Job ID = 2161324 sra ファイルのダウンロード中... Completed: 178859K bytes transferred in 4 seconds (301521K 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 36893 0 36893 0 0 50414 0 --:--:-- --:--:-- --:--:-- 68320 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 8017000 spots for /home/okishinya/chipatlas/results/dm3/SRX017852/SRR038287.sra Written 8017000 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: 00:01:02 8017000 reads; of these: 8017000 (100.00%) were unpaired; of these: 6133681 (76.51%) aligned 0 times 1376847 (17.17%) aligned exactly 1 time 506472 (6.32%) aligned >1 times 23.49% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 189581 / 1883319 = 0.1007 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 12:21:50: # Command line: callpeak -t SRX017852.bam -f BAM -g dm -n SRX017852.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX017852.05 # format = BAM # ChIP-seq file = ['SRX017852.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 12:21:50: # Command line: callpeak -t SRX017852.bam -f BAM -g dm -n SRX017852.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX017852.20 # format = BAM # ChIP-seq file = ['SRX017852.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 12:21:50: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:21:50: # Command line: callpeak -t SRX017852.bam -f BAM -g dm -n SRX017852.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX017852.10 # format = BAM # ChIP-seq file = ['SRX017852.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 12:21:50: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:21:50: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:21:50: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:21:50: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:21:50: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:21:55: 1000000 INFO @ Tue, 21 Apr 2015 12:21:55: 1000000 INFO @ Tue, 21 Apr 2015 12:21:56: 1000000 INFO @ Tue, 21 Apr 2015 12:21:59: #1 tag size is determined as 25 bps INFO @ Tue, 21 Apr 2015 12:21:59: #1 tag size = 25 INFO @ Tue, 21 Apr 2015 12:21:59: #1 total tags in treatment: 1693738 INFO @ Tue, 21 Apr 2015 12:21:59: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:21:59: #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 12:21:59: #1 tag size is determined as 25 bps INFO @ Tue, 21 Apr 2015 12:21:59: #1 tag size = 25 INFO @ Tue, 21 Apr 2015 12:21:59: #1 total tags in treatment: 1693738 INFO @ Tue, 21 Apr 2015 12:21:59: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:21:59: #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 12:21:59: #1 tags after filtering in treatment: 1693732 INFO @ Tue, 21 Apr 2015 12:21:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:21:59: #1 finished! INFO @ Tue, 21 Apr 2015 12:21:59: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:22:00: #1 tags after filtering in treatment: 1693732 INFO @ Tue, 21 Apr 2015 12:22:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:22:00: #1 finished! INFO @ Tue, 21 Apr 2015 12:22:00: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:22:00: #1 tag size is determined as 25 bps INFO @ Tue, 21 Apr 2015 12:22:00: #1 tag size = 25 INFO @ Tue, 21 Apr 2015 12:22:00: #1 total tags in treatment: 1693738 INFO @ Tue, 21 Apr 2015 12:22:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:22:00: #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 12:22:00: #1 tags after filtering in treatment: 1693732 INFO @ Tue, 21 Apr 2015 12:22:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:22:00: #1 finished! INFO @ Tue, 21 Apr 2015 12:22:00: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:22:00: #2 number of paired peaks: 3983 INFO @ Tue, 21 Apr 2015 12:22:00: start model_add_line... INFO @ Tue, 21 Apr 2015 12:22:00: #2 number of paired peaks: 3983 INFO @ Tue, 21 Apr 2015 12:22:00: start model_add_line... INFO @ Tue, 21 Apr 2015 12:22:01: #2 number of paired peaks: 3983 INFO @ Tue, 21 Apr 2015 12:22:01: start model_add_line... INFO @ Tue, 21 Apr 2015 12:22:05: start X-correlation... INFO @ Tue, 21 Apr 2015 12:22:05: end of X-cor INFO @ Tue, 21 Apr 2015 12:22:05: #2 finished! INFO @ Tue, 21 Apr 2015 12:22:05: #2 predicted fragment length is 88 bps INFO @ Tue, 21 Apr 2015 12:22:05: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 21 Apr 2015 12:22:05: #2.2 Generate R script for model : SRX017852.10_model.r INFO @ Tue, 21 Apr 2015 12:22:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:22:05: start X-correlation... INFO @ Tue, 21 Apr 2015 12:22:05: end of X-cor INFO @ Tue, 21 Apr 2015 12:22:05: #2 finished! INFO @ Tue, 21 Apr 2015 12:22:05: #2 predicted fragment length is 88 bps INFO @ Tue, 21 Apr 2015 12:22:05: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 21 Apr 2015 12:22:05: #2.2 Generate R script for model : SRX017852.05_model.r INFO @ Tue, 21 Apr 2015 12:22:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:22:05: start X-correlation... INFO @ Tue, 21 Apr 2015 12:22:05: end of X-cor INFO @ Tue, 21 Apr 2015 12:22:05: #2 finished! INFO @ Tue, 21 Apr 2015 12:22:05: #2 predicted fragment length is 88 bps INFO @ Tue, 21 Apr 2015 12:22:05: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 21 Apr 2015 12:22:05: #2.2 Generate R script for model : SRX017852.20_model.r INFO @ Tue, 21 Apr 2015 12:22:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:22:15: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:22:16: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:22:16: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:22:23: #4 Write output xls file... SRX017852.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:22:23: #4 Write peak in narrowPeak format file... SRX017852.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:22:23: #4 Write summits bed file... SRX017852.20_summits.bed INFO @ Tue, 21 Apr 2015 12:22:23: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1186 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:22:24: #4 Write output xls file... SRX017852.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:22:24: #4 Write peak in narrowPeak format file... SRX017852.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:22:24: #4 Write summits bed file... SRX017852.10_summits.bed INFO @ Tue, 21 Apr 2015 12:22:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2503 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:22:25: #4 Write output xls file... SRX017852.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:22:25: #4 Write peak in narrowPeak format file... SRX017852.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:22:25: #4 Write summits bed file... SRX017852.05_summits.bed INFO @ Tue, 21 Apr 2015 12:22:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4311 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。