Job ID = 2161267 sra ファイルのダウンロード中... Completed: 9414K bytes transferred in 3 seconds (24132K 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 34494 0 34494 0 0 48690 0 --:--:-- --:--:-- --:--:-- 66719 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 469851 spots for /home/okishinya/chipatlas/results/dm3/SRX013111/SRR030377.sra Written 469851 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: 00:00:07 469851 reads; of these: 469851 (100.00%) were unpaired; of these: 42104 (8.96%) aligned 0 times 360847 (76.80%) aligned exactly 1 time 66900 (14.24%) aligned >1 times 91.04% overall alignment rate Time searching: 00:00:07 Overall time: 00:00:07 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] 38895 / 427747 = 0.0909 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 12:09:50: # Command line: callpeak -t SRX013111.bam -f BAM -g dm -n SRX013111.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013111.10 # format = BAM # ChIP-seq file = ['SRX013111.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 12:09:50: # Command line: callpeak -t SRX013111.bam -f BAM -g dm -n SRX013111.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013111.05 # format = BAM # ChIP-seq file = ['SRX013111.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 12:09:50: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:50: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:50: # Command line: callpeak -t SRX013111.bam -f BAM -g dm -n SRX013111.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013111.20 # format = BAM # ChIP-seq file = ['SRX013111.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 12:09:50: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:50: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:50: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:50: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:52: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:52: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:52: #1 total tags in treatment: 388852 INFO @ Tue, 21 Apr 2015 12:09:52: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:52: #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 12:09:52: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:52: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:52: #1 total tags in treatment: 388852 INFO @ Tue, 21 Apr 2015 12:09:52: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:52: #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 12:09:52: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:52: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:52: #1 total tags in treatment: 388852 INFO @ Tue, 21 Apr 2015 12:09:52: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:52: #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 12:09:52: #1 tags after filtering in treatment: 388842 INFO @ Tue, 21 Apr 2015 12:09:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:52: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:52: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:52: #1 tags after filtering in treatment: 388842 INFO @ Tue, 21 Apr 2015 12:09:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:52: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:52: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:52: #1 tags after filtering in treatment: 388842 INFO @ Tue, 21 Apr 2015 12:09:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:52: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:52: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:53: #2 number of paired peaks: 2369 INFO @ Tue, 21 Apr 2015 12:09:53: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:53: #2 number of paired peaks: 2369 INFO @ Tue, 21 Apr 2015 12:09:53: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:53: #2 number of paired peaks: 2369 INFO @ Tue, 21 Apr 2015 12:09:53: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:53: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:53: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:53: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:53: #2 predicted fragment length is 164 bps INFO @ Tue, 21 Apr 2015 12:09:53: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 21 Apr 2015 12:09:53: #2.2 Generate R script for model : SRX013111.20_model.r INFO @ Tue, 21 Apr 2015 12:09:53: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:53: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:53: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:53: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:53: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:53: #2 predicted fragment length is 164 bps INFO @ Tue, 21 Apr 2015 12:09:53: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 21 Apr 2015 12:09:53: #2.2 Generate R script for model : SRX013111.05_model.r INFO @ Tue, 21 Apr 2015 12:09:53: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:53: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:53: #2 predicted fragment length is 164 bps INFO @ Tue, 21 Apr 2015 12:09:53: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 21 Apr 2015 12:09:53: #2.2 Generate R script for model : SRX013111.10_model.r INFO @ Tue, 21 Apr 2015 12:09:53: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:53: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:55: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:57: #4 Write output xls file... SRX013111.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:57: #4 Write peak in narrowPeak format file... SRX013111.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:57: #4 Write summits bed file... SRX013111.20_summits.bed INFO @ Tue, 21 Apr 2015 12:09:57: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:09:57: #4 Write output xls file... SRX013111.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:57: #4 Write peak in narrowPeak format file... SRX013111.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:57: #4 Write summits bed file... SRX013111.10_summits.bed INFO @ Tue, 21 Apr 2015 12:09:57: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (15 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:09:57: #4 Write output xls file... SRX013111.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:57: #4 Write peak in narrowPeak format file... SRX013111.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:57: #4 Write summits bed file... SRX013111.05_summits.bed INFO @ Tue, 21 Apr 2015 12:09:57: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (42 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。