Job ID = 2161914 sra ファイルのダウンロード中... Completed: 255378K bytes transferred in 5 seconds (367075K 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 13456 0 13456 0 0 23151 0 --:--:-- --:--:-- --:--:-- 34502 100 35570 0 35570 0 0 46148 0 --:--:-- --:--:-- --:--:-- 61327 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 9732011 spots for /home/okishinya/chipatlas/results/dm3/SRX040617/SRR097986.sra Written 9732011 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: 00:00:01 Multiseed full-index search: 00:01:48 9732011 reads; of these: 9732011 (100.00%) were unpaired; of these: 4566181 (46.92%) aligned 0 times 4295957 (44.14%) aligned exactly 1 time 869873 (8.94%) aligned >1 times 53.08% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 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] 3754014 / 5165830 = 0.7267 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 13:14:48: # Command line: callpeak -t SRX040617.bam -f BAM -g dm -n SRX040617.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX040617.20 # format = BAM # ChIP-seq file = ['SRX040617.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 13:14:48: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:14:48: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:14:48: # Command line: callpeak -t SRX040617.bam -f BAM -g dm -n SRX040617.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX040617.10 # format = BAM # ChIP-seq file = ['SRX040617.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 13:14:48: # Command line: callpeak -t SRX040617.bam -f BAM -g dm -n SRX040617.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX040617.05 # format = BAM # ChIP-seq file = ['SRX040617.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 13:14:48: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:14:48: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:14:48: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:14:48: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:14:53: 1000000 INFO @ Tue, 21 Apr 2015 13:14:53: 1000000 INFO @ Tue, 21 Apr 2015 13:14:53: 1000000 INFO @ Tue, 21 Apr 2015 13:14:55: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:14:55: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:14:55: #1 total tags in treatment: 1411816 INFO @ Tue, 21 Apr 2015 13:14:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:14:55: #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 13:14:55: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:14:55: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:14:55: #1 total tags in treatment: 1411816 INFO @ Tue, 21 Apr 2015 13:14:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:14:55: #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 13:14:55: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:14:55: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:14:55: #1 total tags in treatment: 1411816 INFO @ Tue, 21 Apr 2015 13:14:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:14:55: #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 13:14:55: #1 tags after filtering in treatment: 1411348 INFO @ Tue, 21 Apr 2015 13:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:14:55: #1 finished! INFO @ Tue, 21 Apr 2015 13:14:55: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:14:56: #1 tags after filtering in treatment: 1411348 INFO @ Tue, 21 Apr 2015 13:14:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:14:56: #1 finished! INFO @ Tue, 21 Apr 2015 13:14:56: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:14:56: #1 tags after filtering in treatment: 1411348 INFO @ Tue, 21 Apr 2015 13:14:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:14:56: #1 finished! INFO @ Tue, 21 Apr 2015 13:14:56: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:14:56: #2 number of paired peaks: 3274 INFO @ Tue, 21 Apr 2015 13:14:56: start model_add_line... INFO @ Tue, 21 Apr 2015 13:14:56: #2 number of paired peaks: 3274 INFO @ Tue, 21 Apr 2015 13:14:56: start model_add_line... INFO @ Tue, 21 Apr 2015 13:14:56: #2 number of paired peaks: 3274 INFO @ Tue, 21 Apr 2015 13:14:56: start model_add_line... INFO @ Tue, 21 Apr 2015 13:14:59: start X-correlation... INFO @ Tue, 21 Apr 2015 13:14:59: end of X-cor INFO @ Tue, 21 Apr 2015 13:14:59: #2 finished! INFO @ Tue, 21 Apr 2015 13:14:59: #2 predicted fragment length is 97 bps INFO @ Tue, 21 Apr 2015 13:14:59: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 21 Apr 2015 13:14:59: #2.2 Generate R script for model : SRX040617.10_model.r INFO @ Tue, 21 Apr 2015 13:14:59: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:14:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:14:59: start X-correlation... INFO @ Tue, 21 Apr 2015 13:14:59: end of X-cor INFO @ Tue, 21 Apr 2015 13:14:59: #2 finished! INFO @ Tue, 21 Apr 2015 13:14:59: #2 predicted fragment length is 97 bps INFO @ Tue, 21 Apr 2015 13:14:59: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 21 Apr 2015 13:14:59: #2.2 Generate R script for model : SRX040617.20_model.r INFO @ Tue, 21 Apr 2015 13:14:59: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:14:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:15:00: start X-correlation... INFO @ Tue, 21 Apr 2015 13:15:00: end of X-cor INFO @ Tue, 21 Apr 2015 13:15:00: #2 finished! INFO @ Tue, 21 Apr 2015 13:15:00: #2 predicted fragment length is 97 bps INFO @ Tue, 21 Apr 2015 13:15:00: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 21 Apr 2015 13:15:00: #2.2 Generate R script for model : SRX040617.05_model.r INFO @ Tue, 21 Apr 2015 13:15:00: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:15:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:15:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:15:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:15:09: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:15:14: #4 Write output xls file... SRX040617.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:15:14: #4 Write peak in narrowPeak format file... SRX040617.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:15:14: #4 Write summits bed file... SRX040617.20_summits.bed INFO @ Tue, 21 Apr 2015 13:15:14: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (865 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:15:15: #4 Write output xls file... SRX040617.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:15:15: #4 Write peak in narrowPeak format file... SRX040617.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:15:15: #4 Write summits bed file... SRX040617.10_summits.bed INFO @ Tue, 21 Apr 2015 13:15:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2253 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:15:17: #4 Write output xls file... SRX040617.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:15:17: #4 Write peak in narrowPeak format file... SRX040617.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:15:17: #4 Write summits bed file... SRX040617.05_summits.bed INFO @ Tue, 21 Apr 2015 13:15:17: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (4545 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。