Job ID = 2161910 sra ファイルのダウンロード中... Completed: 845765K bytes transferred in 10 seconds (687475K 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 29787 0 29787 0 0 39531 0 --:--:-- --:--:-- --:--:-- 52907 100 36290 0 36290 0 0 48102 0 --:--:-- --:--:-- --:--:-- 64343 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 33342680 spots for /home/okishinya/chipatlas/results/dm3/SRX040614/SRR097983.sra Written 33342680 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: 00:13:13 33342680 reads; of these: 33342680 (100.00%) were unpaired; of these: 1598206 (4.79%) aligned 0 times 22108418 (66.31%) aligned exactly 1 time 9636056 (28.90%) aligned >1 times 95.21% overall alignment rate Time searching: 00:13:13 Overall time: 00:13:13 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] 18495765 / 31744474 = 0.5826 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 13:31:38: # Command line: callpeak -t SRX040614.bam -f BAM -g dm -n SRX040614.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX040614.10 # format = BAM # ChIP-seq file = ['SRX040614.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 13:31:38: # Command line: callpeak -t SRX040614.bam -f BAM -g dm -n SRX040614.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX040614.05 # format = BAM # ChIP-seq file = ['SRX040614.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 13:31:38: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:31:38: # Command line: callpeak -t SRX040614.bam -f BAM -g dm -n SRX040614.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX040614.20 # format = BAM # ChIP-seq file = ['SRX040614.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 13:31:38: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:31:38: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:31:38: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:31:38: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:31:38: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:31:43: 1000000 INFO @ Tue, 21 Apr 2015 13:31:45: 1000000 INFO @ Tue, 21 Apr 2015 13:31:45: 1000000 INFO @ Tue, 21 Apr 2015 13:31:49: 2000000 INFO @ Tue, 21 Apr 2015 13:31:51: 2000000 INFO @ Tue, 21 Apr 2015 13:31:51: 2000000 INFO @ Tue, 21 Apr 2015 13:31:54: 3000000 INFO @ Tue, 21 Apr 2015 13:31:58: 3000000 INFO @ Tue, 21 Apr 2015 13:31:58: 3000000 INFO @ Tue, 21 Apr 2015 13:31:59: 4000000 INFO @ Tue, 21 Apr 2015 13:32:03: 4000000 INFO @ Tue, 21 Apr 2015 13:32:03: 4000000 INFO @ Tue, 21 Apr 2015 13:32:04: 5000000 INFO @ Tue, 21 Apr 2015 13:32:08: 5000000 INFO @ Tue, 21 Apr 2015 13:32:08: 5000000 INFO @ Tue, 21 Apr 2015 13:32:09: 6000000 INFO @ Tue, 21 Apr 2015 13:32:13: 6000000 INFO @ Tue, 21 Apr 2015 13:32:14: 6000000 INFO @ Tue, 21 Apr 2015 13:32:14: 7000000 INFO @ Tue, 21 Apr 2015 13:32:19: 7000000 INFO @ Tue, 21 Apr 2015 13:32:19: 7000000 INFO @ Tue, 21 Apr 2015 13:32:19: 8000000 INFO @ Tue, 21 Apr 2015 13:32:24: 8000000 INFO @ Tue, 21 Apr 2015 13:32:25: 9000000 INFO @ Tue, 21 Apr 2015 13:32:25: 8000000 INFO @ Tue, 21 Apr 2015 13:32:30: 9000000 INFO @ Tue, 21 Apr 2015 13:32:30: 10000000 INFO @ Tue, 21 Apr 2015 13:32:30: 9000000 INFO @ Tue, 21 Apr 2015 13:32:35: 11000000 INFO @ Tue, 21 Apr 2015 13:32:35: 10000000 INFO @ Tue, 21 Apr 2015 13:32:36: 10000000 INFO @ Tue, 21 Apr 2015 13:32:40: 12000000 INFO @ Tue, 21 Apr 2015 13:32:41: 11000000 INFO @ Tue, 21 Apr 2015 13:32:42: 11000000 INFO @ Tue, 21 Apr 2015 13:32:45: 13000000 INFO @ Tue, 21 Apr 2015 13:32:46: 12000000 INFO @ Tue, 21 Apr 2015 13:32:47: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:32:47: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:32:47: #1 total tags in treatment: 13248709 INFO @ Tue, 21 Apr 2015 13:32:47: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:32:47: #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 13:32:47: 12000000 INFO @ Tue, 21 Apr 2015 13:32:49: #1 tags after filtering in treatment: 13244722 INFO @ Tue, 21 Apr 2015 13:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:32:49: #1 finished! INFO @ Tue, 21 Apr 2015 13:32:49: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:32:52: #2 number of paired peaks: 1360 INFO @ Tue, 21 Apr 2015 13:32:52: start model_add_line... INFO @ Tue, 21 Apr 2015 13:32:52: 13000000 INFO @ Tue, 21 Apr 2015 13:32:53: 13000000 INFO @ Tue, 21 Apr 2015 13:32:53: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:32:53: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:32:53: #1 total tags in treatment: 13248709 INFO @ Tue, 21 Apr 2015 13:32:53: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:32:53: #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 13:32:54: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:32:54: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:32:54: #1 total tags in treatment: 13248709 INFO @ Tue, 21 Apr 2015 13:32:54: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:32:54: #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 13:32:56: #1 tags after filtering in treatment: 13244722 INFO @ Tue, 21 Apr 2015 13:32:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:32:56: #1 finished! INFO @ Tue, 21 Apr 2015 13:32:56: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:32:57: #1 tags after filtering in treatment: 13244722 INFO @ Tue, 21 Apr 2015 13:32:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:32:57: #1 finished! INFO @ Tue, 21 Apr 2015 13:32:57: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:32:58: #2 number of paired peaks: 1360 INFO @ Tue, 21 Apr 2015 13:32:58: start model_add_line... INFO @ Tue, 21 Apr 2015 13:32:59: #2 number of paired peaks: 1360 INFO @ Tue, 21 Apr 2015 13:32:59: start model_add_line... INFO @ Tue, 21 Apr 2015 13:33:01: start X-correlation... INFO @ Tue, 21 Apr 2015 13:33:01: end of X-cor INFO @ Tue, 21 Apr 2015 13:33:01: #2 finished! INFO @ Tue, 21 Apr 2015 13:33:01: #2 predicted fragment length is 97 bps INFO @ Tue, 21 Apr 2015 13:33:01: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 21 Apr 2015 13:33:01: #2.2 Generate R script for model : SRX040614.10_model.r INFO @ Tue, 21 Apr 2015 13:33:01: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:33:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:33:08: start X-correlation... INFO @ Tue, 21 Apr 2015 13:33:08: end of X-cor INFO @ Tue, 21 Apr 2015 13:33:08: #2 finished! INFO @ Tue, 21 Apr 2015 13:33:08: #2 predicted fragment length is 97 bps INFO @ Tue, 21 Apr 2015 13:33:08: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 21 Apr 2015 13:33:08: #2.2 Generate R script for model : SRX040614.20_model.r INFO @ Tue, 21 Apr 2015 13:33:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:33:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:33:09: start X-correlation... INFO @ Tue, 21 Apr 2015 13:33:09: end of X-cor INFO @ Tue, 21 Apr 2015 13:33:09: #2 finished! INFO @ Tue, 21 Apr 2015 13:33:09: #2 predicted fragment length is 97 bps INFO @ Tue, 21 Apr 2015 13:33:09: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 21 Apr 2015 13:33:09: #2.2 Generate R script for model : SRX040614.05_model.r INFO @ Tue, 21 Apr 2015 13:33:09: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:33:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:34:09: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:34:17: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:34:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:35:12: #4 Write output xls file... SRX040614.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:35:12: #4 Write peak in narrowPeak format file... SRX040614.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:35:12: #4 Write summits bed file... SRX040614.20_summits.bed INFO @ Tue, 21 Apr 2015 13:35:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7578 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:35:18: #4 Write output xls file... SRX040614.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:35:18: #4 Write peak in narrowPeak format file... SRX040614.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:35:18: #4 Write summits bed file... SRX040614.10_summits.bed INFO @ Tue, 21 Apr 2015 13:35:18: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (23017 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:35:49: #4 Write output xls file... SRX040614.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:35:50: #4 Write peak in narrowPeak format file... SRX040614.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:35:50: #4 Write summits bed file... SRX040614.05_summits.bed INFO @ Tue, 21 Apr 2015 13:35:51: Done! pass1 - making usageList (15 chroms): 9 millis pass2 - checking and writing primary data (44927 records, 4 fields): 52 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。