Job ID = 2162426 sra ファイルのダウンロード中... Completed: 495344K bytes transferred in 6 seconds (581642K 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 36852 0 36852 0 0 47216 0 --:--:-- --:--:-- --:--:-- 62567 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 23205866 spots for /home/okishinya/chipatlas/results/dm3/SRX097618/SRR345569.sra Written 23205866 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: 00:06:49 23205866 reads; of these: 23205866 (100.00%) were unpaired; of these: 858266 (3.70%) aligned 0 times 18105557 (78.02%) aligned exactly 1 time 4242043 (18.28%) aligned >1 times 96.30% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9765652 / 22347600 = 0.4370 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 14:06:07: # Command line: callpeak -t SRX097618.bam -f BAM -g dm -n SRX097618.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX097618.10 # format = BAM # ChIP-seq file = ['SRX097618.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 14:06:07: # Command line: callpeak -t SRX097618.bam -f BAM -g dm -n SRX097618.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX097618.20 # format = BAM # ChIP-seq file = ['SRX097618.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 14:06:07: # Command line: callpeak -t SRX097618.bam -f BAM -g dm -n SRX097618.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX097618.05 # format = BAM # ChIP-seq file = ['SRX097618.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 14:06:07: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:06:07: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:06:07: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:06:07: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:06:07: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:06:07: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:06:13: 1000000 INFO @ Tue, 21 Apr 2015 14:06:13: 1000000 INFO @ Tue, 21 Apr 2015 14:06:13: 1000000 INFO @ Tue, 21 Apr 2015 14:06:18: 2000000 INFO @ Tue, 21 Apr 2015 14:06:18: 2000000 INFO @ Tue, 21 Apr 2015 14:06:18: 2000000 INFO @ Tue, 21 Apr 2015 14:06:24: 3000000 INFO @ Tue, 21 Apr 2015 14:06:24: 3000000 INFO @ Tue, 21 Apr 2015 14:06:24: 3000000 INFO @ Tue, 21 Apr 2015 14:06:30: 4000000 INFO @ Tue, 21 Apr 2015 14:06:30: 4000000 INFO @ Tue, 21 Apr 2015 14:06:30: 4000000 INFO @ Tue, 21 Apr 2015 14:06:35: 5000000 INFO @ Tue, 21 Apr 2015 14:06:36: 5000000 INFO @ Tue, 21 Apr 2015 14:06:37: 5000000 INFO @ Tue, 21 Apr 2015 14:06:42: 6000000 INFO @ Tue, 21 Apr 2015 14:06:43: 6000000 INFO @ Tue, 21 Apr 2015 14:06:45: 6000000 INFO @ Tue, 21 Apr 2015 14:06:49: 7000000 INFO @ Tue, 21 Apr 2015 14:06:50: 7000000 INFO @ Tue, 21 Apr 2015 14:06:53: 7000000 INFO @ Tue, 21 Apr 2015 14:06:55: 8000000 INFO @ Tue, 21 Apr 2015 14:06:57: 8000000 INFO @ Tue, 21 Apr 2015 14:07:01: 8000000 INFO @ Tue, 21 Apr 2015 14:07:02: 9000000 INFO @ Tue, 21 Apr 2015 14:07:04: 9000000 INFO @ Tue, 21 Apr 2015 14:07:08: 10000000 INFO @ Tue, 21 Apr 2015 14:07:09: 9000000 INFO @ Tue, 21 Apr 2015 14:07:11: 10000000 INFO @ Tue, 21 Apr 2015 14:07:15: 11000000 INFO @ Tue, 21 Apr 2015 14:07:17: 10000000 INFO @ Tue, 21 Apr 2015 14:07:18: 11000000 INFO @ Tue, 21 Apr 2015 14:07:21: 12000000 INFO @ Tue, 21 Apr 2015 14:07:25: 11000000 INFO @ Tue, 21 Apr 2015 14:07:25: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:07:25: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:07:25: #1 total tags in treatment: 12581948 INFO @ Tue, 21 Apr 2015 14:07:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:07:25: #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 14:07:25: 12000000 INFO @ Tue, 21 Apr 2015 14:07:28: #1 tags after filtering in treatment: 12579635 INFO @ Tue, 21 Apr 2015 14:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:07:28: #1 finished! INFO @ Tue, 21 Apr 2015 14:07:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:07:30: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:07:30: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:07:30: #1 total tags in treatment: 12581948 INFO @ Tue, 21 Apr 2015 14:07:30: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:07:30: #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 14:07:31: #2 number of paired peaks: 4539 INFO @ Tue, 21 Apr 2015 14:07:31: start model_add_line... INFO @ Tue, 21 Apr 2015 14:07:32: #1 tags after filtering in treatment: 12579635 INFO @ Tue, 21 Apr 2015 14:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:07:32: #1 finished! INFO @ Tue, 21 Apr 2015 14:07:32: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:07:32: 12000000 INFO @ Tue, 21 Apr 2015 14:07:35: #2 number of paired peaks: 4539 INFO @ Tue, 21 Apr 2015 14:07:35: start model_add_line... INFO @ Tue, 21 Apr 2015 14:07:36: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:07:36: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:07:36: #1 total tags in treatment: 12581948 INFO @ Tue, 21 Apr 2015 14:07:36: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:07:36: #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 14:07:38: #1 tags after filtering in treatment: 12579635 INFO @ Tue, 21 Apr 2015 14:07:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:07:38: #1 finished! INFO @ Tue, 21 Apr 2015 14:07:38: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:07:41: #2 number of paired peaks: 4539 INFO @ Tue, 21 Apr 2015 14:07:41: start model_add_line... INFO @ Tue, 21 Apr 2015 14:08:04: start X-correlation... INFO @ Tue, 21 Apr 2015 14:08:04: end of X-cor INFO @ Tue, 21 Apr 2015 14:08:04: #2 finished! INFO @ Tue, 21 Apr 2015 14:08:04: #2 predicted fragment length is 155 bps INFO @ Tue, 21 Apr 2015 14:08:04: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 21 Apr 2015 14:08:04: #2.2 Generate R script for model : SRX097618.20_model.r INFO @ Tue, 21 Apr 2015 14:08:04: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:08:08: start X-correlation... INFO @ Tue, 21 Apr 2015 14:08:08: end of X-cor INFO @ Tue, 21 Apr 2015 14:08:08: #2 finished! INFO @ Tue, 21 Apr 2015 14:08:08: #2 predicted fragment length is 155 bps INFO @ Tue, 21 Apr 2015 14:08:08: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 21 Apr 2015 14:08:08: #2.2 Generate R script for model : SRX097618.10_model.r INFO @ Tue, 21 Apr 2015 14:08:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:08:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:08:15: start X-correlation... INFO @ Tue, 21 Apr 2015 14:08:15: end of X-cor INFO @ Tue, 21 Apr 2015 14:08:15: #2 finished! INFO @ Tue, 21 Apr 2015 14:08:15: #2 predicted fragment length is 155 bps INFO @ Tue, 21 Apr 2015 14:08:15: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 21 Apr 2015 14:08:15: #2.2 Generate R script for model : SRX097618.05_model.r INFO @ Tue, 21 Apr 2015 14:08:15: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:08:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:09:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:09:25: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:09:30: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:10:11: #4 Write output xls file... SRX097618.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:10:11: #4 Write peak in narrowPeak format file... SRX097618.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:10:11: #4 Write summits bed file... SRX097618.20_summits.bed INFO @ Tue, 21 Apr 2015 14:10:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6461 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:10:30: #4 Write output xls file... SRX097618.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:10:30: #4 Write peak in narrowPeak format file... SRX097618.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:10:30: #4 Write summits bed file... SRX097618.10_summits.bed INFO @ Tue, 21 Apr 2015 14:10:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9257 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 21 Apr 2015 14:10:36: #4 Write output xls file... SRX097618.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:10:36: #4 Write peak in narrowPeak format file... SRX097618.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:10:37: #4 Write summits bed file... SRX097618.05_summits.bed INFO @ Tue, 21 Apr 2015 14:10:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12308 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。