Job ID = 2162434 sra ファイルのダウンロード中... Completed: 189958K bytes transferred in 5 seconds (277898K 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 5460 0 5460 0 0 9568 0 --:--:-- --:--:-- --:--:-- 14368 100 38440 0 38440 0 0 50563 0 --:--:-- --:--:-- --:--:-- 67557 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 7011050 spots for /home/okishinya/chipatlas/results/dm3/SRX099638/SRR350628.sra Written 7011050 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: 00:03:50 7011050 reads; of these: 7011050 (100.00%) were unpaired; of these: 534323 (7.62%) aligned 0 times 1285318 (18.33%) aligned exactly 1 time 5191409 (74.05%) aligned >1 times 92.38% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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] 5910212 / 6476727 = 0.9125 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 14:01:29: # Command line: callpeak -t SRX099638.bam -f BAM -g dm -n SRX099638.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX099638.05 # format = BAM # ChIP-seq file = ['SRX099638.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 14:01:29: # Command line: callpeak -t SRX099638.bam -f BAM -g dm -n SRX099638.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX099638.20 # format = BAM # ChIP-seq file = ['SRX099638.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 14:01:29: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:01:29: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:01:29: # Command line: callpeak -t SRX099638.bam -f BAM -g dm -n SRX099638.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX099638.10 # format = BAM # ChIP-seq file = ['SRX099638.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 14:01:29: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:01:29: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:01:29: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:01:29: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:01:32: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 14:01:32: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 14:01:32: #1 total tags in treatment: 566515 INFO @ Tue, 21 Apr 2015 14:01:32: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:01:32: #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 14:01:32: #1 tags after filtering in treatment: 566064 INFO @ Tue, 21 Apr 2015 14:01:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:01:32: #1 finished! INFO @ Tue, 21 Apr 2015 14:01:32: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:01:32: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 14:01:32: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 14:01:32: #1 total tags in treatment: 566515 INFO @ Tue, 21 Apr 2015 14:01:32: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:01:32: #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 14:01:32: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 14:01:32: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 14:01:32: #1 total tags in treatment: 566515 INFO @ Tue, 21 Apr 2015 14:01:32: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:01:32: #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 14:01:32: #1 tags after filtering in treatment: 566064 INFO @ Tue, 21 Apr 2015 14:01:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:01:32: #1 finished! INFO @ Tue, 21 Apr 2015 14:01:32: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:01:32: #1 tags after filtering in treatment: 566064 INFO @ Tue, 21 Apr 2015 14:01:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:01:32: #1 finished! INFO @ Tue, 21 Apr 2015 14:01:32: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:01:32: #2 number of paired peaks: 1866 INFO @ Tue, 21 Apr 2015 14:01:32: start model_add_line... INFO @ Tue, 21 Apr 2015 14:01:32: #2 number of paired peaks: 1866 INFO @ Tue, 21 Apr 2015 14:01:32: start model_add_line... INFO @ Tue, 21 Apr 2015 14:01:32: #2 number of paired peaks: 1866 INFO @ Tue, 21 Apr 2015 14:01:32: start model_add_line... INFO @ Tue, 21 Apr 2015 14:01:33: start X-correlation... INFO @ Tue, 21 Apr 2015 14:01:33: end of X-cor INFO @ Tue, 21 Apr 2015 14:01:33: #2 finished! INFO @ Tue, 21 Apr 2015 14:01:33: #2 predicted fragment length is 135 bps INFO @ Tue, 21 Apr 2015 14:01:33: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 21 Apr 2015 14:01:33: #2.2 Generate R script for model : SRX099638.05_model.r INFO @ Tue, 21 Apr 2015 14:01:33: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:01:33: start X-correlation... INFO @ Tue, 21 Apr 2015 14:01:33: end of X-cor INFO @ Tue, 21 Apr 2015 14:01:33: #2 finished! INFO @ Tue, 21 Apr 2015 14:01:33: #2 predicted fragment length is 135 bps INFO @ Tue, 21 Apr 2015 14:01:33: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 21 Apr 2015 14:01:33: #2.2 Generate R script for model : SRX099638.20_model.r INFO @ Tue, 21 Apr 2015 14:01:33: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:01:33: start X-correlation... INFO @ Tue, 21 Apr 2015 14:01:33: end of X-cor INFO @ Tue, 21 Apr 2015 14:01:33: #2 finished! INFO @ Tue, 21 Apr 2015 14:01:33: #2 predicted fragment length is 135 bps INFO @ Tue, 21 Apr 2015 14:01:33: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 21 Apr 2015 14:01:33: #2.2 Generate R script for model : SRX099638.10_model.r INFO @ Tue, 21 Apr 2015 14:01:33: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:01:37: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:01:37: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:01:37: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 21 Apr 2015 14:01:41: #4 Write output xls file... SRX099638.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:01:41: #4 Write peak in narrowPeak format file... SRX099638.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:01:41: #4 Write summits bed file... SRX099638.20_summits.bed INFO @ Tue, 21 Apr 2015 14:01:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2134 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:01:42: #4 Write output xls file... SRX099638.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:01:42: #4 Write output xls file... SRX099638.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:01:42: #4 Write peak in narrowPeak format file... SRX099638.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:01:42: #4 Write peak in narrowPeak format file... SRX099638.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:01:42: #4 Write summits bed file... SRX099638.10_summits.bed INFO @ Tue, 21 Apr 2015 14:01:42: #4 Write summits bed file... SRX099638.05_summits.bed INFO @ Tue, 21 Apr 2015 14:01:42: Done! INFO @ Tue, 21 Apr 2015 14:01:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2757 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3474 records, 4 fields): 6 millis CompletedMACS2peakCalling