Job ID = 2161574 sra ファイルのダウンロード中... Completed: 889472K bytes transferred in 10 seconds (681405K 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 --:--:-- --:--:-- --:--:-- 0 101 2540 0 2540 0 0 4597 0 --:--:-- --:--:-- --:--:-- 7016 100 44931 0 44931 0 0 48251 0 --:--:-- --:--:-- --:--:-- 60635 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 16340773 spots for /home/okishinya/chipatlas/results/dm3/SRX032111/SRR073928.sra Written 16340773 spots total Written 21728558 spots for /home/okishinya/chipatlas/results/dm3/SRX032111/SRR073929.sra Written 21728558 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: 00:13:22 38069331 reads; of these: 38069331 (100.00%) were unpaired; of these: 510292 (1.34%) aligned 0 times 30263673 (79.50%) aligned exactly 1 time 7295366 (19.16%) aligned >1 times 98.66% overall alignment rate Time searching: 00:13:22 Overall time: 00:13:22 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 12 files... [bam_rmdupse_core] 22426894 / 37559039 = 0.5971 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 13:15:43: # Command line: callpeak -t SRX032111.bam -f BAM -g dm -n SRX032111.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX032111.10 # format = BAM # ChIP-seq file = ['SRX032111.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 13:15:43: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:15:43: # Command line: callpeak -t SRX032111.bam -f BAM -g dm -n SRX032111.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX032111.20 # format = BAM # ChIP-seq file = ['SRX032111.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 13:15:43: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:15:43: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:15:43: # Command line: callpeak -t SRX032111.bam -f BAM -g dm -n SRX032111.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX032111.05 # format = BAM # ChIP-seq file = ['SRX032111.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 13:15:43: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:15:43: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:15:43: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:15:48: 1000000 INFO @ Tue, 21 Apr 2015 13:15:48: 1000000 INFO @ Tue, 21 Apr 2015 13:15:48: 1000000 INFO @ Tue, 21 Apr 2015 13:15:53: 2000000 INFO @ Tue, 21 Apr 2015 13:15:54: 2000000 INFO @ Tue, 21 Apr 2015 13:15:54: 2000000 INFO @ Tue, 21 Apr 2015 13:15:59: 3000000 INFO @ Tue, 21 Apr 2015 13:15:59: 3000000 INFO @ Tue, 21 Apr 2015 13:16:00: 3000000 INFO @ Tue, 21 Apr 2015 13:16:05: 4000000 INFO @ Tue, 21 Apr 2015 13:16:05: 4000000 INFO @ Tue, 21 Apr 2015 13:16:05: 4000000 INFO @ Tue, 21 Apr 2015 13:16:10: 5000000 INFO @ Tue, 21 Apr 2015 13:16:10: 5000000 INFO @ Tue, 21 Apr 2015 13:16:11: 5000000 INFO @ Tue, 21 Apr 2015 13:16:16: 6000000 INFO @ Tue, 21 Apr 2015 13:16:16: 6000000 INFO @ Tue, 21 Apr 2015 13:16:16: 6000000 INFO @ Tue, 21 Apr 2015 13:16:21: 7000000 INFO @ Tue, 21 Apr 2015 13:16:22: 7000000 INFO @ Tue, 21 Apr 2015 13:16:22: 7000000 INFO @ Tue, 21 Apr 2015 13:16:27: 8000000 INFO @ Tue, 21 Apr 2015 13:16:27: 8000000 INFO @ Tue, 21 Apr 2015 13:16:28: 8000000 INFO @ Tue, 21 Apr 2015 13:16:32: 9000000 INFO @ Tue, 21 Apr 2015 13:16:33: 9000000 INFO @ Tue, 21 Apr 2015 13:16:34: 9000000 INFO @ Tue, 21 Apr 2015 13:16:38: 10000000 INFO @ Tue, 21 Apr 2015 13:16:38: 10000000 INFO @ Tue, 21 Apr 2015 13:16:39: 10000000 INFO @ Tue, 21 Apr 2015 13:16:44: 11000000 INFO @ Tue, 21 Apr 2015 13:16:44: 11000000 INFO @ Tue, 21 Apr 2015 13:16:45: 11000000 INFO @ Tue, 21 Apr 2015 13:16:49: 12000000 INFO @ Tue, 21 Apr 2015 13:16:49: 12000000 INFO @ Tue, 21 Apr 2015 13:16:50: 12000000 INFO @ Tue, 21 Apr 2015 13:16:54: 13000000 INFO @ Tue, 21 Apr 2015 13:16:55: 13000000 INFO @ Tue, 21 Apr 2015 13:16:56: 13000000 INFO @ Tue, 21 Apr 2015 13:17:00: 14000000 INFO @ Tue, 21 Apr 2015 13:17:00: 14000000 INFO @ Tue, 21 Apr 2015 13:17:01: 14000000 INFO @ Tue, 21 Apr 2015 13:17:05: 15000000 INFO @ Tue, 21 Apr 2015 13:17:06: 15000000 INFO @ Tue, 21 Apr 2015 13:17:06: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:17:06: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:17:06: #1 total tags in treatment: 15132145 INFO @ Tue, 21 Apr 2015 13:17:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:17:06: #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 13:17:07: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:17:07: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:17:07: #1 total tags in treatment: 15132145 INFO @ Tue, 21 Apr 2015 13:17:07: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:17:07: #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 13:17:07: 15000000 INFO @ Tue, 21 Apr 2015 13:17:08: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:17:08: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:17:08: #1 total tags in treatment: 15132145 INFO @ Tue, 21 Apr 2015 13:17:08: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:17:08: #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 13:17:09: #1 tags after filtering in treatment: 15123280 INFO @ Tue, 21 Apr 2015 13:17:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:17:09: #1 finished! INFO @ Tue, 21 Apr 2015 13:17:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:17:10: #1 tags after filtering in treatment: 15123280 INFO @ Tue, 21 Apr 2015 13:17:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:17:10: #1 finished! INFO @ Tue, 21 Apr 2015 13:17:10: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:17:10: #1 tags after filtering in treatment: 15123280 INFO @ Tue, 21 Apr 2015 13:17:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:17:10: #1 finished! INFO @ Tue, 21 Apr 2015 13:17:10: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:17:13: #2 number of paired peaks: 6890 INFO @ Tue, 21 Apr 2015 13:17:13: start model_add_line... INFO @ Tue, 21 Apr 2015 13:17:13: #2 number of paired peaks: 6890 INFO @ Tue, 21 Apr 2015 13:17:13: start model_add_line... INFO @ Tue, 21 Apr 2015 13:17:14: #2 number of paired peaks: 6890 INFO @ Tue, 21 Apr 2015 13:17:14: start model_add_line... INFO @ Tue, 21 Apr 2015 13:18:27: start X-correlation... INFO @ Tue, 21 Apr 2015 13:18:27: end of X-cor INFO @ Tue, 21 Apr 2015 13:18:27: #2 finished! INFO @ Tue, 21 Apr 2015 13:18:27: #2 predicted fragment length is 244 bps INFO @ Tue, 21 Apr 2015 13:18:27: #2 alternative fragment length(s) may be 244 bps INFO @ Tue, 21 Apr 2015 13:18:27: #2.2 Generate R script for model : SRX032111.05_model.r INFO @ Tue, 21 Apr 2015 13:18:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:18:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:18:30: start X-correlation... INFO @ Tue, 21 Apr 2015 13:18:30: end of X-cor INFO @ Tue, 21 Apr 2015 13:18:30: #2 finished! INFO @ Tue, 21 Apr 2015 13:18:30: #2 predicted fragment length is 244 bps INFO @ Tue, 21 Apr 2015 13:18:30: #2 alternative fragment length(s) may be 244 bps INFO @ Tue, 21 Apr 2015 13:18:30: #2.2 Generate R script for model : SRX032111.20_model.r INFO @ Tue, 21 Apr 2015 13:18:30: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:18:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:18:32: start X-correlation... INFO @ Tue, 21 Apr 2015 13:18:32: end of X-cor INFO @ Tue, 21 Apr 2015 13:18:32: #2 finished! INFO @ Tue, 21 Apr 2015 13:18:32: #2 predicted fragment length is 244 bps INFO @ Tue, 21 Apr 2015 13:18:32: #2 alternative fragment length(s) may be 244 bps INFO @ Tue, 21 Apr 2015 13:18:32: #2.2 Generate R script for model : SRX032111.10_model.r INFO @ Tue, 21 Apr 2015 13:18:32: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:18:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:20:17: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:20:17: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:20:20: #3 Call peaks for each chromosome... 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 13:21:33: #4 Write output xls file... SRX032111.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:21:33: #4 Write peak in narrowPeak format file... SRX032111.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:21:33: #4 Write summits bed file... SRX032111.20_summits.bed INFO @ Tue, 21 Apr 2015 13:21:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8166 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:21:41: #4 Write output xls file... SRX032111.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:21:41: #4 Write peak in narrowPeak format file... SRX032111.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:21:41: #4 Write summits bed file... SRX032111.10_summits.bed INFO @ Tue, 21 Apr 2015 13:21:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9987 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:21:43: #4 Write output xls file... SRX032111.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:21:43: #4 Write peak in narrowPeak format file... SRX032111.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:21:43: #4 Write summits bed file... SRX032111.05_summits.bed INFO @ Tue, 21 Apr 2015 13:21:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11666 records, 4 fields): 15 millis CompletedMACS2peakCalling