Job ID = 2237070 sra ファイルのダウンロード中... Completed: 141664K bytes transferred in 6 seconds (182975K 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 36879 0 36879 0 0 49528 0 --:--:-- --:--:-- --:--:-- 66688 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 6956186 spots for /home/okishinya/chipatlas/results/ce10/SRX113608/SRR393708.sra Written 6956186 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: 00:01:41 6956186 reads; of these: 6956186 (100.00%) were unpaired; of these: 1325624 (19.06%) aligned 0 times 3947913 (56.75%) aligned exactly 1 time 1682649 (24.19%) aligned >1 times 80.94% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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] 2732933 / 5630562 = 0.4854 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 11:29:15: # Command line: callpeak -t SRX113608.bam -f BAM -g ce -n SRX113608.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX113608.10 # format = BAM # ChIP-seq file = ['SRX113608.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 11:29:15: # Command line: callpeak -t SRX113608.bam -f BAM -g ce -n SRX113608.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX113608.05 # format = BAM # ChIP-seq file = ['SRX113608.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 11:29:15: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:15: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:15: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:15: # Command line: callpeak -t SRX113608.bam -f BAM -g ce -n SRX113608.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX113608.20 # format = BAM # ChIP-seq file = ['SRX113608.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 11:29:15: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:15: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:15: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:21: 1000000 INFO @ Thu, 30 Apr 2015 11:29:22: 1000000 INFO @ Thu, 30 Apr 2015 11:29:22: 1000000 INFO @ Thu, 30 Apr 2015 11:29:28: 2000000 INFO @ Thu, 30 Apr 2015 11:29:28: 2000000 INFO @ Thu, 30 Apr 2015 11:29:28: 2000000 INFO @ Thu, 30 Apr 2015 11:29:33: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:29:33: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:29:33: #1 total tags in treatment: 2897629 INFO @ Thu, 30 Apr 2015 11:29:33: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:29:33: #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 11:29:33: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:29:33: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:29:33: #1 total tags in treatment: 2897629 INFO @ Thu, 30 Apr 2015 11:29:33: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:29:33: #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 11:29:33: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:29:33: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:29:33: #1 total tags in treatment: 2897629 INFO @ Thu, 30 Apr 2015 11:29:33: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:29:33: #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 11:29:33: #1 tags after filtering in treatment: 2884753 INFO @ Thu, 30 Apr 2015 11:29:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:29:33: #1 finished! INFO @ Thu, 30 Apr 2015 11:29:33: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:29:34: #1 tags after filtering in treatment: 2884753 INFO @ Thu, 30 Apr 2015 11:29:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:29:34: #1 finished! INFO @ Thu, 30 Apr 2015 11:29:34: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:29:34: #1 tags after filtering in treatment: 2884753 INFO @ Thu, 30 Apr 2015 11:29:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:29:34: #1 finished! INFO @ Thu, 30 Apr 2015 11:29:34: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:29:35: #2 number of paired peaks: 3639 INFO @ Thu, 30 Apr 2015 11:29:35: start model_add_line... INFO @ Thu, 30 Apr 2015 11:29:35: #2 number of paired peaks: 3639 INFO @ Thu, 30 Apr 2015 11:29:35: start model_add_line... INFO @ Thu, 30 Apr 2015 11:29:35: #2 number of paired peaks: 3639 INFO @ Thu, 30 Apr 2015 11:29:35: start model_add_line... INFO @ Thu, 30 Apr 2015 11:29:46: start X-correlation... INFO @ Thu, 30 Apr 2015 11:29:46: end of X-cor INFO @ Thu, 30 Apr 2015 11:29:46: #2 finished! INFO @ Thu, 30 Apr 2015 11:29:46: #2 predicted fragment length is 191 bps INFO @ Thu, 30 Apr 2015 11:29:46: #2 alternative fragment length(s) may be 2,191 bps INFO @ Thu, 30 Apr 2015 11:29:46: #2.2 Generate R script for model : SRX113608.10_model.r INFO @ Thu, 30 Apr 2015 11:29:46: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:29:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:29:46: start X-correlation... INFO @ Thu, 30 Apr 2015 11:29:46: end of X-cor INFO @ Thu, 30 Apr 2015 11:29:46: #2 finished! INFO @ Thu, 30 Apr 2015 11:29:46: #2 predicted fragment length is 191 bps INFO @ Thu, 30 Apr 2015 11:29:46: #2 alternative fragment length(s) may be 2,191 bps INFO @ Thu, 30 Apr 2015 11:29:46: #2.2 Generate R script for model : SRX113608.05_model.r INFO @ Thu, 30 Apr 2015 11:29:46: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:29:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:29:46: start X-correlation... INFO @ Thu, 30 Apr 2015 11:29:46: end of X-cor INFO @ Thu, 30 Apr 2015 11:29:46: #2 finished! INFO @ Thu, 30 Apr 2015 11:29:46: #2 predicted fragment length is 191 bps INFO @ Thu, 30 Apr 2015 11:29:46: #2 alternative fragment length(s) may be 2,191 bps INFO @ Thu, 30 Apr 2015 11:29:46: #2.2 Generate R script for model : SRX113608.20_model.r INFO @ Thu, 30 Apr 2015 11:29:46: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:29:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:30:05: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:30:05: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:30:06: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:30:16: #4 Write output xls file... SRX113608.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:30:16: #4 Write peak in narrowPeak format file... SRX113608.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:30:16: #4 Write summits bed file... SRX113608.10_summits.bed INFO @ Thu, 30 Apr 2015 11:30:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:30:18: #4 Write output xls file... SRX113608.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:30:18: #4 Write peak in narrowPeak format file... SRX113608.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:30:18: #4 Write summits bed file... SRX113608.20_summits.bed INFO @ Thu, 30 Apr 2015 11:30:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:30:19: #4 Write output xls file... SRX113608.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:30:19: #4 Write peak in narrowPeak format file... SRX113608.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:30:19: #4 Write summits bed file... SRX113608.05_summits.bed INFO @ Thu, 30 Apr 2015 11:30:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1829 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。