Job ID = 2161244 sra ファイルのダウンロード中... Completed: 133913K bytes transferred in 4 seconds (232376K 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 17816 0 17816 0 0 25667 0 --:--:-- --:--:-- --:--:-- 35419 100 34457 0 34457 0 0 49584 0 --:--:-- --:--:-- --:--:-- 68367 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 5559475 spots for /home/okishinya/chipatlas/results/dm3/SRX013091/SRR030357.sra Written 5559475 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: 00:01:20 5559475 reads; of these: 5559475 (100.00%) were unpaired; of these: 567105 (10.20%) aligned 0 times 4202171 (75.59%) aligned exactly 1 time 790199 (14.21%) aligned >1 times 89.80% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 1899934 / 4992370 = 0.3806 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 12:09:05: # Command line: callpeak -t SRX013091.bam -f BAM -g dm -n SRX013091.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013091.05 # format = BAM # ChIP-seq file = ['SRX013091.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 12:09:05: # Command line: callpeak -t SRX013091.bam -f BAM -g dm -n SRX013091.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013091.20 # format = BAM # ChIP-seq file = ['SRX013091.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 12:09:05: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:05: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:05: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:05: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:05: # Command line: callpeak -t SRX013091.bam -f BAM -g dm -n SRX013091.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013091.10 # format = BAM # ChIP-seq file = ['SRX013091.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 12:09:05: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:05: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:11: 1000000 INFO @ Tue, 21 Apr 2015 12:09:11: 1000000 INFO @ Tue, 21 Apr 2015 12:09:12: 1000000 INFO @ Tue, 21 Apr 2015 12:09:17: 2000000 INFO @ Tue, 21 Apr 2015 12:09:17: 2000000 INFO @ Tue, 21 Apr 2015 12:09:18: 2000000 INFO @ Tue, 21 Apr 2015 12:09:22: 3000000 INFO @ Tue, 21 Apr 2015 12:09:23: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:23: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:23: #1 total tags in treatment: 3092436 INFO @ Tue, 21 Apr 2015 12:09:23: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:23: #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 12:09:23: #1 tags after filtering in treatment: 3092299 INFO @ Tue, 21 Apr 2015 12:09:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:23: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:24: 3000000 INFO @ Tue, 21 Apr 2015 12:09:24: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:24: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:24: #1 total tags in treatment: 3092436 INFO @ Tue, 21 Apr 2015 12:09:24: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:24: #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 12:09:24: #2 number of paired peaks: 4011 INFO @ Tue, 21 Apr 2015 12:09:24: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:24: 3000000 INFO @ Tue, 21 Apr 2015 12:09:25: #1 tags after filtering in treatment: 3092299 INFO @ Tue, 21 Apr 2015 12:09:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:25: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:25: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:25: #1 total tags in treatment: 3092436 INFO @ Tue, 21 Apr 2015 12:09:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:25: #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 12:09:26: #1 tags after filtering in treatment: 3092299 INFO @ Tue, 21 Apr 2015 12:09:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:26: #2 number of paired peaks: 4011 INFO @ Tue, 21 Apr 2015 12:09:26: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:27: #2 number of paired peaks: 4011 INFO @ Tue, 21 Apr 2015 12:09:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:33: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:33: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:33: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:33: #2 predicted fragment length is 180 bps INFO @ Tue, 21 Apr 2015 12:09:33: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 21 Apr 2015 12:09:33: #2.2 Generate R script for model : SRX013091.05_model.r INFO @ Tue, 21 Apr 2015 12:09:33: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:34: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:34: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:34: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:34: #2 predicted fragment length is 180 bps INFO @ Tue, 21 Apr 2015 12:09:34: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 21 Apr 2015 12:09:34: #2.2 Generate R script for model : SRX013091.10_model.r INFO @ Tue, 21 Apr 2015 12:09:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:34: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:34: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:34: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:34: #2 predicted fragment length is 180 bps INFO @ Tue, 21 Apr 2015 12:09:34: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 21 Apr 2015 12:09:34: #2.2 Generate R script for model : SRX013091.20_model.r INFO @ Tue, 21 Apr 2015 12:09:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:51: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:53: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:54: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:05: #4 Write output xls file... SRX013091.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:05: #4 Write peak in narrowPeak format file... SRX013091.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:05: #4 Write summits bed file... SRX013091.05_summits.bed INFO @ Tue, 21 Apr 2015 12:10:05: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (477 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:10:06: #4 Write output xls file... SRX013091.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:06: #4 Write peak in narrowPeak format file... SRX013091.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:06: #4 Write summits bed file... SRX013091.20_summits.bed INFO @ Tue, 21 Apr 2015 12:10:06: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:10:07: #4 Write output xls file... SRX013091.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:07: #4 Write peak in narrowPeak format file... SRX013091.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:07: #4 Write summits bed file... SRX013091.10_summits.bed INFO @ Tue, 21 Apr 2015 12:10:07: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (317 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。