Job ID = 2161145 sra ファイルのダウンロード中... Completed: 159351K bytes transferred in 4 seconds (263980K 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 34548 0 34548 0 0 50070 0 --:--:-- --:--:-- --:--:-- 69234 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 7318708 spots for /home/okishinya/chipatlas/results/dm3/SRX013026/SRR030292.sra Written 7318708 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: 00:01:44 7318708 reads; of these: 7318708 (100.00%) were unpaired; of these: 565361 (7.72%) aligned 0 times 5744034 (78.48%) aligned exactly 1 time 1009313 (13.79%) aligned >1 times 92.28% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:45 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] 436902 / 6753347 = 0.0647 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 12:01:01: # Command line: callpeak -t SRX013026.bam -f BAM -g dm -n SRX013026.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013026.05 # format = BAM # ChIP-seq file = ['SRX013026.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 12:01:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:01:01: # Command line: callpeak -t SRX013026.bam -f BAM -g dm -n SRX013026.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013026.20 # format = BAM # ChIP-seq file = ['SRX013026.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 12:01:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:01:01: # Command line: callpeak -t SRX013026.bam -f BAM -g dm -n SRX013026.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013026.10 # format = BAM # ChIP-seq file = ['SRX013026.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 12:01:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:01:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:01:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:01:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:01:06: 1000000 INFO @ Tue, 21 Apr 2015 12:01:07: 1000000 INFO @ Tue, 21 Apr 2015 12:01:07: 1000000 INFO @ Tue, 21 Apr 2015 12:01:12: 2000000 INFO @ Tue, 21 Apr 2015 12:01:13: 2000000 INFO @ Tue, 21 Apr 2015 12:01:13: 2000000 INFO @ Tue, 21 Apr 2015 12:01:17: 3000000 INFO @ Tue, 21 Apr 2015 12:01:18: 3000000 INFO @ Tue, 21 Apr 2015 12:01:18: 3000000 INFO @ Tue, 21 Apr 2015 12:01:22: 4000000 INFO @ Tue, 21 Apr 2015 12:01:24: 4000000 INFO @ Tue, 21 Apr 2015 12:01:24: 4000000 INFO @ Tue, 21 Apr 2015 12:01:27: 5000000 INFO @ Tue, 21 Apr 2015 12:01:30: 5000000 INFO @ Tue, 21 Apr 2015 12:01:30: 5000000 INFO @ Tue, 21 Apr 2015 12:01:33: 6000000 INFO @ Tue, 21 Apr 2015 12:01:34: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:01:34: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:01:34: #1 total tags in treatment: 6316445 INFO @ Tue, 21 Apr 2015 12:01:34: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:01:34: #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 12:01:36: #1 tags after filtering in treatment: 6316243 INFO @ Tue, 21 Apr 2015 12:01:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:01:36: #1 finished! INFO @ Tue, 21 Apr 2015 12:01:36: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:01:36: 6000000 INFO @ Tue, 21 Apr 2015 12:01:36: 6000000 INFO @ Tue, 21 Apr 2015 12:01:37: #2 number of paired peaks: 2229 INFO @ Tue, 21 Apr 2015 12:01:37: start model_add_line... INFO @ Tue, 21 Apr 2015 12:01:38: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:01:38: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:01:38: #1 total tags in treatment: 6316445 INFO @ Tue, 21 Apr 2015 12:01:38: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:01:38: #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 12:01:38: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:01:38: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:01:38: #1 total tags in treatment: 6316445 INFO @ Tue, 21 Apr 2015 12:01:38: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:01:38: #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 12:01:39: #1 tags after filtering in treatment: 6316243 INFO @ Tue, 21 Apr 2015 12:01:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:01:39: #1 finished! INFO @ Tue, 21 Apr 2015 12:01:39: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:01:39: #1 tags after filtering in treatment: 6316243 INFO @ Tue, 21 Apr 2015 12:01:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:01:39: #1 finished! INFO @ Tue, 21 Apr 2015 12:01:39: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:01:40: #2 number of paired peaks: 2229 INFO @ Tue, 21 Apr 2015 12:01:40: start model_add_line... INFO @ Tue, 21 Apr 2015 12:01:40: #2 number of paired peaks: 2229 INFO @ Tue, 21 Apr 2015 12:01:40: start model_add_line... INFO @ Tue, 21 Apr 2015 12:01:46: start X-correlation... INFO @ Tue, 21 Apr 2015 12:01:46: end of X-cor INFO @ Tue, 21 Apr 2015 12:01:46: #2 finished! INFO @ Tue, 21 Apr 2015 12:01:46: #2 predicted fragment length is 156 bps INFO @ Tue, 21 Apr 2015 12:01:46: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 21 Apr 2015 12:01:46: #2.2 Generate R script for model : SRX013026.20_model.r INFO @ Tue, 21 Apr 2015 12:01:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:01:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:01:49: start X-correlation... INFO @ Tue, 21 Apr 2015 12:01:49: end of X-cor INFO @ Tue, 21 Apr 2015 12:01:49: #2 finished! INFO @ Tue, 21 Apr 2015 12:01:49: #2 predicted fragment length is 156 bps INFO @ Tue, 21 Apr 2015 12:01:49: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 21 Apr 2015 12:01:49: #2.2 Generate R script for model : SRX013026.05_model.r INFO @ Tue, 21 Apr 2015 12:01:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:01:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:01:49: start X-correlation... INFO @ Tue, 21 Apr 2015 12:01:49: end of X-cor INFO @ Tue, 21 Apr 2015 12:01:49: #2 finished! INFO @ Tue, 21 Apr 2015 12:01:49: #2 predicted fragment length is 156 bps INFO @ Tue, 21 Apr 2015 12:01:49: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 21 Apr 2015 12:01:49: #2.2 Generate R script for model : SRX013026.10_model.r INFO @ Tue, 21 Apr 2015 12:01:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:01:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:02:24: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:02:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:02:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:02:52: #4 Write output xls file... SRX013026.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:02:52: #4 Write peak in narrowPeak format file... SRX013026.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:02:52: #4 Write summits bed file... SRX013026.20_summits.bed INFO @ Tue, 21 Apr 2015 12:02:52: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1343 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:02:53: #4 Write output xls file... SRX013026.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:02:53: #4 Write peak in narrowPeak format file... SRX013026.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:02:53: #4 Write summits bed file... SRX013026.10_summits.bed INFO @ Tue, 21 Apr 2015 12:02:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3764 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:02:56: #4 Write output xls file... SRX013026.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:02:56: #4 Write peak in narrowPeak format file... SRX013026.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:02:56: #4 Write summits bed file... SRX013026.05_summits.bed INFO @ Tue, 21 Apr 2015 12:02:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6399 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。