Job ID = 2162167 sra ファイルのダウンロード中... Completed: 136860K bytes transferred in 4 seconds (249567K 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 4000 0 4000 0 0 7951 0 --:--:-- --:--:-- --:--:-- 12779 100 35450 0 35450 0 0 51166 0 --:--:-- --:--:-- --:--:-- 70477 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 7259465 spots for /home/okishinya/chipatlas/results/dm3/SRX050603/SRR139085.sra Written 7259465 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: 00:01:42 7259465 reads; of these: 7259465 (100.00%) were unpaired; of these: 217281 (2.99%) aligned 0 times 6031345 (83.08%) aligned exactly 1 time 1010839 (13.92%) aligned >1 times 97.01% overall alignment rate Time searching: 00:01:42 Overall time: 00:01:42 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] 931359 / 7042184 = 0.1323 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 13:35:54: # Command line: callpeak -t SRX050603.bam -f BAM -g dm -n SRX050603.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX050603.05 # format = BAM # ChIP-seq file = ['SRX050603.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 13:35:54: # Command line: callpeak -t SRX050603.bam -f BAM -g dm -n SRX050603.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX050603.20 # format = BAM # ChIP-seq file = ['SRX050603.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 13:35:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:35:54: # Command line: callpeak -t SRX050603.bam -f BAM -g dm -n SRX050603.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX050603.10 # format = BAM # ChIP-seq file = ['SRX050603.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 13:35:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:35:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:35:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:35:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:35:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:35:59: 1000000 INFO @ Tue, 21 Apr 2015 13:35:59: 1000000 INFO @ Tue, 21 Apr 2015 13:35:59: 1000000 INFO @ Tue, 21 Apr 2015 13:36:05: 2000000 INFO @ Tue, 21 Apr 2015 13:36:05: 2000000 INFO @ Tue, 21 Apr 2015 13:36:05: 2000000 INFO @ Tue, 21 Apr 2015 13:36:10: 3000000 INFO @ Tue, 21 Apr 2015 13:36:10: 3000000 INFO @ Tue, 21 Apr 2015 13:36:10: 3000000 INFO @ Tue, 21 Apr 2015 13:36:15: 4000000 INFO @ Tue, 21 Apr 2015 13:36:15: 4000000 INFO @ Tue, 21 Apr 2015 13:36:15: 4000000 INFO @ Tue, 21 Apr 2015 13:36:20: 5000000 INFO @ Tue, 21 Apr 2015 13:36:20: 5000000 INFO @ Tue, 21 Apr 2015 13:36:20: 5000000 INFO @ Tue, 21 Apr 2015 13:36:25: 6000000 INFO @ Tue, 21 Apr 2015 13:36:25: 6000000 INFO @ Tue, 21 Apr 2015 13:36:26: 6000000 INFO @ Tue, 21 Apr 2015 13:36:26: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:36:26: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:36:26: #1 total tags in treatment: 6110825 INFO @ Tue, 21 Apr 2015 13:36:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:36:26: #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 13:36:26: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:36:26: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:36:26: #1 total tags in treatment: 6110825 INFO @ Tue, 21 Apr 2015 13:36:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:36:26: #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 13:36:26: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:36:26: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:36:26: #1 total tags in treatment: 6110825 INFO @ Tue, 21 Apr 2015 13:36:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:36:26: #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 13:36:27: #1 tags after filtering in treatment: 6110482 INFO @ Tue, 21 Apr 2015 13:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:36:27: #1 finished! INFO @ Tue, 21 Apr 2015 13:36:27: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:36:27: #1 tags after filtering in treatment: 6110482 INFO @ Tue, 21 Apr 2015 13:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:36:27: #1 finished! INFO @ Tue, 21 Apr 2015 13:36:27: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:36:27: #1 tags after filtering in treatment: 6110482 INFO @ Tue, 21 Apr 2015 13:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:36:27: #1 finished! INFO @ Tue, 21 Apr 2015 13:36:27: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:36:29: #2 number of paired peaks: 3266 INFO @ Tue, 21 Apr 2015 13:36:29: start model_add_line... INFO @ Tue, 21 Apr 2015 13:36:29: #2 number of paired peaks: 3266 INFO @ Tue, 21 Apr 2015 13:36:29: start model_add_line... INFO @ Tue, 21 Apr 2015 13:36:29: #2 number of paired peaks: 3266 INFO @ Tue, 21 Apr 2015 13:36:29: start model_add_line... INFO @ Tue, 21 Apr 2015 13:36:40: start X-correlation... INFO @ Tue, 21 Apr 2015 13:36:40: start X-correlation... INFO @ Tue, 21 Apr 2015 13:36:40: end of X-cor INFO @ Tue, 21 Apr 2015 13:36:40: #2 finished! INFO @ Tue, 21 Apr 2015 13:36:40: #2 predicted fragment length is 98 bps INFO @ Tue, 21 Apr 2015 13:36:40: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 21 Apr 2015 13:36:40: #2.2 Generate R script for model : SRX050603.10_model.r INFO @ Tue, 21 Apr 2015 13:36:40: end of X-cor INFO @ Tue, 21 Apr 2015 13:36:40: #2 finished! INFO @ Tue, 21 Apr 2015 13:36:40: #2 predicted fragment length is 98 bps INFO @ Tue, 21 Apr 2015 13:36:40: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 21 Apr 2015 13:36:40: #2.2 Generate R script for model : SRX050603.05_model.r INFO @ Tue, 21 Apr 2015 13:36:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:36:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:36:41: start X-correlation... INFO @ Tue, 21 Apr 2015 13:36:41: end of X-cor INFO @ Tue, 21 Apr 2015 13:36:41: #2 finished! INFO @ Tue, 21 Apr 2015 13:36:41: #2 predicted fragment length is 98 bps INFO @ Tue, 21 Apr 2015 13:36:41: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 21 Apr 2015 13:36:41: #2.2 Generate R script for model : SRX050603.20_model.r INFO @ Tue, 21 Apr 2015 13:36:41: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:36:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:37:13: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:37:16: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:37:16: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:37:43: #4 Write output xls file... SRX050603.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:37:43: #4 Write peak in narrowPeak format file... SRX050603.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:37:43: #4 Write summits bed file... SRX050603.05_summits.bed INFO @ Tue, 21 Apr 2015 13:37:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8175 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:37:44: #4 Write output xls file... SRX050603.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:37:44: #4 Write peak in narrowPeak format file... SRX050603.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:37:44: #4 Write summits bed file... SRX050603.20_summits.bed INFO @ Tue, 21 Apr 2015 13:37:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3450 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:37:45: #4 Write output xls file... SRX050603.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:37:45: #4 Write peak in narrowPeak format file... SRX050603.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:37:45: #4 Write summits bed file... SRX050603.10_summits.bed INFO @ Tue, 21 Apr 2015 13:37:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5385 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。