Job ID = 2162425 sra ファイルのダウンロード中... Completed: 740101K bytes transferred in 9 seconds (656735K 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 25120 0 25120 0 0 28848 0 --:--:-- --:--:-- --:--:-- 36941 100 36866 0 36866 0 0 42295 0 --:--:-- --:--:-- --:--:-- 54135 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 32402765 spots for /home/okishinya/chipatlas/results/dm3/SRX097617/SRR345568.sra Written 32402765 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: 00:10:41 32402765 reads; of these: 32402765 (100.00%) were unpaired; of these: 1096475 (3.38%) aligned 0 times 23937630 (73.88%) aligned exactly 1 time 7368660 (22.74%) aligned >1 times 96.62% overall alignment rate Time searching: 00:10:41 Overall time: 00:10:41 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] 10141097 / 31306290 = 0.3239 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 14:12:33: # Command line: callpeak -t SRX097617.bam -f BAM -g dm -n SRX097617.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX097617.20 # format = BAM # ChIP-seq file = ['SRX097617.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 14:12:33: # Command line: callpeak -t SRX097617.bam -f BAM -g dm -n SRX097617.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX097617.05 # format = BAM # ChIP-seq file = ['SRX097617.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 14:12:33: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:12:33: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:12:33: # Command line: callpeak -t SRX097617.bam -f BAM -g dm -n SRX097617.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX097617.10 # format = BAM # ChIP-seq file = ['SRX097617.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 14:12:33: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:12:33: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:12:33: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:12:33: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:12:38: 1000000 INFO @ Tue, 21 Apr 2015 14:12:38: 1000000 INFO @ Tue, 21 Apr 2015 14:12:38: 1000000 INFO @ Tue, 21 Apr 2015 14:12:42: 2000000 INFO @ Tue, 21 Apr 2015 14:12:42: 2000000 INFO @ Tue, 21 Apr 2015 14:12:43: 2000000 INFO @ Tue, 21 Apr 2015 14:12:47: 3000000 INFO @ Tue, 21 Apr 2015 14:12:47: 3000000 INFO @ Tue, 21 Apr 2015 14:12:48: 3000000 INFO @ Tue, 21 Apr 2015 14:12:52: 4000000 INFO @ Tue, 21 Apr 2015 14:12:52: 4000000 INFO @ Tue, 21 Apr 2015 14:12:53: 4000000 INFO @ Tue, 21 Apr 2015 14:12:57: 5000000 INFO @ Tue, 21 Apr 2015 14:12:57: 5000000 INFO @ Tue, 21 Apr 2015 14:12:58: 5000000 INFO @ Tue, 21 Apr 2015 14:13:02: 6000000 INFO @ Tue, 21 Apr 2015 14:13:02: 6000000 INFO @ Tue, 21 Apr 2015 14:13:03: 6000000 INFO @ Tue, 21 Apr 2015 14:13:07: 7000000 INFO @ Tue, 21 Apr 2015 14:13:07: 7000000 INFO @ Tue, 21 Apr 2015 14:13:08: 7000000 INFO @ Tue, 21 Apr 2015 14:13:12: 8000000 INFO @ Tue, 21 Apr 2015 14:13:12: 8000000 INFO @ Tue, 21 Apr 2015 14:13:13: 8000000 INFO @ Tue, 21 Apr 2015 14:13:17: 9000000 INFO @ Tue, 21 Apr 2015 14:13:17: 9000000 INFO @ Tue, 21 Apr 2015 14:13:18: 9000000 INFO @ Tue, 21 Apr 2015 14:13:21: 10000000 INFO @ Tue, 21 Apr 2015 14:13:22: 10000000 INFO @ Tue, 21 Apr 2015 14:13:24: 10000000 INFO @ Tue, 21 Apr 2015 14:13:26: 11000000 INFO @ Tue, 21 Apr 2015 14:13:27: 11000000 INFO @ Tue, 21 Apr 2015 14:13:29: 11000000 INFO @ Tue, 21 Apr 2015 14:13:31: 12000000 INFO @ Tue, 21 Apr 2015 14:13:33: 12000000 INFO @ Tue, 21 Apr 2015 14:13:34: 12000000 INFO @ Tue, 21 Apr 2015 14:13:36: 13000000 INFO @ Tue, 21 Apr 2015 14:13:38: 13000000 INFO @ Tue, 21 Apr 2015 14:13:39: 13000000 INFO @ Tue, 21 Apr 2015 14:13:41: 14000000 INFO @ Tue, 21 Apr 2015 14:13:43: 14000000 INFO @ Tue, 21 Apr 2015 14:13:44: 14000000 INFO @ Tue, 21 Apr 2015 14:13:46: 15000000 INFO @ Tue, 21 Apr 2015 14:13:48: 15000000 INFO @ Tue, 21 Apr 2015 14:13:50: 15000000 INFO @ Tue, 21 Apr 2015 14:13:50: 16000000 INFO @ Tue, 21 Apr 2015 14:13:53: 16000000 INFO @ Tue, 21 Apr 2015 14:13:55: 16000000 INFO @ Tue, 21 Apr 2015 14:13:55: 17000000 INFO @ Tue, 21 Apr 2015 14:13:58: 17000000 INFO @ Tue, 21 Apr 2015 14:14:00: 18000000 INFO @ Tue, 21 Apr 2015 14:14:00: 17000000 INFO @ Tue, 21 Apr 2015 14:14:03: 18000000 INFO @ Tue, 21 Apr 2015 14:14:05: 19000000 INFO @ Tue, 21 Apr 2015 14:14:06: 18000000 INFO @ Tue, 21 Apr 2015 14:14:08: 19000000 INFO @ Tue, 21 Apr 2015 14:14:10: 20000000 INFO @ Tue, 21 Apr 2015 14:14:11: 19000000 INFO @ Tue, 21 Apr 2015 14:14:13: 20000000 INFO @ Tue, 21 Apr 2015 14:14:15: 21000000 INFO @ Tue, 21 Apr 2015 14:14:16: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:14:16: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:14:16: #1 total tags in treatment: 21165193 INFO @ Tue, 21 Apr 2015 14:14:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:14:16: #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 14:14:16: 20000000 INFO @ Tue, 21 Apr 2015 14:14:18: 21000000 INFO @ Tue, 21 Apr 2015 14:14:20: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:14:20: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:14:20: #1 total tags in treatment: 21165193 INFO @ Tue, 21 Apr 2015 14:14:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:14:20: #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 14:14:20: #1 tags after filtering in treatment: 21161548 INFO @ Tue, 21 Apr 2015 14:14:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:14:20: #1 finished! INFO @ Tue, 21 Apr 2015 14:14:20: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:14:21: 21000000 INFO @ Tue, 21 Apr 2015 14:14:22: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:14:22: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:14:22: #1 total tags in treatment: 21165193 INFO @ Tue, 21 Apr 2015 14:14:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:14:22: #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 14:14:23: #1 tags after filtering in treatment: 21161548 INFO @ Tue, 21 Apr 2015 14:14:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:14:23: #1 finished! INFO @ Tue, 21 Apr 2015 14:14:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:14:24: #2 number of paired peaks: 1289 INFO @ Tue, 21 Apr 2015 14:14:24: start model_add_line... INFO @ Tue, 21 Apr 2015 14:14:26: #1 tags after filtering in treatment: 21161548 INFO @ Tue, 21 Apr 2015 14:14:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:14:26: #1 finished! INFO @ Tue, 21 Apr 2015 14:14:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:14:27: #2 number of paired peaks: 1289 INFO @ Tue, 21 Apr 2015 14:14:27: start model_add_line... INFO @ Tue, 21 Apr 2015 14:14:30: #2 number of paired peaks: 1289 INFO @ Tue, 21 Apr 2015 14:14:30: start model_add_line... INFO @ Tue, 21 Apr 2015 14:14:43: start X-correlation... INFO @ Tue, 21 Apr 2015 14:14:43: end of X-cor INFO @ Tue, 21 Apr 2015 14:14:43: #2 finished! INFO @ Tue, 21 Apr 2015 14:14:43: #2 predicted fragment length is 97 bps INFO @ Tue, 21 Apr 2015 14:14:43: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 21 Apr 2015 14:14:43: #2.2 Generate R script for model : SRX097617.10_model.r INFO @ Tue, 21 Apr 2015 14:14:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:14:45: start X-correlation... INFO @ Tue, 21 Apr 2015 14:14:45: end of X-cor INFO @ Tue, 21 Apr 2015 14:14:45: #2 finished! INFO @ Tue, 21 Apr 2015 14:14:45: #2 predicted fragment length is 97 bps INFO @ Tue, 21 Apr 2015 14:14:45: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 21 Apr 2015 14:14:45: #2.2 Generate R script for model : SRX097617.05_model.r INFO @ Tue, 21 Apr 2015 14:14:45: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:14:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:14:49: start X-correlation... INFO @ Tue, 21 Apr 2015 14:14:49: end of X-cor INFO @ Tue, 21 Apr 2015 14:14:49: #2 finished! INFO @ Tue, 21 Apr 2015 14:14:49: #2 predicted fragment length is 97 bps INFO @ Tue, 21 Apr 2015 14:14:49: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 21 Apr 2015 14:14:49: #2.2 Generate R script for model : SRX097617.20_model.r INFO @ Tue, 21 Apr 2015 14:14:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:16:28: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:16:31: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:16:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:17:46: #4 Write output xls file... SRX097617.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:17:47: #4 Write peak in narrowPeak format file... SRX097617.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:17:47: #4 Write summits bed file... SRX097617.10_summits.bed INFO @ Tue, 21 Apr 2015 14:17:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6028 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:17:51: #4 Write output xls file... SRX097617.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:17:51: #4 Write peak in narrowPeak format file... SRX097617.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:17:51: #4 Write summits bed file... SRX097617.20_summits.bed INFO @ Tue, 21 Apr 2015 14:17:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3199 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:17:54: #4 Write output xls file... SRX097617.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:17:54: #4 Write peak in narrowPeak format file... SRX097617.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:17:54: #4 Write summits bed file... SRX097617.05_summits.bed INFO @ Tue, 21 Apr 2015 14:17:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9663 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。