Job ID = 2162166 sra ファイルのダウンロード中... Completed: 105914K bytes transferred in 4 seconds (201412K 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 35446 0 35446 0 0 47904 0 --:--:-- --:--:-- --:--:-- 64682 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 5715475 spots for /home/okishinya/chipatlas/results/dm3/SRX050602/SRR139084.sra Written 5715475 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:26 5715475 reads; of these: 5715475 (100.00%) were unpaired; of these: 162579 (2.84%) aligned 0 times 4541788 (79.46%) aligned exactly 1 time 1011108 (17.69%) aligned >1 times 97.16% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 326058 / 5552896 = 0.0587 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 13:34:30: # Command line: callpeak -t SRX050602.bam -f BAM -g dm -n SRX050602.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX050602.10 # format = BAM # ChIP-seq file = ['SRX050602.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 13:34:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:34:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:34:30: # Command line: callpeak -t SRX050602.bam -f BAM -g dm -n SRX050602.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX050602.05 # format = BAM # ChIP-seq file = ['SRX050602.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 13:34:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:34:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:34:30: # Command line: callpeak -t SRX050602.bam -f BAM -g dm -n SRX050602.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX050602.20 # format = BAM # ChIP-seq file = ['SRX050602.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 13:34:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:34:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:34:35: 1000000 INFO @ Tue, 21 Apr 2015 13:34:35: 1000000 INFO @ Tue, 21 Apr 2015 13:34:35: 1000000 INFO @ Tue, 21 Apr 2015 13:34:40: 2000000 INFO @ Tue, 21 Apr 2015 13:34:40: 2000000 INFO @ Tue, 21 Apr 2015 13:34:40: 2000000 INFO @ Tue, 21 Apr 2015 13:34:44: 3000000 INFO @ Tue, 21 Apr 2015 13:34:45: 3000000 INFO @ Tue, 21 Apr 2015 13:34:45: 3000000 INFO @ Tue, 21 Apr 2015 13:34:49: 4000000 INFO @ Tue, 21 Apr 2015 13:34:49: 4000000 INFO @ Tue, 21 Apr 2015 13:34:50: 4000000 INFO @ Tue, 21 Apr 2015 13:34:54: 5000000 INFO @ Tue, 21 Apr 2015 13:34:54: 5000000 INFO @ Tue, 21 Apr 2015 13:34:55: 5000000 INFO @ Tue, 21 Apr 2015 13:34:55: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:34:55: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:34:55: #1 total tags in treatment: 5226838 INFO @ Tue, 21 Apr 2015 13:34:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:34:55: #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 13:34:55: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:34:55: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:34:55: #1 total tags in treatment: 5226838 INFO @ Tue, 21 Apr 2015 13:34:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:34:55: #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 13:34:56: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:34:56: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:34:56: #1 total tags in treatment: 5226838 INFO @ Tue, 21 Apr 2015 13:34:56: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:34:56: #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 13:34:56: #1 tags after filtering in treatment: 5226706 INFO @ Tue, 21 Apr 2015 13:34:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:34:56: #1 finished! INFO @ Tue, 21 Apr 2015 13:34:56: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:34:56: #1 tags after filtering in treatment: 5226706 INFO @ Tue, 21 Apr 2015 13:34:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:34:56: #1 finished! INFO @ Tue, 21 Apr 2015 13:34:56: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:34:57: #1 tags after filtering in treatment: 5226706 INFO @ Tue, 21 Apr 2015 13:34:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:34:57: #1 finished! INFO @ Tue, 21 Apr 2015 13:34:57: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:34:57: #2 number of paired peaks: 1165 INFO @ Tue, 21 Apr 2015 13:34:57: start model_add_line... INFO @ Tue, 21 Apr 2015 13:34:57: #2 number of paired peaks: 1165 INFO @ Tue, 21 Apr 2015 13:34:57: start model_add_line... INFO @ Tue, 21 Apr 2015 13:34:58: #2 number of paired peaks: 1165 INFO @ Tue, 21 Apr 2015 13:34:58: start model_add_line... INFO @ Tue, 21 Apr 2015 13:35:01: start X-correlation... INFO @ Tue, 21 Apr 2015 13:35:01: end of X-cor INFO @ Tue, 21 Apr 2015 13:35:01: #2 finished! INFO @ Tue, 21 Apr 2015 13:35:01: #2 predicted fragment length is 92 bps INFO @ Tue, 21 Apr 2015 13:35:01: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 21 Apr 2015 13:35:01: #2.2 Generate R script for model : SRX050602.10_model.r INFO @ Tue, 21 Apr 2015 13:35:01: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:35:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:35:01: start X-correlation... INFO @ Tue, 21 Apr 2015 13:35:01: end of X-cor INFO @ Tue, 21 Apr 2015 13:35:01: #2 finished! INFO @ Tue, 21 Apr 2015 13:35:01: #2 predicted fragment length is 92 bps INFO @ Tue, 21 Apr 2015 13:35:01: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 21 Apr 2015 13:35:01: #2.2 Generate R script for model : SRX050602.20_model.r INFO @ Tue, 21 Apr 2015 13:35:01: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:35:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:35:01: start X-correlation... INFO @ Tue, 21 Apr 2015 13:35:02: end of X-cor INFO @ Tue, 21 Apr 2015 13:35:02: #2 finished! INFO @ Tue, 21 Apr 2015 13:35:02: #2 predicted fragment length is 92 bps INFO @ Tue, 21 Apr 2015 13:35:02: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 21 Apr 2015 13:35:02: #2.2 Generate R script for model : SRX050602.05_model.r INFO @ Tue, 21 Apr 2015 13:35:02: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:35:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:35:31: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:35:31: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:35:33: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:35:54: #4 Write output xls file... SRX050602.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:35:54: #4 Write peak in narrowPeak format file... SRX050602.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:35:54: #4 Write summits bed file... SRX050602.10_summits.bed INFO @ Tue, 21 Apr 2015 13:35:54: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2695 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:35:55: #4 Write output xls file... SRX050602.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:35:55: #4 Write peak in narrowPeak format file... SRX050602.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:35:55: #4 Write summits bed file... SRX050602.05_summits.bed INFO @ Tue, 21 Apr 2015 13:35:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4248 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:35:57: #4 Write output xls file... SRX050602.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:35:57: #4 Write peak in narrowPeak format file... SRX050602.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:35:57: #4 Write summits bed file... SRX050602.20_summits.bed INFO @ Tue, 21 Apr 2015 13:35:57: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1490 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。