Job ID = 2161150 sra ファイルのダウンロード中... Completed: 115768K bytes transferred in 4 seconds (209270K 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 14121 0 14121 0 0 20790 0 --:--:-- --:--:-- --:--:-- 28936 100 34848 0 34848 0 0 51231 0 --:--:-- --:--:-- --:--:-- 71263 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 4769560 spots for /home/okishinya/chipatlas/results/dm3/SRX013030/SRR030296.sra Written 4769560 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: 00:00:01 Multiseed full-index search: 00:00:58 4769560 reads; of these: 4769560 (100.00%) were unpaired; of these: 884724 (18.55%) aligned 0 times 3378412 (70.83%) aligned exactly 1 time 506424 (10.62%) aligned >1 times 81.45% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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] 943485 / 3884836 = 0.2429 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 11:59:58: # Command line: callpeak -t SRX013030.bam -f BAM -g dm -n SRX013030.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013030.20 # format = BAM # ChIP-seq file = ['SRX013030.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 11:59:58: # Command line: callpeak -t SRX013030.bam -f BAM -g dm -n SRX013030.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013030.05 # format = BAM # ChIP-seq file = ['SRX013030.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 11:59:58: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:59:58: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:59:58: # Command line: callpeak -t SRX013030.bam -f BAM -g dm -n SRX013030.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013030.10 # format = BAM # ChIP-seq file = ['SRX013030.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 11:59:58: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:59:58: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:59:58: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:59:58: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:00:03: 1000000 INFO @ Tue, 21 Apr 2015 12:00:03: 1000000 INFO @ Tue, 21 Apr 2015 12:00:03: 1000000 INFO @ Tue, 21 Apr 2015 12:00:08: 2000000 INFO @ Tue, 21 Apr 2015 12:00:08: 2000000 INFO @ Tue, 21 Apr 2015 12:00:08: 2000000 INFO @ Tue, 21 Apr 2015 12:00:13: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:00:13: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:00:13: #1 total tags in treatment: 2941351 INFO @ Tue, 21 Apr 2015 12:00:13: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:00:13: #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 12:00:13: #1 tags after filtering in treatment: 2941279 INFO @ Tue, 21 Apr 2015 12:00:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:00:13: #1 finished! INFO @ Tue, 21 Apr 2015 12:00:13: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:00:14: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:00:14: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:00:14: #1 total tags in treatment: 2941351 INFO @ Tue, 21 Apr 2015 12:00:14: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:00:14: #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 12:00:14: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:00:14: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:00:14: #1 total tags in treatment: 2941351 INFO @ Tue, 21 Apr 2015 12:00:14: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:00:14: #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 12:00:14: #1 tags after filtering in treatment: 2941279 INFO @ Tue, 21 Apr 2015 12:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:00:14: #1 finished! INFO @ Tue, 21 Apr 2015 12:00:14: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:00:14: #1 tags after filtering in treatment: 2941279 INFO @ Tue, 21 Apr 2015 12:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:00:14: #1 finished! INFO @ Tue, 21 Apr 2015 12:00:14: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:00:14: #2 number of paired peaks: 3903 INFO @ Tue, 21 Apr 2015 12:00:14: start model_add_line... INFO @ Tue, 21 Apr 2015 12:00:15: #2 number of paired peaks: 3903 INFO @ Tue, 21 Apr 2015 12:00:15: start model_add_line... INFO @ Tue, 21 Apr 2015 12:00:15: #2 number of paired peaks: 3903 INFO @ Tue, 21 Apr 2015 12:00:15: start model_add_line... INFO @ Tue, 21 Apr 2015 12:00:21: start X-correlation... INFO @ Tue, 21 Apr 2015 12:00:21: end of X-cor INFO @ Tue, 21 Apr 2015 12:00:21: #2 finished! INFO @ Tue, 21 Apr 2015 12:00:21: #2 predicted fragment length is 189 bps INFO @ Tue, 21 Apr 2015 12:00:21: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 21 Apr 2015 12:00:21: #2.2 Generate R script for model : SRX013030.05_model.r INFO @ Tue, 21 Apr 2015 12:00:21: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:00:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:00:22: start X-correlation... INFO @ Tue, 21 Apr 2015 12:00:22: end of X-cor INFO @ Tue, 21 Apr 2015 12:00:22: #2 finished! INFO @ Tue, 21 Apr 2015 12:00:22: #2 predicted fragment length is 189 bps INFO @ Tue, 21 Apr 2015 12:00:22: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 21 Apr 2015 12:00:22: #2.2 Generate R script for model : SRX013030.20_model.r INFO @ Tue, 21 Apr 2015 12:00:22: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:00:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:00:22: start X-correlation... INFO @ Tue, 21 Apr 2015 12:00:22: end of X-cor INFO @ Tue, 21 Apr 2015 12:00:22: #2 finished! INFO @ Tue, 21 Apr 2015 12:00:22: #2 predicted fragment length is 189 bps INFO @ Tue, 21 Apr 2015 12:00:22: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 21 Apr 2015 12:00:22: #2.2 Generate R script for model : SRX013030.10_model.r INFO @ Tue, 21 Apr 2015 12:00:22: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:00:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:00:39: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:00:40: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:00:40: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:00:54: #4 Write output xls file... SRX013030.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:00:54: #4 Write peak in narrowPeak format file... SRX013030.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:00:54: #4 Write summits bed file... SRX013030.20_summits.bed INFO @ Tue, 21 Apr 2015 12:00:54: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1538 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:00:55: #4 Write output xls file... SRX013030.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:00:55: #4 Write peak in narrowPeak format file... SRX013030.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:00:55: #4 Write summits bed file... SRX013030.10_summits.bed INFO @ Tue, 21 Apr 2015 12:00:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3352 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:00:56: #4 Write output xls file... SRX013030.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:00:56: #4 Write peak in narrowPeak format file... SRX013030.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:00:56: #4 Write summits bed file... SRX013030.05_summits.bed INFO @ Tue, 21 Apr 2015 12:00:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4923 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。