Job ID = 2161421 sra ファイルのダウンロード中... Completed: 707988K bytes transferred in 8 seconds (675590K 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 35829 0 35829 0 0 48849 0 --:--:-- --:--:-- --:--:-- 66105 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 26808386 spots for /home/okishinya/chipatlas/results/dm3/SRX026739/SRR065625.sra Written 26808386 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: 00:07:34 26808386 reads; of these: 26808386 (100.00%) were unpaired; of these: 10443853 (38.96%) aligned 0 times 10742516 (40.07%) aligned exactly 1 time 5622017 (20.97%) aligned >1 times 61.04% overall alignment rate Time searching: 00:07:35 Overall time: 00:07:35 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10252704 / 16364533 = 0.6265 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 12:49:01: # Command line: callpeak -t SRX026739.bam -f BAM -g dm -n SRX026739.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX026739.20 # format = BAM # ChIP-seq file = ['SRX026739.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 12:49:01: # Command line: callpeak -t SRX026739.bam -f BAM -g dm -n SRX026739.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX026739.10 # format = BAM # ChIP-seq file = ['SRX026739.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 12:49:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:49:01: # Command line: callpeak -t SRX026739.bam -f BAM -g dm -n SRX026739.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX026739.05 # format = BAM # ChIP-seq file = ['SRX026739.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 12:49:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:49:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:49:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:49:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:49:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:49:07: 1000000 INFO @ Tue, 21 Apr 2015 12:49:08: 1000000 INFO @ Tue, 21 Apr 2015 12:49:08: 1000000 INFO @ Tue, 21 Apr 2015 12:49:13: 2000000 INFO @ Tue, 21 Apr 2015 12:49:14: 2000000 INFO @ Tue, 21 Apr 2015 12:49:14: 2000000 INFO @ Tue, 21 Apr 2015 12:49:20: 3000000 INFO @ Tue, 21 Apr 2015 12:49:20: 3000000 INFO @ Tue, 21 Apr 2015 12:49:21: 3000000 INFO @ Tue, 21 Apr 2015 12:49:26: 4000000 INFO @ Tue, 21 Apr 2015 12:49:26: 4000000 INFO @ Tue, 21 Apr 2015 12:49:28: 4000000 INFO @ Tue, 21 Apr 2015 12:49:32: 5000000 INFO @ Tue, 21 Apr 2015 12:49:32: 5000000 INFO @ Tue, 21 Apr 2015 12:49:34: 5000000 INFO @ Tue, 21 Apr 2015 12:49:39: 6000000 INFO @ Tue, 21 Apr 2015 12:49:39: 6000000 INFO @ Tue, 21 Apr 2015 12:49:39: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 12:49:39: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 12:49:39: #1 total tags in treatment: 6111829 INFO @ Tue, 21 Apr 2015 12:49:39: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:49:39: #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 12:49:39: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 12:49:39: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 12:49:39: #1 total tags in treatment: 6111829 INFO @ Tue, 21 Apr 2015 12:49:39: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:49:39: #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 12:49:40: #1 tags after filtering in treatment: 6109595 INFO @ Tue, 21 Apr 2015 12:49:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:49:40: #1 finished! INFO @ Tue, 21 Apr 2015 12:49:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:49:41: #1 tags after filtering in treatment: 6109595 INFO @ Tue, 21 Apr 2015 12:49:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:49:41: #1 finished! INFO @ Tue, 21 Apr 2015 12:49:41: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:49:41: 6000000 INFO @ Tue, 21 Apr 2015 12:49:41: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 12:49:41: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 12:49:41: #1 total tags in treatment: 6111829 INFO @ Tue, 21 Apr 2015 12:49:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:49:41: #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 12:49:42: #2 number of paired peaks: 1838 INFO @ Tue, 21 Apr 2015 12:49:42: start model_add_line... INFO @ Tue, 21 Apr 2015 12:49:42: #2 number of paired peaks: 1838 INFO @ Tue, 21 Apr 2015 12:49:42: start model_add_line... INFO @ Tue, 21 Apr 2015 12:49:43: #1 tags after filtering in treatment: 6109595 INFO @ Tue, 21 Apr 2015 12:49:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:49:43: #1 finished! INFO @ Tue, 21 Apr 2015 12:49:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:49:44: #2 number of paired peaks: 1838 INFO @ Tue, 21 Apr 2015 12:49:44: start model_add_line... INFO @ Tue, 21 Apr 2015 12:49:48: start X-correlation... INFO @ Tue, 21 Apr 2015 12:49:48: end of X-cor INFO @ Tue, 21 Apr 2015 12:49:48: #2 finished! INFO @ Tue, 21 Apr 2015 12:49:48: #2 predicted fragment length is 162 bps INFO @ Tue, 21 Apr 2015 12:49:48: #2 alternative fragment length(s) may be 162 bps INFO @ Tue, 21 Apr 2015 12:49:48: #2.2 Generate R script for model : SRX026739.20_model.r INFO @ Tue, 21 Apr 2015 12:49:48: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:49:49: start X-correlation... INFO @ Tue, 21 Apr 2015 12:49:49: end of X-cor INFO @ Tue, 21 Apr 2015 12:49:49: #2 finished! INFO @ Tue, 21 Apr 2015 12:49:49: #2 predicted fragment length is 162 bps INFO @ Tue, 21 Apr 2015 12:49:49: #2 alternative fragment length(s) may be 162 bps INFO @ Tue, 21 Apr 2015 12:49:49: #2.2 Generate R script for model : SRX026739.05_model.r INFO @ Tue, 21 Apr 2015 12:49:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:49:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:49:50: start X-correlation... INFO @ Tue, 21 Apr 2015 12:49:50: end of X-cor INFO @ Tue, 21 Apr 2015 12:49:50: #2 finished! INFO @ Tue, 21 Apr 2015 12:49:50: #2 predicted fragment length is 162 bps INFO @ Tue, 21 Apr 2015 12:49:50: #2 alternative fragment length(s) may be 162 bps INFO @ Tue, 21 Apr 2015 12:49:50: #2.2 Generate R script for model : SRX026739.10_model.r INFO @ Tue, 21 Apr 2015 12:49:50: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:49:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:50:23: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:50:24: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:50:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:50:51: #4 Write output xls file... SRX026739.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:50:51: #4 Write peak in narrowPeak format file... SRX026739.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:50:51: #4 Write summits bed file... SRX026739.20_summits.bed INFO @ Tue, 21 Apr 2015 12:50:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1865 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:50:55: #4 Write output xls file... SRX026739.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:50:55: #4 Write peak in narrowPeak format file... SRX026739.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:50:55: #4 Write summits bed file... SRX026739.10_summits.bed INFO @ Tue, 21 Apr 2015 12:50:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4358 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:50:56: #4 Write output xls file... SRX026739.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:50:56: #4 Write peak in narrowPeak format file... SRX026739.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:50:56: #4 Write summits bed file... SRX026739.05_summits.bed INFO @ Tue, 21 Apr 2015 12:50:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8017 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。