Job ID = 2161146 sra ファイルのダウンロード中... Completed: 143843K bytes transferred in 4 seconds (263668K 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 34735 0 34735 0 0 46836 0 --:--:-- --:--:-- --:--:-- 63154 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 6941252 spots for /home/okishinya/chipatlas/results/dm3/SRX013027/SRR030293.sra Written 6941252 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: 00:01:39 6941252 reads; of these: 6941252 (100.00%) were unpaired; of these: 845165 (12.18%) aligned 0 times 5183227 (74.67%) aligned exactly 1 time 912860 (13.15%) aligned >1 times 87.82% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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] 706745 / 6096087 = 0.1159 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 12:00:56: # Command line: callpeak -t SRX013027.bam -f BAM -g dm -n SRX013027.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013027.20 # format = BAM # ChIP-seq file = ['SRX013027.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 12:00:56: # Command line: callpeak -t SRX013027.bam -f BAM -g dm -n SRX013027.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013027.10 # format = BAM # ChIP-seq file = ['SRX013027.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 12:00:56: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:00:56: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:00:56: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:00:56: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:00:56: # Command line: callpeak -t SRX013027.bam -f BAM -g dm -n SRX013027.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013027.05 # format = BAM # ChIP-seq file = ['SRX013027.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 12:00:56: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:00:56: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:01:01: 1000000 INFO @ Tue, 21 Apr 2015 12:01:01: 1000000 INFO @ Tue, 21 Apr 2015 12:01:01: 1000000 INFO @ Tue, 21 Apr 2015 12:01:06: 2000000 INFO @ Tue, 21 Apr 2015 12:01:06: 2000000 INFO @ Tue, 21 Apr 2015 12:01:06: 2000000 INFO @ Tue, 21 Apr 2015 12:01:12: 3000000 INFO @ Tue, 21 Apr 2015 12:01:12: 3000000 INFO @ Tue, 21 Apr 2015 12:01:12: 3000000 INFO @ Tue, 21 Apr 2015 12:01:17: 4000000 INFO @ Tue, 21 Apr 2015 12:01:17: 4000000 INFO @ Tue, 21 Apr 2015 12:01:17: 4000000 INFO @ Tue, 21 Apr 2015 12:01:22: 5000000 INFO @ Tue, 21 Apr 2015 12:01:22: 5000000 INFO @ Tue, 21 Apr 2015 12:01:23: 5000000 INFO @ Tue, 21 Apr 2015 12:01:24: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:01:24: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:01:24: #1 total tags in treatment: 5389342 INFO @ Tue, 21 Apr 2015 12:01:24: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:01:24: #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 12:01:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:01:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:01:25: #1 total tags in treatment: 5389342 INFO @ Tue, 21 Apr 2015 12:01:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:01:25: #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 12:01:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:01:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:01:25: #1 total tags in treatment: 5389342 INFO @ Tue, 21 Apr 2015 12:01:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:01:25: #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 12:01:25: #1 tags after filtering in treatment: 5389118 INFO @ Tue, 21 Apr 2015 12:01:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:01:25: #1 finished! INFO @ Tue, 21 Apr 2015 12:01:25: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:01:26: #1 tags after filtering in treatment: 5389118 INFO @ Tue, 21 Apr 2015 12:01:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:01:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:01:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:01:26: #1 tags after filtering in treatment: 5389118 INFO @ Tue, 21 Apr 2015 12:01:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:01:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:01:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:01:27: #2 number of paired peaks: 4831 INFO @ Tue, 21 Apr 2015 12:01:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:01:27: #2 number of paired peaks: 4831 INFO @ Tue, 21 Apr 2015 12:01:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:01:27: #2 number of paired peaks: 4831 INFO @ Tue, 21 Apr 2015 12:01:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:01:44: start X-correlation... INFO @ Tue, 21 Apr 2015 12:01:44: end of X-cor INFO @ Tue, 21 Apr 2015 12:01:44: #2 finished! INFO @ Tue, 21 Apr 2015 12:01:44: #2 predicted fragment length is 198 bps INFO @ Tue, 21 Apr 2015 12:01:44: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 21 Apr 2015 12:01:44: #2.2 Generate R script for model : SRX013027.05_model.r INFO @ Tue, 21 Apr 2015 12:01:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:01:44: start X-correlation... INFO @ Tue, 21 Apr 2015 12:01:44: end of X-cor INFO @ Tue, 21 Apr 2015 12:01:44: #2 finished! INFO @ Tue, 21 Apr 2015 12:01:44: #2 predicted fragment length is 198 bps INFO @ Tue, 21 Apr 2015 12:01:44: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 21 Apr 2015 12:01:44: #2.2 Generate R script for model : SRX013027.20_model.r INFO @ Tue, 21 Apr 2015 12:01:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:01:44: start X-correlation... INFO @ Tue, 21 Apr 2015 12:01:44: end of X-cor INFO @ Tue, 21 Apr 2015 12:01:44: #2 finished! INFO @ Tue, 21 Apr 2015 12:01:44: #2 predicted fragment length is 198 bps INFO @ Tue, 21 Apr 2015 12:01:44: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 21 Apr 2015 12:01:44: #2.2 Generate R script for model : SRX013027.10_model.r INFO @ Tue, 21 Apr 2015 12:01:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:02:16: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:02:17: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:02:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:02:46: #4 Write output xls file... SRX013027.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:02:46: #4 Write peak in narrowPeak format file... SRX013027.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:02:46: #4 Write summits bed file... SRX013027.20_summits.bed INFO @ Tue, 21 Apr 2015 12:02:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3624 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:02:47: #4 Write output xls file... SRX013027.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:02:47: #4 Write peak in narrowPeak format file... SRX013027.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:02:47: #4 Write summits bed file... SRX013027.10_summits.bed INFO @ Tue, 21 Apr 2015 12:02:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5355 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:02:49: #4 Write output xls file... SRX013027.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:02:49: #4 Write peak in narrowPeak format file... SRX013027.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:02:49: #4 Write summits bed file... SRX013027.05_summits.bed INFO @ Tue, 21 Apr 2015 12:02:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6820 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。