Job ID = 2162387 sra ファイルのダウンロード中... Completed: 891427K bytes transferred in 12 seconds (603615K bits/sec), in 3 files, 4 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 36015 0 36015 0 0 48742 0 --:--:-- --:--:-- --:--:-- 65840 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 6343045 spots for /home/okishinya/chipatlas/results/dm3/SRX066246/SRR222075.sra Written 6343045 spots total Written 6657591 spots for /home/okishinya/chipatlas/results/dm3/SRX066246/SRR222076.sra Written 6657591 spots total Written 26266943 spots for /home/okishinya/chipatlas/results/dm3/SRX066246/SRR222077.sra Written 26266943 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: 00:10:11 39267579 reads; of these: 39267579 (100.00%) were unpaired; of these: 1765072 (4.49%) aligned 0 times 32454872 (82.65%) aligned exactly 1 time 5047635 (12.85%) aligned >1 times 95.51% overall alignment rate Time searching: 00:10:11 Overall time: 00:10:11 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] 20513497 / 37502507 = 0.5470 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 13:58:13: # Command line: callpeak -t SRX066246.bam -f BAM -g dm -n SRX066246.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX066246.10 # format = BAM # ChIP-seq file = ['SRX066246.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 13:58:13: # Command line: callpeak -t SRX066246.bam -f BAM -g dm -n SRX066246.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX066246.20 # format = BAM # ChIP-seq file = ['SRX066246.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 13:58:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:58:13: # Command line: callpeak -t SRX066246.bam -f BAM -g dm -n SRX066246.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX066246.05 # format = BAM # ChIP-seq file = ['SRX066246.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 13:58:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:58:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:58:13: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:58:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:58:13: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:58:19: 1000000 INFO @ Tue, 21 Apr 2015 13:58:19: 1000000 INFO @ Tue, 21 Apr 2015 13:58:19: 1000000 INFO @ Tue, 21 Apr 2015 13:58:24: 2000000 INFO @ Tue, 21 Apr 2015 13:58:24: 2000000 INFO @ Tue, 21 Apr 2015 13:58:24: 2000000 INFO @ Tue, 21 Apr 2015 13:58:29: 3000000 INFO @ Tue, 21 Apr 2015 13:58:29: 3000000 INFO @ Tue, 21 Apr 2015 13:58:30: 3000000 INFO @ Tue, 21 Apr 2015 13:58:34: 4000000 INFO @ Tue, 21 Apr 2015 13:58:35: 4000000 INFO @ Tue, 21 Apr 2015 13:58:35: 4000000 INFO @ Tue, 21 Apr 2015 13:58:39: 5000000 INFO @ Tue, 21 Apr 2015 13:58:40: 5000000 INFO @ Tue, 21 Apr 2015 13:58:40: 5000000 INFO @ Tue, 21 Apr 2015 13:58:44: 6000000 INFO @ Tue, 21 Apr 2015 13:58:46: 6000000 INFO @ Tue, 21 Apr 2015 13:58:46: 6000000 INFO @ Tue, 21 Apr 2015 13:58:49: 7000000 INFO @ Tue, 21 Apr 2015 13:58:51: 7000000 INFO @ Tue, 21 Apr 2015 13:58:51: 7000000 INFO @ Tue, 21 Apr 2015 13:58:55: 8000000 INFO @ Tue, 21 Apr 2015 13:58:57: 8000000 INFO @ Tue, 21 Apr 2015 13:58:57: 8000000 INFO @ Tue, 21 Apr 2015 13:59:00: 9000000 INFO @ Tue, 21 Apr 2015 13:59:02: 9000000 INFO @ Tue, 21 Apr 2015 13:59:03: 9000000 INFO @ Tue, 21 Apr 2015 13:59:05: 10000000 INFO @ Tue, 21 Apr 2015 13:59:08: 10000000 INFO @ Tue, 21 Apr 2015 13:59:08: 10000000 INFO @ Tue, 21 Apr 2015 13:59:10: 11000000 INFO @ Tue, 21 Apr 2015 13:59:13: 11000000 INFO @ Tue, 21 Apr 2015 13:59:14: 11000000 INFO @ Tue, 21 Apr 2015 13:59:15: 12000000 INFO @ Tue, 21 Apr 2015 13:59:19: 12000000 INFO @ Tue, 21 Apr 2015 13:59:20: 12000000 INFO @ Tue, 21 Apr 2015 13:59:20: 13000000 INFO @ Tue, 21 Apr 2015 13:59:25: 13000000 INFO @ Tue, 21 Apr 2015 13:59:25: 14000000 INFO @ Tue, 21 Apr 2015 13:59:26: 13000000 INFO @ Tue, 21 Apr 2015 13:59:31: 15000000 INFO @ Tue, 21 Apr 2015 13:59:31: 14000000 INFO @ Tue, 21 Apr 2015 13:59:32: 14000000 INFO @ Tue, 21 Apr 2015 13:59:36: 16000000 INFO @ Tue, 21 Apr 2015 13:59:36: 15000000 INFO @ Tue, 21 Apr 2015 13:59:38: 15000000 INFO @ Tue, 21 Apr 2015 13:59:41: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:59:41: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:59:41: #1 total tags in treatment: 16989010 INFO @ Tue, 21 Apr 2015 13:59:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:59:41: #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 13:59:42: 16000000 INFO @ Tue, 21 Apr 2015 13:59:44: 16000000 INFO @ Tue, 21 Apr 2015 13:59:44: #1 tags after filtering in treatment: 16983335 INFO @ Tue, 21 Apr 2015 13:59:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:59:44: #1 finished! INFO @ Tue, 21 Apr 2015 13:59:44: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:59:47: #2 number of paired peaks: 2494 INFO @ Tue, 21 Apr 2015 13:59:47: start model_add_line... INFO @ Tue, 21 Apr 2015 13:59:48: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:59:48: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:59:48: #1 total tags in treatment: 16989010 INFO @ Tue, 21 Apr 2015 13:59:48: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:59:48: #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 13:59:49: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:59:49: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:59:49: #1 total tags in treatment: 16989010 INFO @ Tue, 21 Apr 2015 13:59:49: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:59:49: #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 13:59:51: #1 tags after filtering in treatment: 16983335 INFO @ Tue, 21 Apr 2015 13:59:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:59:51: #1 finished! INFO @ Tue, 21 Apr 2015 13:59:51: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:59:52: #1 tags after filtering in treatment: 16983335 INFO @ Tue, 21 Apr 2015 13:59:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:59:52: #1 finished! INFO @ Tue, 21 Apr 2015 13:59:52: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:59:54: #2 number of paired peaks: 2494 INFO @ Tue, 21 Apr 2015 13:59:54: start model_add_line... INFO @ Tue, 21 Apr 2015 13:59:56: #2 number of paired peaks: 2494 INFO @ Tue, 21 Apr 2015 13:59:56: start model_add_line... INFO @ Tue, 21 Apr 2015 14:00:12: start X-correlation... INFO @ Tue, 21 Apr 2015 14:00:12: end of X-cor INFO @ Tue, 21 Apr 2015 14:00:12: #2 finished! INFO @ Tue, 21 Apr 2015 14:00:12: #2 predicted fragment length is 99 bps INFO @ Tue, 21 Apr 2015 14:00:12: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 21 Apr 2015 14:00:12: #2.2 Generate R script for model : SRX066246.20_model.r INFO @ Tue, 21 Apr 2015 14:00:12: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:00:19: start X-correlation... INFO @ Tue, 21 Apr 2015 14:00:19: end of X-cor INFO @ Tue, 21 Apr 2015 14:00:19: #2 finished! INFO @ Tue, 21 Apr 2015 14:00:19: #2 predicted fragment length is 99 bps INFO @ Tue, 21 Apr 2015 14:00:19: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 21 Apr 2015 14:00:19: #2.2 Generate R script for model : SRX066246.10_model.r INFO @ Tue, 21 Apr 2015 14:00:19: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:00:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:00:22: start X-correlation... INFO @ Tue, 21 Apr 2015 14:00:22: end of X-cor INFO @ Tue, 21 Apr 2015 14:00:22: #2 finished! INFO @ Tue, 21 Apr 2015 14:00:22: #2 predicted fragment length is 99 bps INFO @ Tue, 21 Apr 2015 14:00:22: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 21 Apr 2015 14:00:22: #2.2 Generate R script for model : SRX066246.05_model.r INFO @ Tue, 21 Apr 2015 14:00:22: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:00:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:01:42: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:01:49: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:01:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:02:49: #4 Write output xls file... SRX066246.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:02:50: #4 Write peak in narrowPeak format file... SRX066246.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:02:50: #4 Write summits bed file... SRX066246.20_summits.bed INFO @ Tue, 21 Apr 2015 14:02:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6086 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:02:59: #4 Write output xls file... SRX066246.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:03:00: #4 Write peak in narrowPeak format file... SRX066246.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:03:00: #4 Write summits bed file... SRX066246.10_summits.bed INFO @ Tue, 21 Apr 2015 14:03:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9262 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:03:14: #4 Write output xls file... SRX066246.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:03:15: #4 Write peak in narrowPeak format file... SRX066246.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:03:15: #4 Write summits bed file... SRX066246.05_summits.bed INFO @ Tue, 21 Apr 2015 14:03:15: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12746 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。