Job ID = 2161261 sra ファイルのダウンロード中... Completed: 10265K bytes transferred in 3 seconds (26085K 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 34120 0 34120 0 0 49986 0 --:--:-- --:--:-- --:--:-- 69490 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 445788 spots for /home/okishinya/chipatlas/results/dm3/SRX013105/SRR030371.sra Written 445788 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: 00:00:06 445788 reads; of these: 445788 (100.00%) were unpaired; of these: 47950 (10.76%) aligned 0 times 358574 (80.44%) aligned exactly 1 time 39264 (8.81%) aligned >1 times 89.24% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 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] 15689 / 397838 = 0.0394 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 12:09:19: # Command line: callpeak -t SRX013105.bam -f BAM -g dm -n SRX013105.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013105.05 # format = BAM # ChIP-seq file = ['SRX013105.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 12:09:19: # Command line: callpeak -t SRX013105.bam -f BAM -g dm -n SRX013105.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013105.10 # format = BAM # ChIP-seq file = ['SRX013105.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 12:09:19: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:19: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:19: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:19: # Command line: callpeak -t SRX013105.bam -f BAM -g dm -n SRX013105.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013105.20 # format = BAM # ChIP-seq file = ['SRX013105.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 12:09:19: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:19: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:19: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:21: #1 total tags in treatment: 382149 INFO @ Tue, 21 Apr 2015 12:09:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:21: #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 12:09:21: #1 tags after filtering in treatment: 382143 INFO @ Tue, 21 Apr 2015 12:09:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:21: #1 total tags in treatment: 382149 INFO @ Tue, 21 Apr 2015 12:09:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:21: #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 12:09:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:21: #1 total tags in treatment: 382149 INFO @ Tue, 21 Apr 2015 12:09:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:21: #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 12:09:21: #1 tags after filtering in treatment: 382143 INFO @ Tue, 21 Apr 2015 12:09:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:21: #1 tags after filtering in treatment: 382143 INFO @ Tue, 21 Apr 2015 12:09:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:22: #2 number of paired peaks: 3672 INFO @ Tue, 21 Apr 2015 12:09:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:22: #2 number of paired peaks: 3672 INFO @ Tue, 21 Apr 2015 12:09:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:22: #2 number of paired peaks: 3672 INFO @ Tue, 21 Apr 2015 12:09:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:23: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:23: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:23: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:23: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:23: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:23: #2 predicted fragment length is 185 bps INFO @ Tue, 21 Apr 2015 12:09:23: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 21 Apr 2015 12:09:23: #2.2 Generate R script for model : SRX013105.20_model.r INFO @ Tue, 21 Apr 2015 12:09:23: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:23: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:23: #2 predicted fragment length is 185 bps INFO @ Tue, 21 Apr 2015 12:09:23: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 21 Apr 2015 12:09:23: #2.2 Generate R script for model : SRX013105.05_model.r INFO @ Tue, 21 Apr 2015 12:09:23: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:23: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:23: #2 predicted fragment length is 185 bps INFO @ Tue, 21 Apr 2015 12:09:23: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 21 Apr 2015 12:09:23: #2.2 Generate R script for model : SRX013105.10_model.r INFO @ Tue, 21 Apr 2015 12:09:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:25: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:25: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:25: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:27: #4 Write output xls file... SRX013105.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:27: #4 Write peak in narrowPeak format file... SRX013105.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:27: #4 Write summits bed file... SRX013105.05_summits.bed INFO @ Tue, 21 Apr 2015 12:09:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (141 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:09:27: #4 Write output xls file... SRX013105.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:27: #4 Write peak in narrowPeak format file... SRX013105.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:27: #4 Write summits bed file... SRX013105.10_summits.bed INFO @ Tue, 21 Apr 2015 12:09:27: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:09:27: #4 Write output xls file... SRX013105.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:27: #4 Write peak in narrowPeak format file... SRX013105.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:27: #4 Write summits bed file... SRX013105.20_summits.bed INFO @ Tue, 21 Apr 2015 12:09:27: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。