Job ID = 2161264 sra ファイルのダウンロード中... Completed: 220183K bytes transferred in 5 seconds (342401K 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 --:--:-- --:--:-- --:--:-- 0 101 2540 0 2540 0 0 4596 0 --:--:-- --:--:-- --:--:-- 7016 100 34469 0 34469 0 0 46448 0 --:--:-- --:--:-- --:--:-- 62443 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 8604186 spots for /home/okishinya/chipatlas/results/dm3/SRX013108/SRR030374.sra Written 8604186 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: 00:00:57 8604186 reads; of these: 8604186 (100.00%) were unpaired; of these: 6415824 (74.57%) aligned 0 times 1913514 (22.24%) aligned exactly 1 time 274848 (3.19%) aligned >1 times 25.43% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 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] 1437191 / 2188362 = 0.6567 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 12:11:12: # Command line: callpeak -t SRX013108.bam -f BAM -g dm -n SRX013108.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013108.05 # format = BAM # ChIP-seq file = ['SRX013108.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 12:11:12: # Command line: callpeak -t SRX013108.bam -f BAM -g dm -n SRX013108.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013108.10 # format = BAM # ChIP-seq file = ['SRX013108.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 12:11:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:11:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:11:12: # Command line: callpeak -t SRX013108.bam -f BAM -g dm -n SRX013108.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013108.20 # format = BAM # ChIP-seq file = ['SRX013108.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 12:11:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:11:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:11:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:11:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:11:16: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:11:16: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:11:16: #1 total tags in treatment: 751171 INFO @ Tue, 21 Apr 2015 12:11:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:11:16: #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 12:11:16: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:11:16: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:11:16: #1 total tags in treatment: 751171 INFO @ Tue, 21 Apr 2015 12:11:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:11:16: #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 12:11:16: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:11:16: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:11:16: #1 total tags in treatment: 751171 INFO @ Tue, 21 Apr 2015 12:11:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:11:16: #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 12:11:16: #1 tags after filtering in treatment: 750953 INFO @ Tue, 21 Apr 2015 12:11:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:11:16: #1 finished! INFO @ Tue, 21 Apr 2015 12:11:16: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:11:16: #1 tags after filtering in treatment: 750953 INFO @ Tue, 21 Apr 2015 12:11:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:11:16: #1 finished! INFO @ Tue, 21 Apr 2015 12:11:16: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:11:16: #1 tags after filtering in treatment: 750953 INFO @ Tue, 21 Apr 2015 12:11:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:11:16: #1 finished! INFO @ Tue, 21 Apr 2015 12:11:16: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:11:17: #2 number of paired peaks: 1347 INFO @ Tue, 21 Apr 2015 12:11:17: start model_add_line... INFO @ Tue, 21 Apr 2015 12:11:17: #2 number of paired peaks: 1347 INFO @ Tue, 21 Apr 2015 12:11:17: start model_add_line... INFO @ Tue, 21 Apr 2015 12:11:17: #2 number of paired peaks: 1347 INFO @ Tue, 21 Apr 2015 12:11:17: start model_add_line... INFO @ Tue, 21 Apr 2015 12:11:17: start X-correlation... INFO @ Tue, 21 Apr 2015 12:11:17: start X-correlation... INFO @ Tue, 21 Apr 2015 12:11:17: end of X-cor INFO @ Tue, 21 Apr 2015 12:11:17: end of X-cor INFO @ Tue, 21 Apr 2015 12:11:17: #2 finished! INFO @ Tue, 21 Apr 2015 12:11:17: #2 finished! INFO @ Tue, 21 Apr 2015 12:11:17: #2 predicted fragment length is 74 bps INFO @ Tue, 21 Apr 2015 12:11:17: #2 predicted fragment length is 74 bps INFO @ Tue, 21 Apr 2015 12:11:17: #2 alternative fragment length(s) may be 60,74 bps INFO @ Tue, 21 Apr 2015 12:11:17: #2 alternative fragment length(s) may be 60,74 bps INFO @ Tue, 21 Apr 2015 12:11:17: #2.2 Generate R script for model : SRX013108.20_model.r INFO @ Tue, 21 Apr 2015 12:11:17: #2.2 Generate R script for model : SRX013108.05_model.r INFO @ Tue, 21 Apr 2015 12:11:17: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:11:17: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:11:17: start X-correlation... INFO @ Tue, 21 Apr 2015 12:11:17: end of X-cor INFO @ Tue, 21 Apr 2015 12:11:17: #2 finished! INFO @ Tue, 21 Apr 2015 12:11:17: #2 predicted fragment length is 74 bps INFO @ Tue, 21 Apr 2015 12:11:17: #2 alternative fragment length(s) may be 60,74 bps INFO @ Tue, 21 Apr 2015 12:11:17: #2.2 Generate R script for model : SRX013108.10_model.r INFO @ Tue, 21 Apr 2015 12:11:17: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:11:22: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:11:22: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:11:22: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:11:25: #4 Write output xls file... SRX013108.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:11:25: #4 Write peak in narrowPeak format file... SRX013108.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:11:25: #4 Write summits bed file... SRX013108.20_summits.bed INFO @ Tue, 21 Apr 2015 12:11:25: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (55 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:11:25: #4 Write output xls file... SRX013108.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:11:25: #4 Write peak in narrowPeak format file... SRX013108.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:11:25: #4 Write summits bed file... SRX013108.05_summits.bed INFO @ Tue, 21 Apr 2015 12:11:25: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:11:25: #4 Write output xls file... SRX013108.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:11:25: #4 Write peak in narrowPeak format file... SRX013108.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:11:25: #4 Write summits bed file... SRX013108.10_summits.bed INFO @ Tue, 21 Apr 2015 12:11:25: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (124 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。