Job ID = 2161283 sra ファイルのダウンロード中... Completed: 442241K bytes transferred in 6 seconds (557383K bits/sec), in 2 files, 3 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 17828 0 17828 0 0 24992 0 --:--:-- --:--:-- --:--:-- 34153 100 34360 0 34360 0 0 48113 0 --:--:-- --:--:-- --:--:-- 65697 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 9617745 spots for /home/okishinya/chipatlas/results/dm3/SRX016149/SRR034707.sra Written 9617745 spots total Written 9752434 spots for /home/okishinya/chipatlas/results/dm3/SRX016149/SRR034706.sra Written 9752434 spots total 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: 00:04:10 19370179 reads; of these: 19370179 (100.00%) were unpaired; of these: 266572 (1.38%) aligned 0 times 17541937 (90.56%) aligned exactly 1 time 1561670 (8.06%) aligned >1 times 98.62% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 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_sort_core] merging from 8 files... [bam_rmdupse_core] 13688264 / 19103607 = 0.7165 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 12:19:49: # Command line: callpeak -t SRX016149.bam -f BAM -g dm -n SRX016149.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX016149.20 # format = BAM # ChIP-seq file = ['SRX016149.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 12:19:49: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:19:49: # Command line: callpeak -t SRX016149.bam -f BAM -g dm -n SRX016149.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX016149.05 # format = BAM # ChIP-seq file = ['SRX016149.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 12:19:49: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:19:49: # Command line: callpeak -t SRX016149.bam -f BAM -g dm -n SRX016149.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX016149.10 # format = BAM # ChIP-seq file = ['SRX016149.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 12:19:49: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:19:49: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:19:49: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:19:49: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:19:54: 1000000 INFO @ Tue, 21 Apr 2015 12:19:54: 1000000 INFO @ Tue, 21 Apr 2015 12:19:55: 1000000 INFO @ Tue, 21 Apr 2015 12:20:01: 2000000 INFO @ Tue, 21 Apr 2015 12:20:01: 2000000 INFO @ Tue, 21 Apr 2015 12:20:01: 2000000 INFO @ Tue, 21 Apr 2015 12:20:07: 3000000 INFO @ Tue, 21 Apr 2015 12:20:08: 3000000 INFO @ Tue, 21 Apr 2015 12:20:08: 3000000 INFO @ Tue, 21 Apr 2015 12:20:14: 4000000 INFO @ Tue, 21 Apr 2015 12:20:14: 4000000 INFO @ Tue, 21 Apr 2015 12:20:15: 4000000 INFO @ Tue, 21 Apr 2015 12:20:20: 5000000 INFO @ Tue, 21 Apr 2015 12:20:20: 5000000 INFO @ Tue, 21 Apr 2015 12:20:21: 5000000 INFO @ Tue, 21 Apr 2015 12:20:22: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:20:22: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:20:22: #1 total tags in treatment: 5415343 INFO @ Tue, 21 Apr 2015 12:20:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:20:22: #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 12:20:22: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:20:22: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:20:22: #1 total tags in treatment: 5415343 INFO @ Tue, 21 Apr 2015 12:20:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:20:22: #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 12:20:23: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:20:23: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:20:23: #1 total tags in treatment: 5415343 INFO @ Tue, 21 Apr 2015 12:20:23: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:20:23: #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 12:20:23: #1 tags after filtering in treatment: 5415082 INFO @ Tue, 21 Apr 2015 12:20:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:20:23: #1 finished! INFO @ Tue, 21 Apr 2015 12:20:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:20:23: #1 tags after filtering in treatment: 5415082 INFO @ Tue, 21 Apr 2015 12:20:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:20:23: #1 finished! INFO @ Tue, 21 Apr 2015 12:20:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:20:24: #1 tags after filtering in treatment: 5415082 INFO @ Tue, 21 Apr 2015 12:20:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:20:24: #1 finished! INFO @ Tue, 21 Apr 2015 12:20:24: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:20:25: #2 number of paired peaks: 3036 INFO @ Tue, 21 Apr 2015 12:20:25: start model_add_line... INFO @ Tue, 21 Apr 2015 12:20:25: #2 number of paired peaks: 3036 INFO @ Tue, 21 Apr 2015 12:20:25: start model_add_line... INFO @ Tue, 21 Apr 2015 12:20:25: #2 number of paired peaks: 3036 INFO @ Tue, 21 Apr 2015 12:20:25: start model_add_line... INFO @ Tue, 21 Apr 2015 12:20:34: start X-correlation... INFO @ Tue, 21 Apr 2015 12:20:34: end of X-cor INFO @ Tue, 21 Apr 2015 12:20:34: #2 finished! INFO @ Tue, 21 Apr 2015 12:20:34: #2 predicted fragment length is 235 bps INFO @ Tue, 21 Apr 2015 12:20:34: #2 alternative fragment length(s) may be 235 bps INFO @ Tue, 21 Apr 2015 12:20:34: #2.2 Generate R script for model : SRX016149.10_model.r INFO @ Tue, 21 Apr 2015 12:20:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:20:35: start X-correlation... INFO @ Tue, 21 Apr 2015 12:20:35: end of X-cor INFO @ Tue, 21 Apr 2015 12:20:35: #2 finished! INFO @ Tue, 21 Apr 2015 12:20:35: #2 predicted fragment length is 235 bps INFO @ Tue, 21 Apr 2015 12:20:35: #2 alternative fragment length(s) may be 235 bps INFO @ Tue, 21 Apr 2015 12:20:35: #2.2 Generate R script for model : SRX016149.20_model.r INFO @ Tue, 21 Apr 2015 12:20:35: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:20:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:20:35: start X-correlation... INFO @ Tue, 21 Apr 2015 12:20:35: end of X-cor INFO @ Tue, 21 Apr 2015 12:20:35: #2 finished! INFO @ Tue, 21 Apr 2015 12:20:35: #2 predicted fragment length is 235 bps INFO @ Tue, 21 Apr 2015 12:20:35: #2 alternative fragment length(s) may be 235 bps INFO @ Tue, 21 Apr 2015 12:20:35: #2.2 Generate R script for model : SRX016149.05_model.r INFO @ Tue, 21 Apr 2015 12:20:35: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:20:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:21:04: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:21:06: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:21:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:21:27: #4 Write output xls file... SRX016149.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:21:27: #4 Write peak in narrowPeak format file... SRX016149.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:21:27: #4 Write summits bed file... SRX016149.10_summits.bed INFO @ Tue, 21 Apr 2015 12:21:27: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1645 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:21:29: #4 Write output xls file... SRX016149.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:21:29: #4 Write peak in narrowPeak format file... SRX016149.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:21:29: #4 Write summits bed file... SRX016149.20_summits.bed INFO @ Tue, 21 Apr 2015 12:21:29: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (517 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:21:36: #4 Write output xls file... SRX016149.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:21:36: #4 Write peak in narrowPeak format file... SRX016149.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:21:36: #4 Write summits bed file... SRX016149.05_summits.bed INFO @ Tue, 21 Apr 2015 12:21:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4222 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。