Job ID = 2161084 sra ファイルのダウンロード中... Completed: 179096K bytes transferred in 5 seconds (291633K 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 34453 0 34453 0 0 49702 0 --:--:-- --:--:-- --:--:-- 68631 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 7859161 spots for /home/okishinya/chipatlas/results/dm3/SRX013015/SRR030281.sra Written 7859161 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: 00:01:34 7859161 reads; of these: 7859161 (100.00%) were unpaired; of these: 758865 (9.66%) aligned 0 times 6484021 (82.50%) aligned exactly 1 time 616275 (7.84%) aligned >1 times 90.34% overall alignment rate Time searching: 00:01:34 Overall time: 00:01:34 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] 752535 / 7100296 = 0.1060 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 11:58:15: # Command line: callpeak -t SRX013015.bam -f BAM -g dm -n SRX013015.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013015.05 # format = BAM # ChIP-seq file = ['SRX013015.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 11:58:15: # Command line: callpeak -t SRX013015.bam -f BAM -g dm -n SRX013015.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013015.10 # format = BAM # ChIP-seq file = ['SRX013015.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 11:58:15: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:58:15: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:58:15: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:58:15: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:58:15: # Command line: callpeak -t SRX013015.bam -f BAM -g dm -n SRX013015.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013015.20 # format = BAM # ChIP-seq file = ['SRX013015.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 11:58:15: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:58:15: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:58:20: 1000000 INFO @ Tue, 21 Apr 2015 11:58:21: 1000000 INFO @ Tue, 21 Apr 2015 11:58:21: 1000000 INFO @ Tue, 21 Apr 2015 11:58:25: 2000000 INFO @ Tue, 21 Apr 2015 11:58:27: 2000000 INFO @ Tue, 21 Apr 2015 11:58:27: 2000000 INFO @ Tue, 21 Apr 2015 11:58:31: 3000000 INFO @ Tue, 21 Apr 2015 11:58:33: 3000000 INFO @ Tue, 21 Apr 2015 11:58:33: 3000000 INFO @ Tue, 21 Apr 2015 11:58:36: 4000000 INFO @ Tue, 21 Apr 2015 11:58:39: 4000000 INFO @ Tue, 21 Apr 2015 11:58:39: 4000000 INFO @ Tue, 21 Apr 2015 11:58:41: 5000000 INFO @ Tue, 21 Apr 2015 11:58:45: 5000000 INFO @ Tue, 21 Apr 2015 11:58:45: 5000000 INFO @ Tue, 21 Apr 2015 11:58:47: 6000000 INFO @ Tue, 21 Apr 2015 11:58:49: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:58:49: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:58:49: #1 total tags in treatment: 6347761 INFO @ Tue, 21 Apr 2015 11:58:49: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:58:49: #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 11:58:50: #1 tags after filtering in treatment: 6347372 INFO @ Tue, 21 Apr 2015 11:58:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:58:50: #1 finished! INFO @ Tue, 21 Apr 2015 11:58:50: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:58:51: 6000000 INFO @ Tue, 21 Apr 2015 11:58:51: 6000000 INFO @ Tue, 21 Apr 2015 11:58:51: #2 number of paired peaks: 5309 INFO @ Tue, 21 Apr 2015 11:58:51: start model_add_line... INFO @ Tue, 21 Apr 2015 11:58:53: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:58:53: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:58:53: #1 total tags in treatment: 6347761 INFO @ Tue, 21 Apr 2015 11:58:53: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:58:53: #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 11:58:53: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 11:58:53: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 11:58:53: #1 total tags in treatment: 6347761 INFO @ Tue, 21 Apr 2015 11:58:53: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 11:58:53: #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 11:58:55: #1 tags after filtering in treatment: 6347372 INFO @ Tue, 21 Apr 2015 11:58:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:58:55: #1 finished! INFO @ Tue, 21 Apr 2015 11:58:55: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:58:55: #1 tags after filtering in treatment: 6347372 INFO @ Tue, 21 Apr 2015 11:58:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 11:58:55: #1 finished! INFO @ Tue, 21 Apr 2015 11:58:55: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 11:58:56: #2 number of paired peaks: 5309 INFO @ Tue, 21 Apr 2015 11:58:56: start model_add_line... INFO @ Tue, 21 Apr 2015 11:58:56: #2 number of paired peaks: 5309 INFO @ Tue, 21 Apr 2015 11:58:56: start model_add_line... INFO @ Tue, 21 Apr 2015 11:59:11: start X-correlation... INFO @ Tue, 21 Apr 2015 11:59:12: end of X-cor INFO @ Tue, 21 Apr 2015 11:59:12: #2 finished! INFO @ Tue, 21 Apr 2015 11:59:12: #2 predicted fragment length is 150 bps INFO @ Tue, 21 Apr 2015 11:59:12: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 21 Apr 2015 11:59:12: #2.2 Generate R script for model : SRX013015.20_model.r INFO @ Tue, 21 Apr 2015 11:59:12: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:59:16: start X-correlation... INFO @ Tue, 21 Apr 2015 11:59:16: end of X-cor INFO @ Tue, 21 Apr 2015 11:59:16: #2 finished! INFO @ Tue, 21 Apr 2015 11:59:16: #2 predicted fragment length is 150 bps INFO @ Tue, 21 Apr 2015 11:59:16: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 21 Apr 2015 11:59:16: #2.2 Generate R script for model : SRX013015.05_model.r INFO @ Tue, 21 Apr 2015 11:59:16: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:59:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:59:17: start X-correlation... INFO @ Tue, 21 Apr 2015 11:59:17: end of X-cor INFO @ Tue, 21 Apr 2015 11:59:17: #2 finished! INFO @ Tue, 21 Apr 2015 11:59:17: #2 predicted fragment length is 150 bps INFO @ Tue, 21 Apr 2015 11:59:17: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 21 Apr 2015 11:59:17: #2.2 Generate R script for model : SRX013015.10_model.r INFO @ Tue, 21 Apr 2015 11:59:17: #3 Call peaks... INFO @ Tue, 21 Apr 2015 11:59:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 11:59:49: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:59:53: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 11:59:53: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:00:16: #4 Write output xls file... SRX013015.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:00:16: #4 Write peak in narrowPeak format file... SRX013015.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:00:16: #4 Write summits bed file... SRX013015.20_summits.bed INFO @ Tue, 21 Apr 2015 12:00:16: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (2426 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:00:25: #4 Write output xls file... SRX013015.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:00:25: #4 Write peak in narrowPeak format file... SRX013015.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:00:25: #4 Write summits bed file... SRX013015.10_summits.bed INFO @ Tue, 21 Apr 2015 12:00:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5041 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:00:30: #4 Write output xls file... SRX013015.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:00:30: #4 Write peak in narrowPeak format file... SRX013015.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:00:30: #4 Write summits bed file... SRX013015.05_summits.bed INFO @ Tue, 21 Apr 2015 12:00:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7171 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。