Job ID = 2161907 sra ファイルのダウンロード中... Completed: 332567K bytes transferred in 5 seconds (454364K 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 2547 0 2547 0 0 4113 0 --:--:-- --:--:-- --:--:-- 5937 100 35679 0 35679 0 0 44101 0 --:--:-- --:--:-- --:--:-- 57639 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 12133630 spots for /home/okishinya/chipatlas/results/dm3/SRX040611/SRR097980.sra Written 12133630 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: 00:02:22 12133630 reads; of these: 12133630 (100.00%) were unpaired; of these: 605503 (4.99%) aligned 0 times 11078682 (91.31%) aligned exactly 1 time 449445 (3.70%) aligned >1 times 95.01% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 6323532 / 11528127 = 0.5485 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 13:13:28: # Command line: callpeak -t SRX040611.bam -f BAM -g dm -n SRX040611.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX040611.10 # format = BAM # ChIP-seq file = ['SRX040611.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 13:13:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:13:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:13:28: # Command line: callpeak -t SRX040611.bam -f BAM -g dm -n SRX040611.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX040611.20 # format = BAM # ChIP-seq file = ['SRX040611.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 13:13:28: # Command line: callpeak -t SRX040611.bam -f BAM -g dm -n SRX040611.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX040611.05 # format = BAM # ChIP-seq file = ['SRX040611.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 13:13:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:13:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:13:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:13:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:13:34: 1000000 INFO @ Tue, 21 Apr 2015 13:13:35: 1000000 INFO @ Tue, 21 Apr 2015 13:13:35: 1000000 INFO @ Tue, 21 Apr 2015 13:13:40: 2000000 INFO @ Tue, 21 Apr 2015 13:13:42: 2000000 INFO @ Tue, 21 Apr 2015 13:13:42: 2000000 INFO @ Tue, 21 Apr 2015 13:13:46: 3000000 INFO @ Tue, 21 Apr 2015 13:13:48: 3000000 INFO @ Tue, 21 Apr 2015 13:13:48: 3000000 INFO @ Tue, 21 Apr 2015 13:13:52: 4000000 INFO @ Tue, 21 Apr 2015 13:13:55: 4000000 INFO @ Tue, 21 Apr 2015 13:13:55: 4000000 INFO @ Tue, 21 Apr 2015 13:13:58: 5000000 INFO @ Tue, 21 Apr 2015 13:13:59: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:13:59: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:13:59: #1 total tags in treatment: 5204595 INFO @ Tue, 21 Apr 2015 13:13:59: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:13:59: #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 13:14:00: #1 tags after filtering in treatment: 5201733 INFO @ Tue, 21 Apr 2015 13:14:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:14:00: #1 finished! INFO @ Tue, 21 Apr 2015 13:14:00: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:14:02: #2 number of paired peaks: 11000 INFO @ Tue, 21 Apr 2015 13:14:02: start model_add_line... INFO @ Tue, 21 Apr 2015 13:14:02: 5000000 INFO @ Tue, 21 Apr 2015 13:14:02: 5000000 INFO @ Tue, 21 Apr 2015 13:14:04: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:14:04: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:14:04: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:14:04: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:14:04: #1 total tags in treatment: 5204595 INFO @ Tue, 21 Apr 2015 13:14:04: #1 total tags in treatment: 5204595 INFO @ Tue, 21 Apr 2015 13:14:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:14:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:14:04: #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 13:14:04: #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 13:14:04: #1 tags after filtering in treatment: 5201733 INFO @ Tue, 21 Apr 2015 13:14:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:14:04: #1 finished! INFO @ Tue, 21 Apr 2015 13:14:04: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:14:04: #1 tags after filtering in treatment: 5201733 INFO @ Tue, 21 Apr 2015 13:14:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:14:04: #1 finished! INFO @ Tue, 21 Apr 2015 13:14:04: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:14:07: #2 number of paired peaks: 11000 INFO @ Tue, 21 Apr 2015 13:14:07: start model_add_line... INFO @ Tue, 21 Apr 2015 13:14:07: #2 number of paired peaks: 11000 INFO @ Tue, 21 Apr 2015 13:14:07: start model_add_line... 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 13:15:12: start X-correlation... INFO @ Tue, 21 Apr 2015 13:15:12: end of X-cor INFO @ Tue, 21 Apr 2015 13:15:12: #2 finished! INFO @ Tue, 21 Apr 2015 13:15:12: #2 predicted fragment length is 226 bps INFO @ Tue, 21 Apr 2015 13:15:12: #2 alternative fragment length(s) may be 226 bps INFO @ Tue, 21 Apr 2015 13:15:12: #2.2 Generate R script for model : SRX040611.20_model.r INFO @ Tue, 21 Apr 2015 13:15:12: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:15:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:15:18: start X-correlation... INFO @ Tue, 21 Apr 2015 13:15:18: end of X-cor INFO @ Tue, 21 Apr 2015 13:15:18: #2 finished! INFO @ Tue, 21 Apr 2015 13:15:18: #2 predicted fragment length is 226 bps INFO @ Tue, 21 Apr 2015 13:15:18: #2 alternative fragment length(s) may be 226 bps INFO @ Tue, 21 Apr 2015 13:15:18: #2.2 Generate R script for model : SRX040611.10_model.r INFO @ Tue, 21 Apr 2015 13:15:18: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:15:19: start X-correlation... INFO @ Tue, 21 Apr 2015 13:15:19: end of X-cor INFO @ Tue, 21 Apr 2015 13:15:19: #2 finished! INFO @ Tue, 21 Apr 2015 13:15:19: #2 predicted fragment length is 226 bps INFO @ Tue, 21 Apr 2015 13:15:19: #2 alternative fragment length(s) may be 226 bps INFO @ Tue, 21 Apr 2015 13:15:19: #2.2 Generate R script for model : SRX040611.05_model.r INFO @ Tue, 21 Apr 2015 13:15:19: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:15:52: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:16:00: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:16:01: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:16:24: #4 Write output xls file... SRX040611.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:16:24: #4 Write peak in narrowPeak format file... SRX040611.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:16:24: #4 Write summits bed file... SRX040611.20_summits.bed INFO @ Tue, 21 Apr 2015 13:16:24: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6060 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:16:34: #4 Write output xls file... SRX040611.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:16:34: #4 Write peak in narrowPeak format file... SRX040611.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:16:34: #4 Write summits bed file... SRX040611.10_summits.bed INFO @ Tue, 21 Apr 2015 13:16:34: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7000 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:16:38: #4 Write output xls file... SRX040611.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:16:38: #4 Write peak in narrowPeak format file... SRX040611.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:16:38: #4 Write summits bed file... SRX040611.05_summits.bed INFO @ Tue, 21 Apr 2015 13:16:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7661 records, 4 fields): 11 millis CompletedMACS2peakCalling