Job ID = 2161344 sra ファイルのダウンロード中... Completed: 561527K bytes transferred in 7 seconds (618973K 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 9839 0 9839 0 0 17499 0 --:--:-- --:--:-- --:--:-- 26448 100 35374 0 35374 0 0 47055 0 --:--:-- --:--:-- --:--:-- 63055 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 17364041 spots for /home/okishinya/chipatlas/results/dm3/SRX020693/SRR060800.sra Written 17364041 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: 00:02:53 17364041 reads; of these: 17364041 (100.00%) were unpaired; of these: 10325012 (59.46%) aligned 0 times 5646569 (32.52%) aligned exactly 1 time 1392460 (8.02%) aligned >1 times 40.54% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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] 1590861 / 7039029 = 0.2260 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 12:30:23: # Command line: callpeak -t SRX020693.bam -f BAM -g dm -n SRX020693.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX020693.05 # format = BAM # ChIP-seq file = ['SRX020693.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 12:30:23: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:30:23: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:30:23: # Command line: callpeak -t SRX020693.bam -f BAM -g dm -n SRX020693.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX020693.20 # format = BAM # ChIP-seq file = ['SRX020693.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 12:30:23: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:30:23: # Command line: callpeak -t SRX020693.bam -f BAM -g dm -n SRX020693.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX020693.10 # format = BAM # ChIP-seq file = ['SRX020693.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 12:30:23: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:30:23: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:30:23: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:30:28: 1000000 INFO @ Tue, 21 Apr 2015 12:30:28: 1000000 INFO @ Tue, 21 Apr 2015 12:30:28: 1000000 INFO @ Tue, 21 Apr 2015 12:30:33: 2000000 INFO @ Tue, 21 Apr 2015 12:30:33: 2000000 INFO @ Tue, 21 Apr 2015 12:30:34: 2000000 INFO @ Tue, 21 Apr 2015 12:30:38: 3000000 INFO @ Tue, 21 Apr 2015 12:30:38: 3000000 INFO @ Tue, 21 Apr 2015 12:30:39: 3000000 INFO @ Tue, 21 Apr 2015 12:30:43: 4000000 INFO @ Tue, 21 Apr 2015 12:30:43: 4000000 INFO @ Tue, 21 Apr 2015 12:30:44: 4000000 INFO @ Tue, 21 Apr 2015 12:30:48: 5000000 INFO @ Tue, 21 Apr 2015 12:30:48: 5000000 INFO @ Tue, 21 Apr 2015 12:30:50: 5000000 INFO @ Tue, 21 Apr 2015 12:30:51: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:30:51: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:30:51: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:30:51: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:30:51: #1 total tags in treatment: 5448168 INFO @ Tue, 21 Apr 2015 12:30:51: #1 total tags in treatment: 5448168 INFO @ Tue, 21 Apr 2015 12:30:51: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:30:51: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:30:51: #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 12:30:51: #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 12:30:52: #1 tags after filtering in treatment: 5447039 INFO @ Tue, 21 Apr 2015 12:30:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:30:52: #1 finished! INFO @ Tue, 21 Apr 2015 12:30:52: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:30:52: #1 tags after filtering in treatment: 5447039 INFO @ Tue, 21 Apr 2015 12:30:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:30:52: #1 finished! INFO @ Tue, 21 Apr 2015 12:30:52: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:30:52: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:30:52: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:30:52: #1 total tags in treatment: 5448168 INFO @ Tue, 21 Apr 2015 12:30:52: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:30:52: #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 12:30:53: #2 number of paired peaks: 4249 INFO @ Tue, 21 Apr 2015 12:30:53: start model_add_line... INFO @ Tue, 21 Apr 2015 12:30:53: #2 number of paired peaks: 4249 INFO @ Tue, 21 Apr 2015 12:30:53: start model_add_line... INFO @ Tue, 21 Apr 2015 12:30:53: #1 tags after filtering in treatment: 5447039 INFO @ Tue, 21 Apr 2015 12:30:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:30:53: #1 finished! INFO @ Tue, 21 Apr 2015 12:30:53: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:30:55: #2 number of paired peaks: 4249 INFO @ Tue, 21 Apr 2015 12:30:55: start model_add_line... INFO @ Tue, 21 Apr 2015 12:31:09: start X-correlation... INFO @ Tue, 21 Apr 2015 12:31:09: end of X-cor INFO @ Tue, 21 Apr 2015 12:31:09: #2 finished! INFO @ Tue, 21 Apr 2015 12:31:09: #2 predicted fragment length is 76 bps INFO @ Tue, 21 Apr 2015 12:31:09: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 21 Apr 2015 12:31:09: #2.2 Generate R script for model : SRX020693.20_model.r INFO @ Tue, 21 Apr 2015 12:31:09: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:31:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:31:09: start X-correlation... INFO @ Tue, 21 Apr 2015 12:31:09: end of X-cor INFO @ Tue, 21 Apr 2015 12:31:09: #2 finished! INFO @ Tue, 21 Apr 2015 12:31:09: #2 predicted fragment length is 76 bps INFO @ Tue, 21 Apr 2015 12:31:09: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 21 Apr 2015 12:31:09: #2.2 Generate R script for model : SRX020693.05_model.r INFO @ Tue, 21 Apr 2015 12:31:09: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:31:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:31:10: start X-correlation... INFO @ Tue, 21 Apr 2015 12:31:10: end of X-cor INFO @ Tue, 21 Apr 2015 12:31:10: #2 finished! INFO @ Tue, 21 Apr 2015 12:31:10: #2 predicted fragment length is 76 bps INFO @ Tue, 21 Apr 2015 12:31:10: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 21 Apr 2015 12:31:10: #2.2 Generate R script for model : SRX020693.10_model.r INFO @ Tue, 21 Apr 2015 12:31:10: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:31:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:31:39: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:31:39: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:31:40: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:32:02: #4 Write output xls file... SRX020693.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:32:02: #4 Write peak in narrowPeak format file... SRX020693.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:32:02: #4 Write summits bed file... SRX020693.20_summits.bed INFO @ Tue, 21 Apr 2015 12:32:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2778 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:32:03: #4 Write output xls file... SRX020693.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:32:04: #4 Write peak in narrowPeak format file... SRX020693.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:32:04: #4 Write summits bed file... SRX020693.10_summits.bed INFO @ Tue, 21 Apr 2015 12:32:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6898 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:32:09: #4 Write output xls file... SRX020693.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:32:10: #4 Write peak in narrowPeak format file... SRX020693.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:32:10: #4 Write summits bed file... SRX020693.05_summits.bed INFO @ Tue, 21 Apr 2015 12:32:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11346 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。