Job ID = 2161243 sra ファイルのダウンロード中... Completed: 148103K bytes transferred in 4 seconds (256550K 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 12759 0 12759 0 0 22329 0 --:--:-- --:--:-- --:--:-- 33488 100 34750 0 34750 0 0 45671 0 --:--:-- --:--:-- --:--:-- 60964 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 7308316 spots for /home/okishinya/chipatlas/results/dm3/SRX013090/SRR030356.sra Written 7308316 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: 00:01:43 7308316 reads; of these: 7308316 (100.00%) were unpaired; of these: 196669 (2.69%) aligned 0 times 6158904 (84.27%) aligned exactly 1 time 952743 (13.04%) aligned >1 times 97.31% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 1009979 / 7111647 = 0.1420 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 12:09:54: # Command line: callpeak -t SRX013090.bam -f BAM -g dm -n SRX013090.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013090.05 # format = BAM # ChIP-seq file = ['SRX013090.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 12:09:54: # Command line: callpeak -t SRX013090.bam -f BAM -g dm -n SRX013090.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013090.10 # format = BAM # ChIP-seq file = ['SRX013090.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 12:09:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:54: # Command line: callpeak -t SRX013090.bam -f BAM -g dm -n SRX013090.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013090.20 # format = BAM # ChIP-seq file = ['SRX013090.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 12:09:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:09:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:59: 1000000 INFO @ Tue, 21 Apr 2015 12:09:59: 1000000 INFO @ Tue, 21 Apr 2015 12:09:59: 1000000 INFO @ Tue, 21 Apr 2015 12:10:04: 2000000 INFO @ Tue, 21 Apr 2015 12:10:04: 2000000 INFO @ Tue, 21 Apr 2015 12:10:04: 2000000 INFO @ Tue, 21 Apr 2015 12:10:09: 3000000 INFO @ Tue, 21 Apr 2015 12:10:09: 3000000 INFO @ Tue, 21 Apr 2015 12:10:09: 3000000 INFO @ Tue, 21 Apr 2015 12:10:14: 4000000 INFO @ Tue, 21 Apr 2015 12:10:14: 4000000 INFO @ Tue, 21 Apr 2015 12:10:14: 4000000 INFO @ Tue, 21 Apr 2015 12:10:19: 5000000 INFO @ Tue, 21 Apr 2015 12:10:19: 5000000 INFO @ Tue, 21 Apr 2015 12:10:19: 5000000 INFO @ Tue, 21 Apr 2015 12:10:24: 6000000 INFO @ Tue, 21 Apr 2015 12:10:24: 6000000 INFO @ Tue, 21 Apr 2015 12:10:24: 6000000 INFO @ Tue, 21 Apr 2015 12:10:24: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:10:24: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:10:24: #1 total tags in treatment: 6101668 INFO @ Tue, 21 Apr 2015 12:10:24: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:10:24: #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 12:10:24: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:10:24: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:10:24: #1 total tags in treatment: 6101668 INFO @ Tue, 21 Apr 2015 12:10:24: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:10:24: #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 12:10:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:10:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:10:25: #1 total tags in treatment: 6101668 INFO @ Tue, 21 Apr 2015 12:10:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:10:25: #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 12:10:25: #1 tags after filtering in treatment: 6101371 INFO @ Tue, 21 Apr 2015 12:10:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:10:25: #1 finished! INFO @ Tue, 21 Apr 2015 12:10:25: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:10:25: #1 tags after filtering in treatment: 6101371 INFO @ Tue, 21 Apr 2015 12:10:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:10:25: #1 finished! INFO @ Tue, 21 Apr 2015 12:10:25: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:10:26: #1 tags after filtering in treatment: 6101371 INFO @ Tue, 21 Apr 2015 12:10:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:10:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:10:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:10:27: #2 number of paired peaks: 4650 INFO @ Tue, 21 Apr 2015 12:10:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:10:27: #2 number of paired peaks: 4650 INFO @ Tue, 21 Apr 2015 12:10:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:10:27: #2 number of paired peaks: 4650 INFO @ Tue, 21 Apr 2015 12:10:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:10:46: start X-correlation... INFO @ Tue, 21 Apr 2015 12:10:46: end of X-cor INFO @ Tue, 21 Apr 2015 12:10:46: #2 finished! INFO @ Tue, 21 Apr 2015 12:10:46: #2 predicted fragment length is 194 bps INFO @ Tue, 21 Apr 2015 12:10:46: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 21 Apr 2015 12:10:46: #2.2 Generate R script for model : SRX013090.20_model.r INFO @ Tue, 21 Apr 2015 12:10:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:10:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:10:46: start X-correlation... INFO @ Tue, 21 Apr 2015 12:10:46: end of X-cor INFO @ Tue, 21 Apr 2015 12:10:46: #2 finished! INFO @ Tue, 21 Apr 2015 12:10:46: #2 predicted fragment length is 194 bps INFO @ Tue, 21 Apr 2015 12:10:46: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 21 Apr 2015 12:10:46: #2.2 Generate R script for model : SRX013090.05_model.r INFO @ Tue, 21 Apr 2015 12:10:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:10:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:10:46: start X-correlation... INFO @ Tue, 21 Apr 2015 12:10:46: end of X-cor INFO @ Tue, 21 Apr 2015 12:10:46: #2 finished! INFO @ Tue, 21 Apr 2015 12:10:46: #2 predicted fragment length is 194 bps INFO @ Tue, 21 Apr 2015 12:10:46: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 21 Apr 2015 12:10:46: #2.2 Generate R script for model : SRX013090.10_model.r INFO @ Tue, 21 Apr 2015 12:10:47: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:10:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:11:25: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:11:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:11:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:11:50: #4 Write output xls file... SRX013090.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:11:50: #4 Write peak in narrowPeak format file... SRX013090.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:11:50: #4 Write summits bed file... SRX013090.20_summits.bed INFO @ Tue, 21 Apr 2015 12:11:50: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (474 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:11:53: #4 Write output xls file... SRX013090.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:11:53: #4 Write peak in narrowPeak format file... SRX013090.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:11:53: #4 Write summits bed file... SRX013090.10_summits.bed INFO @ Tue, 21 Apr 2015 12:11:53: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1519 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:11:56: #4 Write output xls file... SRX013090.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:11:56: #4 Write peak in narrowPeak format file... SRX013090.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:11:56: #4 Write summits bed file... SRX013090.05_summits.bed INFO @ Tue, 21 Apr 2015 12:11:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3827 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。