Job ID = 2161201 sra ファイルのダウンロード中... Completed: 43304K bytes transferred in 3 seconds (89470K 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 34425 0 34425 0 0 50614 0 --:--:-- --:--:-- --:--:-- 70398 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 1936311 spots for /home/okishinya/chipatlas/results/dm3/SRX013049/SRR030315.sra Written 1936311 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:24 1936311 reads; of these: 1936311 (100.00%) were unpaired; of these: 176661 (9.12%) aligned 0 times 1585607 (81.89%) aligned exactly 1 time 174043 (8.99%) aligned >1 times 90.88% overall alignment rate Time searching: 00:00:25 Overall time: 00:00:25 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] 570817 / 1759650 = 0.3244 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 12:02:01: # Command line: callpeak -t SRX013049.bam -f BAM -g dm -n SRX013049.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013049.10 # format = BAM # ChIP-seq file = ['SRX013049.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 12:02:01: # Command line: callpeak -t SRX013049.bam -f BAM -g dm -n SRX013049.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013049.05 # format = BAM # ChIP-seq file = ['SRX013049.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 12:02:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:02:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:02:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:02:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:02:01: # Command line: callpeak -t SRX013049.bam -f BAM -g dm -n SRX013049.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013049.20 # format = BAM # ChIP-seq file = ['SRX013049.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 12:02:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:02:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:02:07: 1000000 INFO @ Tue, 21 Apr 2015 12:02:08: 1000000 INFO @ Tue, 21 Apr 2015 12:02:08: 1000000 INFO @ Tue, 21 Apr 2015 12:02:08: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:02:08: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:02:08: #1 total tags in treatment: 1188833 INFO @ Tue, 21 Apr 2015 12:02:08: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:02:08: #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 12:02:08: #1 tags after filtering in treatment: 1188806 INFO @ Tue, 21 Apr 2015 12:02:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:02:08: #1 finished! INFO @ Tue, 21 Apr 2015 12:02:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:02:09: #2 number of paired peaks: 4549 INFO @ Tue, 21 Apr 2015 12:02:09: start model_add_line... INFO @ Tue, 21 Apr 2015 12:02:09: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:02:09: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:02:09: #1 total tags in treatment: 1188833 INFO @ Tue, 21 Apr 2015 12:02:09: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:02:09: #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 12:02:09: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:02:09: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:02:09: #1 total tags in treatment: 1188833 INFO @ Tue, 21 Apr 2015 12:02:09: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:02:09: #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 12:02:09: #1 tags after filtering in treatment: 1188806 INFO @ Tue, 21 Apr 2015 12:02:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:02:09: #1 finished! INFO @ Tue, 21 Apr 2015 12:02:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:02:09: #1 tags after filtering in treatment: 1188806 INFO @ Tue, 21 Apr 2015 12:02:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:02:09: #1 finished! INFO @ Tue, 21 Apr 2015 12:02:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:02:10: #2 number of paired peaks: 4549 INFO @ Tue, 21 Apr 2015 12:02:10: start model_add_line... INFO @ Tue, 21 Apr 2015 12:02:10: #2 number of paired peaks: 4549 INFO @ Tue, 21 Apr 2015 12:02:10: start model_add_line... INFO @ Tue, 21 Apr 2015 12:02:13: start X-correlation... INFO @ Tue, 21 Apr 2015 12:02:13: end of X-cor INFO @ Tue, 21 Apr 2015 12:02:13: #2 finished! INFO @ Tue, 21 Apr 2015 12:02:13: #2 predicted fragment length is 253 bps INFO @ Tue, 21 Apr 2015 12:02:13: #2 alternative fragment length(s) may be 253 bps INFO @ Tue, 21 Apr 2015 12:02:13: #2.2 Generate R script for model : SRX013049.20_model.r INFO @ Tue, 21 Apr 2015 12:02:13: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:02:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:02:14: start X-correlation... INFO @ Tue, 21 Apr 2015 12:02:14: end of X-cor INFO @ Tue, 21 Apr 2015 12:02:14: #2 finished! INFO @ Tue, 21 Apr 2015 12:02:14: #2 predicted fragment length is 253 bps INFO @ Tue, 21 Apr 2015 12:02:14: #2 alternative fragment length(s) may be 253 bps INFO @ Tue, 21 Apr 2015 12:02:14: #2.2 Generate R script for model : SRX013049.05_model.r INFO @ Tue, 21 Apr 2015 12:02:14: start X-correlation... INFO @ Tue, 21 Apr 2015 12:02:14: end of X-cor INFO @ Tue, 21 Apr 2015 12:02:14: #2 finished! INFO @ Tue, 21 Apr 2015 12:02:14: #2 predicted fragment length is 253 bps INFO @ Tue, 21 Apr 2015 12:02:14: #2 alternative fragment length(s) may be 253 bps INFO @ Tue, 21 Apr 2015 12:02:14: #2.2 Generate R script for model : SRX013049.10_model.r INFO @ Tue, 21 Apr 2015 12:02:14: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:02:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:02:14: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:02:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:02:22: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:02:22: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:02:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 21 Apr 2015 12:02:27: #4 Write output xls file... SRX013049.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:02:27: #4 Write peak in narrowPeak format file... SRX013049.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:02:27: #4 Write summits bed file... SRX013049.20_summits.bed INFO @ Tue, 21 Apr 2015 12:02:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (342 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:02:28: #4 Write output xls file... SRX013049.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:02:28: #4 Write peak in narrowPeak format file... SRX013049.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:02:28: #4 Write summits bed file... SRX013049.10_summits.bed INFO @ Tue, 21 Apr 2015 12:02:28: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1003 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:02:28: #4 Write output xls file... SRX013049.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:02:28: #4 Write peak in narrowPeak format file... SRX013049.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:02:28: #4 Write summits bed file... SRX013049.05_summits.bed INFO @ Tue, 21 Apr 2015 12:02:28: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (2323 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。