Job ID = 2237027 sra ファイルのダウンロード中... Completed: 121239K bytes transferred in 4 seconds (213571K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 38015 0 38015 0 0 55855 0 --:--:-- --:--:-- --:--:-- 77740 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 6303653 spots for /home/okishinya/chipatlas/results/ce10/SRX080082/SRR298902.sra Written 6303653 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: 00:00:42 6303653 reads; of these: 6303653 (100.00%) were unpaired; of these: 3765019 (59.73%) aligned 0 times 2182998 (34.63%) aligned exactly 1 time 355636 (5.64%) aligned >1 times 40.27% overall alignment rate Time searching: 00:00:42 Overall time: 00:00:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 586910 / 2538634 = 0.2312 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, 30 Apr 2015 11:25:21: # Command line: callpeak -t SRX080082.bam -f BAM -g ce -n SRX080082.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080082.10 # format = BAM # ChIP-seq file = ['SRX080082.bam'] # control file = None # effective genome size = 9.00e+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 INFO @ Thu, 30 Apr 2015 11:25:21: # Command line: callpeak -t SRX080082.bam -f BAM -g ce -n SRX080082.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080082.05 # format = BAM # ChIP-seq file = ['SRX080082.bam'] # control file = None # effective genome size = 9.00e+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 INFO @ Thu, 30 Apr 2015 11:25:21: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:21: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:21: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:21: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:21: # Command line: callpeak -t SRX080082.bam -f BAM -g ce -n SRX080082.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080082.20 # format = BAM # ChIP-seq file = ['SRX080082.bam'] # control file = None # effective genome size = 9.00e+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 INFO @ Thu, 30 Apr 2015 11:25:21: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:21: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:26: 1000000 INFO @ Thu, 30 Apr 2015 11:25:26: 1000000 INFO @ Thu, 30 Apr 2015 11:25:26: 1000000 INFO @ Thu, 30 Apr 2015 11:25:31: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:31: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:31: #1 total tags in treatment: 1951724 INFO @ Thu, 30 Apr 2015 11:25:31: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:25:31: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:31: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:31: #1 total tags in treatment: 1951724 INFO @ Thu, 30 Apr 2015 11:25:31: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:25:31: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:31: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:31: #1 total tags in treatment: 1951724 INFO @ Thu, 30 Apr 2015 11:25:31: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:25:31: #1 tags after filtering in treatment: 1951630 INFO @ Thu, 30 Apr 2015 11:25:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:31: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:31: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:31: #1 tags after filtering in treatment: 1951630 INFO @ Thu, 30 Apr 2015 11:25:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:31: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:31: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:31: #1 tags after filtering in treatment: 1951630 INFO @ Thu, 30 Apr 2015 11:25:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:31: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:31: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:31: #2 number of paired peaks: 2378 INFO @ Thu, 30 Apr 2015 11:25:31: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:32: #2 number of paired peaks: 2378 INFO @ Thu, 30 Apr 2015 11:25:32: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:32: #2 number of paired peaks: 2378 INFO @ Thu, 30 Apr 2015 11:25:32: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:36: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:36: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:36: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:36: #2 predicted fragment length is 139 bps INFO @ Thu, 30 Apr 2015 11:25:36: #2 alternative fragment length(s) may be 139 bps INFO @ Thu, 30 Apr 2015 11:25:36: #2.2 Generate R script for model : SRX080082.10_model.r INFO @ Thu, 30 Apr 2015 11:25:36: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:36: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:36: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:36: #2 predicted fragment length is 139 bps INFO @ Thu, 30 Apr 2015 11:25:36: #2 alternative fragment length(s) may be 139 bps INFO @ Thu, 30 Apr 2015 11:25:36: #2.2 Generate R script for model : SRX080082.20_model.r INFO @ Thu, 30 Apr 2015 11:25:36: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:36: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:36: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:36: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:36: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:36: #2 predicted fragment length is 139 bps INFO @ Thu, 30 Apr 2015 11:25:36: #2 alternative fragment length(s) may be 139 bps INFO @ Thu, 30 Apr 2015 11:25:36: #2.2 Generate R script for model : SRX080082.05_model.r INFO @ Thu, 30 Apr 2015 11:25:36: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:49: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:49: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:49: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:58: #4 Write output xls file... SRX080082.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:58: #4 Write peak in narrowPeak format file... SRX080082.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:58: #4 Write summits bed file... SRX080082.20_summits.bed INFO @ Thu, 30 Apr 2015 11:25:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1693 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write output xls file... SRX080082.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write peak in narrowPeak format file... SRX080082.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write summits bed file... SRX080082.10_summits.bed INFO @ Thu, 30 Apr 2015 11:25:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2668 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write output xls file... SRX080082.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write peak in narrowPeak format file... SRX080082.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write summits bed file... SRX080082.05_summits.bed INFO @ Thu, 30 Apr 2015 11:25:59: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3702 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。