_line... INFO @ Fri, 28 Jul 2017 11:26:37: start X-correlation... INFO @ Fri, 28 Jul 2017 11:26:37: #2 number of paired peaks: 378 WARNING @ Fri, 28 Jul 2017 11:26:37: Fewer paired peaks (378) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 378 pairs to build model! INFO @ Fri, 28 Jul 2017 11:26:37: start model_add_line... INFO @ Fri, 28 Jul 2017 11:26:37: #2 number of paired peaks: 378 WARNING @ Fri, 28 Jul 2017 11:26:37: Fewer paired peaks (378) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 378 pairs to build model! INFO @ Fri, 28 Jul 2017 11:26:37: start model_add_line... INFO @ Fri, 28 Jul 2017 11:26:37: start X-correlation... INFO @ Fri, 28 Jul 2017 11:26:37: start X-correlation... INFO @ Fri, 28 Jul 2017 11:26:37: end of X-cor INFO @ Fri, 28 Jul 2017 11:26:37: end of X-cor INFO @ Fri, 28 Jul 2017 11:26:37: #2 finished! INFO @ Fri, 28 Jul 2017 11:26:37: #2 finished! INFO @ Fri, 28 Jul 2017 11:26:37: end of X-cor INFO @ Fri, 28 Jul 2017 11:26:37: #2 predicted fragment length is 119 bps INFO @ Fri, 28 Jul 2017 11:26:37: #2 predicted fragment length is 119 bps INFO @ Fri, 28 Jul 2017 11:26:37: #2 finished! INFO @ Fri, 28 Jul 2017 11:26:37: #2 alternative fragment length(s) may be 119,122,137,154 bps INFO @ Fri, 28 Jul 2017 11:26:37: #2 alternative fragment length(s) may be 119,122,137,154 bps INFO @ Fri, 28 Jul 2017 11:26:37: #2 predicted fragment length is 119 bps INFO @ Fri, 28 Jul 2017 11:26:37: #2.2 Generate R script for model : SRX1514715.10_model.r INFO @ Fri, 28 Jul 2017 11:26:37: #2.2 Generate R script for model : SRX1514715.20_model.r INFO @ Fri, 28 Jul 2017 11:26:37: #2 alternative fragment length(s) may be 119,122,137,154 bps INFO @ Fri, 28 Jul 2017 11:26:37: #2.2 Generate R script for model : SRX1514715.05_model.r INFO @ Fri, 28 Jul 2017 11:26:37: #3 Call peaks... INFO @ Fri, 28 Jul 2017 11:26:37: #3 Call peaks... INFO @ Fri, 28 Jul 2017 11:26:37: #3 Call peaks... INFO @ Fri, 28 Jul 2017 11:26:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 28 Jul 2017 11:26:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 28 Jul 2017 11:26:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 28 Jul 2017 11:26:38: #3 Call peaks for each chromosome... INFO @ Fri, 28 Jul 2017 11:26:38: #3 Call peaks for each chromosome... INFO @ Fri, 28 Jul 2017 11:26:38: #3 Call peaks for each chromosome... INFO @ Fri, 28 Jul 2017 11:26:38: #4 Write output xls file... SRX1514715.20_peaks.xls INFO @ Fri, 28 Jul 2017 11:26:38: #4 Write output xls file... SRX1514715.10_peaks.xls INFO @ Fri, 28 Jul 2017 11:26:38: #4 Write output xls file... SRX1514715.05_peaks.xls INFO @ Fri, 28 Jul 2017 11:26:38: #4 Write peak in narrowPeak format file... SRX1514715.10_peaks.narrowPeak INFO @ Fri, 28 Jul 2017 11:26:38: #4 Write peak in narrowPeak format file... SRX1514715.05_peaks.narrowPeak INFO @ Fri, 28 Jul 2017 11:26:38: #4 Write summits bed file... SRX1514715.10_summits.bed INFO @ Fri, 28 Jul 2017 11:26:38: #4 Write summits bed file... SRX1514715.05_summits.bed INFO @ Fri, 28 Jul 2017 11:26:38: Done! INFO @ Fri, 28 Jul 2017 11:26:38: Done! pass1 - making usageList (17 chroms): 0 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 28 Jul 2017 11:26:39: #4 Write peak in narrowPeak format file... SRX1514715.20_peaks.narrowPeak INFO @ Fri, 28 Jul 2017 11:26:39: #4 Write summits bed file... SRX1514715.20_summits.bed INFO @ Fri, 28 Jul 2017 11:26:39: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (31 records, 4 fields): 2 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (135 records, 4 fields): 328 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。