Job ID = 2162409 sra ファイルのダウンロード中... Completed: 394136K bytes transferred in 6 seconds (487091K 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 --:--:-- --:--:-- --:--:-- 0 101 5467 0 5467 0 0 9627 0 --:--:-- --:--:-- --:--:-- 14501 100 36122 0 36122 0 0 47659 0 --:--:-- --:--:-- --:--:-- 63707 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 22089961 spots for /home/okishinya/chipatlas/results/dm3/SRX085405/SRR317183.sra Written 22089961 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: 00:04:18 22089961 reads; of these: 22089961 (100.00%) were unpaired; of these: 8194381 (37.10%) aligned 0 times 11976064 (54.21%) aligned exactly 1 time 1919516 (8.69%) aligned >1 times 62.90% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 10405645 / 13895580 = 0.7488 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 @ Tue, 21 Apr 2015 13:57:00: # Command line: callpeak -t SRX085405.bam -f BAM -g dm -n SRX085405.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX085405.20 # format = BAM # ChIP-seq file = ['SRX085405.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 13:57:00: # Command line: callpeak -t SRX085405.bam -f BAM -g dm -n SRX085405.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX085405.10 # format = BAM # ChIP-seq file = ['SRX085405.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 13:57:00: # Command line: callpeak -t SRX085405.bam -f BAM -g dm -n SRX085405.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX085405.05 # format = BAM # ChIP-seq file = ['SRX085405.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 13:57:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:57:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:57:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:57:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:57:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:57:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:57:08: 1000000 INFO @ Tue, 21 Apr 2015 13:57:08: 1000000 INFO @ Tue, 21 Apr 2015 13:57:08: 1000000 INFO @ Tue, 21 Apr 2015 13:57:15: 2000000 INFO @ Tue, 21 Apr 2015 13:57:15: 2000000 INFO @ Tue, 21 Apr 2015 13:57:15: 2000000 INFO @ Tue, 21 Apr 2015 13:57:22: 3000000 INFO @ Tue, 21 Apr 2015 13:57:22: 3000000 INFO @ Tue, 21 Apr 2015 13:57:22: 3000000 INFO @ Tue, 21 Apr 2015 13:57:26: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:57:26: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:57:26: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:57:26: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:57:26: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:57:26: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:57:26: #1 total tags in treatment: 3489935 INFO @ Tue, 21 Apr 2015 13:57:26: #1 total tags in treatment: 3489935 INFO @ Tue, 21 Apr 2015 13:57:26: #1 total tags in treatment: 3489935 INFO @ Tue, 21 Apr 2015 13:57:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:57:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:57:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:57:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:57:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:57:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:57:27: #1 tags after filtering in treatment: 3489196 INFO @ Tue, 21 Apr 2015 13:57:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:57:27: #1 finished! INFO @ Tue, 21 Apr 2015 13:57:27: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:57:27: #1 tags after filtering in treatment: 3489196 INFO @ Tue, 21 Apr 2015 13:57:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:57:27: #1 finished! INFO @ Tue, 21 Apr 2015 13:57:27: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:57:27: #1 tags after filtering in treatment: 3489196 INFO @ Tue, 21 Apr 2015 13:57:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:57:27: #1 finished! INFO @ Tue, 21 Apr 2015 13:57:27: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:57:28: #2 number of paired peaks: 2730 INFO @ Tue, 21 Apr 2015 13:57:28: start model_add_line... INFO @ Tue, 21 Apr 2015 13:57:28: #2 number of paired peaks: 2730 INFO @ Tue, 21 Apr 2015 13:57:28: start model_add_line... INFO @ Tue, 21 Apr 2015 13:57:28: #2 number of paired peaks: 2730 INFO @ Tue, 21 Apr 2015 13:57:28: start model_add_line... INFO @ Tue, 21 Apr 2015 13:57:36: start X-correlation... INFO @ Tue, 21 Apr 2015 13:57:36: end of X-cor INFO @ Tue, 21 Apr 2015 13:57:36: #2 finished! INFO @ Tue, 21 Apr 2015 13:57:36: #2 predicted fragment length is 119 bps INFO @ Tue, 21 Apr 2015 13:57:36: #2 alternative fragment length(s) may be 119 bps INFO @ Tue, 21 Apr 2015 13:57:36: #2.2 Generate R script for model : SRX085405.05_model.r INFO @ Tue, 21 Apr 2015 13:57:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:57:36: start X-correlation... INFO @ Tue, 21 Apr 2015 13:57:36: end of X-cor INFO @ Tue, 21 Apr 2015 13:57:36: #2 finished! INFO @ Tue, 21 Apr 2015 13:57:36: #2 predicted fragment length is 119 bps INFO @ Tue, 21 Apr 2015 13:57:36: #2 alternative fragment length(s) may be 119 bps INFO @ Tue, 21 Apr 2015 13:57:36: #2.2 Generate R script for model : SRX085405.10_model.r INFO @ Tue, 21 Apr 2015 13:57:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:57:36: start X-correlation... INFO @ Tue, 21 Apr 2015 13:57:36: end of X-cor INFO @ Tue, 21 Apr 2015 13:57:36: #2 finished! INFO @ Tue, 21 Apr 2015 13:57:36: #2 predicted fragment length is 119 bps INFO @ Tue, 21 Apr 2015 13:57:36: #2 alternative fragment length(s) may be 119 bps INFO @ Tue, 21 Apr 2015 13:57:36: #2.2 Generate R script for model : SRX085405.20_model.r INFO @ Tue, 21 Apr 2015 13:57:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:57:57: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:57:58: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:57:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 21 Apr 2015 13:58:15: #4 Write output xls file... SRX085405.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:58:15: #4 Write peak in narrowPeak format file... SRX085405.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:58:15: #4 Write summits bed file... SRX085405.20_summits.bed INFO @ Tue, 21 Apr 2015 13:58:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2784 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:58:16: #4 Write output xls file... SRX085405.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:58:16: #4 Write peak in narrowPeak format file... SRX085405.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:58:16: #4 Write output xls file... SRX085405.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:58:16: #4 Write summits bed file... SRX085405.10_summits.bed INFO @ Tue, 21 Apr 2015 13:58:16: Done! INFO @ Tue, 21 Apr 2015 13:58:16: #4 Write peak in narrowPeak format file... SRX085405.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:58:16: #4 Write summits bed file... SRX085405.05_summits.bed pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3780 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:58:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5340 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。