User:Lindenb/Notebook/UMR915/2012/03/05: Difference between revisions
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updated GATK | updated GATK | ||
<pre>$ java -jar /usr/local/package/gatk/GenomeAnalysisTK-1.4-37-g0b29d54/GenomeAnalysisTK.jar -T DepthOfCoverage -omitBaseOutput -omitLocusTable -R /GENOTYPAGE/data/pubdb/ucsc/hg19/chromosomes/hg19.fa -I _jeter.bam -L PCCR.hg19.bed -o _jeter.coverage | |||
INFO 15:46:02,567 RodBindingArgumentTypeDescriptor - Dynamically determined type of PCCR.hg19.bed to be BED | |||
INFO 15:46:02,604 HelpFormatter - --------------------------------------------------------------------------------- | |||
INFO 15:46:02,604 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.4-37-g0b29d54, Compiled 2012/02/27 19:56:39 | |||
INFO 15:46:02,605 HelpFormatter - Copyright (c) 2010 The Broad Institute | |||
INFO 15:46:02,605 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki | |||
INFO 15:46:02,605 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa | |||
INFO 15:46:02,606 HelpFormatter - Program Args: -T DepthOfCoverage -omitBaseOutput -omitLocusTable -R /GENOTYPAGE/data/pubdb/ucsc/hg19/chromosomes/hg19.fa -I _jeter.bam -L PCCR.hg19.bed -o _jeter.coverage | |||
INFO 15:46:02,606 HelpFormatter - Date/Time: 2012/03/05 15:46:02 | |||
INFO 15:46:02,606 HelpFormatter - --------------------------------------------------------------------------------- | |||
INFO 15:46:02,607 HelpFormatter - --------------------------------------------------------------------------------- | |||
INFO 15:46:02,624 GenomeAnalysisEngine - Strictness is SILENT | |||
INFO 15:46:02,675 SAMDataSource$SAMReaders - Initializing SAMRecords in serial | |||
INFO 15:46:02,693 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 | |||
INFO 15:46:04,550 DepthOfCoverageWalker - Per-Locus Depth of Coverage output was omitted | |||
INFO 15:46:04,799 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] | |||
INFO 15:46:04,799 TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining | |||
INFO 15:46:34,838 TraversalEngine - chr1:12953045 2.30e+06 30.3 s 13.2 s 0.9% 55.3 m 54.8 m | |||
INFO 15:47:04,826 TraversalEngine - chr1:22902927 3.82e+06 60.3 s 15.8 s 1.6% 63.5 m 62.5 m | |||
INFO 15:47:34,906 TraversalEngine - chr1:38006313 5.82e+06 90.4 s 15.5 s 2.5% 59.5 m 57.9 m | |||
INFO 15:48:04,919 TraversalEngine - chr1:50310781 7.74e+06 2.0 m 15.6 s 3.3% 60.7 m 58.7 m | |||
INFO 15:48:34,943 TraversalEngine - chr1:74940943 8.77e+06 2.5 m 17.1 s 4.0% 63.0 m 60.5 m | |||
INFO 15:49:04,949 TraversalEngine - chr1:95363394 9.61e+06 3.0 m 18.8 s 4.5% 66.2 m 63.2 m | |||
INFO 15:49:35,001 TraversalEngine - chr1:114133136 1.07e+07 3.5 m 19.7 s 5.1% 68.9 m 65.4 m | |||
INFO 15:50:05,230 TraversalEngine - chr1:145293475 1.15e+07 4.0 m 21.0 s 5.5% 73.1 m 69.0 m | |||
INFO 15:50:35,254 TraversalEngine - chr1:148756537 1.22e+07 4.5 m 22.1 s 5.7% 78.7 m 74.1 m | |||
INFO 15:51:05,429 TraversalEngine - chr1:152382718 1.31e+07 5.0 m 22.9 s 6.1% 81.9 m 76.9 m | |||
INFO 15:51:35,432 TraversalEngine - chr1:159557688 1.53e+07 5.5 m 21.7 s 6.9% 79.9 m 74.4 m | |||
INFO 15:52:05,535 TraversalEngine - chr1:174957825 1.64e+07 6.0 m 22.0 s 7.6% 79.6 m 73.6 m | |||
INFO 15:52:35,564 TraversalEngine - chr1:197112474 1.75e+07 6.5 m 22.4 s 8.2% 79.7 m 73.2 m | |||
INFO 15:53:05,669 TraversalEngine - chr1:212241541 1.89e+07 7.0 m 22.3 s 8.9% 78.7 m 71.7 m | |||
INFO 15:53:35,779 TraversalEngine - chr1:232650196 2.02e+07 7.5 m 22.4 s 9.7% 77.8 m 70.3 m | |||
INFO 15:54:05,817 TraversalEngine - chr1:248512195 2.08e+07 8.0 m 23.1 s 10.2% 78.8 m 70.8 m | |||
INFO 15:54:35,820 TraversalEngine - chr2:26541793 2.18e+07 8.5 m 23.4 s 10.8% 78.7 m 70.2 m | |||
INFO 15:55:05,939 TraversalEngine - chr2:42979334 2.34e+07 9.0 m 23.2 s 11.5% 78.4 m 69.4 m | |||
INFO 15:55:35,999 TraversalEngine - chr2:69098212 2.43e+07 9.5 m 23.5 s 12.1% 78.5 m 69.0 m | |||
INFO 15:56:06,064 TraversalEngine - chr2:87420612 2.56e+07 10.0 m 23.5 s 12.8% 78.5 m 68.5 m | |||
INFO 15:56:36,166 TraversalEngine - chr2:102501806 2.66e+07 10.5 m 23.8 s 13.3% 79.4 m 68.9 m | |||
INFO 15:57:06,795 TraversalEngine - chr2:113147040 2.71e+07 11.0 m 24.4 s 13.6% 81.3 m 70.3 m | |||
INFO 15:57:36,818 TraversalEngine - chr2:135965129 2.80e+07 11.5 m 24.7 s 14.1% 81.8 m 70.2 m | |||
INFO 15:58:06,997 TraversalEngine - chr2:162226669 2.87e+07 12.0 m 25.1 s 14.6% 82.4 m 70.4 m | |||
INFO 15:58:37,012 TraversalEngine - chr2:178364420 2.96e+07 12.5 m 25.4 s 15.2% 82.6 m 70.0 m | |||
INFO 15:59:07,028 TraversalEngine - chr2:179621063 3.09e+07 13.0 m 25.3 s 15.5% 84.3 m 71.3 m | |||
INFO 15:59:37,041 TraversalEngine - chr2:201534345 3.19e+07 13.5 m 25.5 s 16.0% 84.5 m 71.0 m | |||
INFO 16:00:07,080 TraversalEngine - chr2:216299504 3.27e+07 14.0 m 25.7 s 16.5% 84.9 m 70.8 m | |||
INFO 16:00:37,101 TraversalEngine - chr2:234181617 3.47e+07 14.5 m 25.2 s 17.3% 83.9 m 69.4 m | |||
INFO 16:01:07,160 TraversalEngine - chr3:11851189 3.61e+07 15.0 m 25.0 s 18.1% 83.0 m 68.0 m | |||
INFO 16:01:37,222 TraversalEngine - chr3:38607966 3.72e+07 15.5 m 25.1 s 18.8% 82.8 m 67.2 m | |||
INFO 16:02:07,274 TraversalEngine - chr3:49201365 3.95e+07 16.0 m 24.4 s 19.6% 82.0 m 65.9 m | |||
INFO 16:02:37,347 TraversalEngine - chr3:63638404 4.18e+07 16.5 m 23.8 s 20.4% 81.1 m 64.6 m | |||
INFO 16:03:07,389 TraversalEngine - chr3:107778305 4.24e+07 17.0 m 24.1 s 20.9% 81.6 m 64.6 m | |||
INFO 16:03:37,411 TraversalEngine - chr3:124437796 4.32e+07 17.5 m 24.4 s 21.5% 81.7 m 64.2 m | |||
INFO 16:04:07,468 TraversalEngine - chr3:142525004 4.43e+07 18.0 m 24.4 s 22.2% 81.4 m 63.4 m | |||
INFO 16:04:37,947 TraversalEngine - chr3:172163093 4.51e+07 18.6 m 24.7 s 22.7% 81.6 m 63.1 m | |||
INFO 16:05:08,080 TraversalEngine - chr3:195511758 4.64e+07 19.1 m 24.6 s 23.4% 81.5 m 62.4 m | |||
INFO 16:05:38,311 TraversalEngine - chr4:9401016 4.76e+07 19.6 m 24.7 s 24.1% 81.3 m 61.7 m | |||
INFO 16:06:08,424 TraversalEngine - chr4:44691249 4.83e+07 20.1 m 24.9 s 24.6% 81.5 m 61.5 m | |||
INFO 16:06:38,570 TraversalEngine - chr4:73968224 4.91e+07 20.6 m 25.1 s 25.1% 81.8 m 61.2 m | |||
INFO 16:07:08,644 TraversalEngine - chr4:95561441 4.99e+07 21.1 m 25.4 s 25.7% 81.9 m 60.9 m | |||
INFO 16:07:38,669 TraversalEngine - chr4:123857249 5.07e+07 21.6 m 25.5 s 26.3% 82.0 m 60.4 m | |||
INFO 16:08:08,739 TraversalEngine - chr4:159136361 5.14e+07 22.1 m 25.8 s 26.9% 82.1 m 60.1 m | |||
INFO 16:08:39,042 TraversalEngine - chr4:190981641 5.21e+07 22.6 m 26.0 s 27.4% 82.5 m 59.9 m | |||
INFO 16:09:09,130 TraversalEngine - chr5:37183807 5.31e+07 23.1 m 26.1 s 28.0% 82.3 m 59.2 m | |||
INFO 16:09:39,133 TraversalEngine - chr5:67589577 5.39e+07 23.6 m 26.2 s 28.6% 82.4 m 58.9 m | |||
INFO 16:10:09,165 TraversalEngine - chr5:80762868 5.46e+07 24.1 m 26.5 s 29.1% 82.8 m 58.7 m | |||
INFO 16:10:39,166 TraversalEngine - chr5:118835178 5.53e+07 24.6 m 26.6 s 29.6% 83.0 m 58.4 m | |||
INFO 16:11:09,216 TraversalEngine - chr5:140050925 5.65e+07 25.1 m 26.6 s 30.3% 82.8 m 57.8 m | |||
INFO 16:11:39,294 TraversalEngine - chr5:151125893 5.76e+07 25.6 m 26.6 s 30.9% 82.7 m 57.1 m | |||
INFO 16:12:09,341 TraversalEngine - chr5:179013366 5.88e+07 26.1 m 26.6 s 31.7% 82.4 m 56.3 m | |||
INFO 16:12:39,407 TraversalEngine - chr6:25779329 5.98e+07 26.6 m 26.7 s 32.3% 82.3 m 55.7 m | |||
INFO 16:13:09,494 TraversalEngine - chr6:31970082 6.17e+07 27.1 m 26.4 s 33.0% 82.1 m 55.0 m | |||
INFO 16:13:39,517 TraversalEngine - chr6:43271871 6.43e+07 27.6 m 25.7 s 33.9% 81.4 m 53.8 m | |||
INFO 16:14:09,679 TraversalEngine - chr6:62442650 6.54e+07 28.1 m 25.8 s 34.4% 81.6 m 53.5 m | |||
INFO 16:14:39,746 TraversalEngine - chr6:91233448 6.63e+07 28.6 m 25.9 s 35.0% 81.6 m 53.0 m | |||
INFO 16:15:09,785 TraversalEngine - chr6:123658853 6.72e+07 29.1 m 26.0 s 35.6% 81.6 m 52.5 m | |||
INFO 16:15:39,789 TraversalEngine - chr6:147042690 6.79e+07 29.6 m 26.1 s 36.2% 81.7 m 52.1 m | |||
INFO 16:16:09,839 TraversalEngine - chr6:167570907 6.88e+07 30.1 m 26.3 s 36.8% 81.8 m 51.7 m | |||
INFO 16:16:40,040 TraversalEngine - chr7:20687564 7.00e+07 30.6 m 26.2 s 37.5% 81.6 m 51.0 m | |||
INFO 16:17:10,069 TraversalEngine - chr7:44294228 7.09e+07 31.1 m 26.3 s 38.1% 81.6 m 50.5 m | |||
INFO 16:17:40,277 TraversalEngine - chr7:74943797 7.19e+07 31.6 m 26.4 s 38.7% 81.6 m 50.0 m | |||
INFO 16:18:10,352 TraversalEngine - chr7:93518466 7.26e+07 32.1 m 26.5 s 39.3% 81.8 m 49.7 m | |||
INFO 16:18:40,483 TraversalEngine - chr7:100676544 7.40e+07 32.6 m 26.4 s 39.8% 81.9 m 49.3 m | |||
INFO 16:19:10,512 TraversalEngine - chr7:116960804 7.49e+07 33.1 m 26.5 s 40.3% 82.1 m 49.0 m | |||
INFO 16:19:40,584 TraversalEngine - chr7:140373233 7.60e+07 33.6 m 26.5 s 41.0% 82.0 m 48.4 m | |||
INFO 16:20:10,634 TraversalEngine - chr7:154774881 7.74e+07 34.1 m 26.4 s 41.6% 81.9 m 47.8 m | |||
INFO 16:20:40,686 TraversalEngine - chr8:15519796 7.80e+07 34.6 m 26.6 s 42.1% 82.2 m 47.6 m | |||
INFO 16:21:10,741 TraversalEngine - chr8:38034692 7.91e+07 35.1 m 26.6 s 42.8% 82.1 m 47.0 m | |||
INFO 16:21:40,826 TraversalEngine - chr8:70488386 8.00e+07 35.6 m 26.7 s 43.4% 82.1 m 46.5 m | |||
INFO 16:22:10,877 TraversalEngine - chr8:103281349 8.07e+07 36.1 m 26.8 s 44.0% 82.1 m 46.0 m | |||
INFO 16:22:40,886 TraversalEngine - chr8:134145808 8.15e+07 36.6 m 26.9 s 44.5% 82.2 m 45.6 m | |||
INFO 16:23:10,963 TraversalEngine - chr9:18661968 8.35e+07 37.1 m 26.7 s 45.4% 81.7 m 44.5 m | |||
INFO 16:23:41,037 TraversalEngine - chr9:37442427 8.49e+07 37.6 m 26.6 s 46.0% 81.7 m 44.1 m | |||
INFO 16:24:11,114 TraversalEngine - chr9:70871874 8.52e+07 38.1 m 26.8 s 46.3% 82.3 m 44.2 m | |||
INFO 16:24:41,129 TraversalEngine - chr9:95418779 8.59e+07 38.6 m 27.0 s 46.9% 82.4 m 43.8 m | |||
INFO 16:25:11,139 TraversalEngine - chr9:114151910 8.68e+07 39.1 m 27.0 s 47.5% 82.3 m 43.2 m | |||
INFO 16:25:41,161 TraversalEngine - chr9:131343216 8.83e+07 39.6 m 26.9 s 48.3% 82.0 m 42.4 m | |||
INFO 16:26:11,278 TraversalEngine - chr10:5789958 9.13e+07 40.1 m 26.4 s 49.4% 81.2 m 41.1 m | |||
INFO 16:26:41,348 TraversalEngine - chr10:29169105 9.22e+07 40.6 m 26.4 s 50.0% 81.1 m 40.5 m | |||
INFO 16:27:11,402 TraversalEngine - chr10:50599255 9.28e+07 41.1 m 26.6 s 50.5% 81.4 m 40.2 m | |||
INFO 16:27:41,436 TraversalEngine - chr10:73892870 9.38e+07 41.6 m 26.6 s 51.1% 81.4 m 39.8 m | |||
INFO 16:28:11,443 TraversalEngine - chr10:95069838 9.49e+07 42.1 m 26.6 s 51.8% 81.4 m 39.2 m | |||
INFO 16:28:41,461 TraversalEngine - chr10:105947244 9.66e+07 42.6 m 26.5 s 52.5% 81.1 m 38.5 m | |||
INFO 16:29:11,528 TraversalEngine - chr10:127797216 9.76e+07 43.1 m 26.5 s 53.2% 81.1 m 38.0 m | |||
INFO 16:29:41,638 TraversalEngine - chr11:5718554 9.99e+07 43.6 m 26.2 s 54.0% 80.8 m 37.1 m | |||
INFO 16:30:11,704 TraversalEngine - chr11:18420934 1.01e+08 44.1 m 26.2 s 54.7% 80.7 m 36.6 m | |||
INFO 16:30:41,725 TraversalEngine - chr11:48131654 1.02e+08 44.6 m 26.1 s 55.4% 80.6 m 35.9 m | |||
INFO 16:31:11,837 TraversalEngine - chr11:59829988 1.03e+08 45.1 m 26.3 s 55.8% 80.9 m 35.8 m | |||
INFO 16:31:41,883 TraversalEngine - chr11:67258295 1.06e+08 45.6 m 25.8 s 56.8% 80.3 m 34.7 m | |||
INFO 16:32:12,167 TraversalEngine - chr11:89534773 1.07e+08 46.1 m 25.8 s 57.6% 80.1 m 33.9 m | |||
INFO 16:32:42,291 TraversalEngine - chr11:108382050 1.08e+08 46.6 m 25.9 s 58.1% 80.3 m 33.7 m | |||
INFO 16:33:12,561 TraversalEngine - chr11:124056341 1.10e+08 47.1 m 25.8 s 58.8% 80.2 m 33.0 m | |||
INFO 16:33:42,578 TraversalEngine - chr12:7060801 1.11e+08 47.6 m 25.7 s 59.6% 80.0 m 32.4 m | |||
INFO 16:34:12,625 TraversalEngine - chr12:21422680 1.12e+08 48.1 m 25.7 s 60.1% 80.1 m 32.0 m | |||
INFO 16:34:42,737 TraversalEngine - chr12:46231482 1.13e+08 48.6 m 25.8 s 60.7% 80.2 m 31.5 m | |||
INFO 16:35:12,768 TraversalEngine - chr12:54967139 1.15e+08 49.1 m 25.5 s 61.5% 79.9 m 30.8 m | |||
INFO 16:35:42,823 TraversalEngine - chr12:68052355 1.17e+08 49.6 m 25.4 s 62.1% 79.9 m 30.2 m | |||
INFO 16:36:12,878 TraversalEngine - chr12:97337512 1.18e+08 50.1 m 25.4 s 62.7% 79.9 m 29.8 m | |||
INFO 16:36:42,898 TraversalEngine - chr12:112669451 1.19e+08 50.6 m 25.4 s 63.4% 79.9 m 29.3 m | |||
INFO 16:37:12,953 TraversalEngine - chr12:131649715 1.21e+08 51.1 m 25.4 s 64.2% 79.7 m 28.5 m | |||
INFO 16:37:42,954 TraversalEngine - chr13:34410256 1.22e+08 51.6 m 25.4 s 64.8% 79.6 m 28.0 m | |||
INFO 16:38:13,028 TraversalEngine - chr13:57743317 1.23e+08 52.1 m 25.5 s 65.4% 79.7 m 27.6 m | |||
INFO 16:38:43,037 TraversalEngine - chr13:114164602 1.24e+08 52.6 m 25.5 s 66.1% 79.6 m 27.0 m | |||
INFO 16:39:13,074 TraversalEngine - chr14:31070929 1.26e+08 53.1 m 25.4 s 66.8% 79.6 m 26.5 m | |||
INFO 16:39:43,174 TraversalEngine - chr14:58471784 1.27e+08 53.6 m 25.4 s 67.4% 79.6 m 25.9 m | |||
INFO 16:40:13,260 TraversalEngine - chr14:75276076 1.28e+08 54.1 m 25.4 s 68.1% 79.5 m 25.4 m | |||
INFO 16:40:43,295 TraversalEngine - chr14:101370029 1.29e+08 54.6 m 25.4 s 68.8% 79.4 m 24.7 m | |||
INFO 16:41:13,352 TraversalEngine - chr15:31198095 1.30e+08 55.1 m 25.4 s 69.5% 79.4 m 24.2 m | |||
INFO 16:41:43,378 TraversalEngine - chr15:43328716 1.32e+08 55.6 m 25.3 s 70.1% 79.3 m 23.7 m | |||
INFO 16:42:13,415 TraversalEngine - chr15:52903468 1.33e+08 56.1 m 25.3 s 70.7% 79.4 m 23.3 m | |||
INFO 16:42:44,145 TraversalEngine - chr15:69011163 1.34e+08 56.7 m 25.3 s 71.3% 79.4 m 22.8 m | |||
INFO 16:43:14,184 TraversalEngine - chr15:84657398 1.35e+08 57.2 m 25.3 s 72.1% 79.3 m 22.2 m | |||
INFO 16:43:44,195 TraversalEngine - chr16:789692 1.37e+08 57.7 m 25.2 s 72.8% 79.2 m 21.5 m | |||
INFO 16:44:14,225 TraversalEngine - chr16:15931975 1.40e+08 58.2 m 24.9 s 73.8% 78.8 m 20.6 m | |||
INFO 16:44:44,456 TraversalEngine - chr16:22530534 1.41e+08 58.7 m 25.0 s 74.2% 79.1 m 20.4 m | |||
INFO 16:45:14,472 TraversalEngine - chr16:47292530 1.43e+08 59.2 m 24.9 s 75.0% 78.9 m 19.7 m | |||
INFO 16:45:44,571 TraversalEngine - chr16:69143290 1.45e+08 59.7 m 24.7 s 75.9% 78.6 m 19.0 m | |||
INFO 16:46:14,592 TraversalEngine - chr16:84228835 1.46e+08 60.2 m 24.7 s 76.5% 78.6 m 18.5 m | |||
INFO 16:46:44,605 TraversalEngine - chr17:7160372 1.49e+08 60.7 m 24.5 s 77.5% 78.2 m 17.6 m | |||
INFO 16:47:14,708 TraversalEngine - chr17:16635202 1.51e+08 61.2 m 24.4 s 78.3% 78.2 m 17.0 m | |||
INFO 16:47:44,740 TraversalEngine - chr17:30202424 1.53e+08 61.7 m 24.3 s 79.0% 78.0 m 16.4 m | |||
INFO 16:48:14,838 TraversalEngine - chr17:39086206 1.54e+08 62.2 m 24.2 s 79.7% 78.0 m 15.9 m | |||
INFO 16:48:45,028 TraversalEngine - chr17:45198290 1.56e+08 62.7 m 24.1 s 80.4% 78.0 m 15.3 m | |||
INFO 16:49:15,072 TraversalEngine - chr17:60683461 1.57e+08 63.2 m 24.1 s 81.1% 77.9 m 14.7 m | |||
INFO 16:49:45,126 TraversalEngine - chr17:74570515 1.60e+08 63.7 m 23.9 s 82.0% 77.7 m 14.0 m | |||
INFO 16:50:15,153 TraversalEngine - chr18:13741552 1.62e+08 64.2 m 23.8 s 82.9% 77.4 m 13.2 m | |||
INFO 16:50:45,254 TraversalEngine - chr18:44549376 1.63e+08 64.7 m 23.9 s 83.5% 77.5 m 12.8 m | |||
INFO 16:51:15,260 TraversalEngine - chr19:2189732 1.64e+08 65.2 m 23.8 s 84.4% 77.2 m 12.0 m | |||
INFO 16:51:45,325 TraversalEngine - chr19:9868613 1.66e+08 65.7 m 23.7 s 85.4% 76.9 m 11.3 m | |||
INFO 16:52:15,331 TraversalEngine - chr19:17394596 1.69e+08 66.2 m 23.5 s 86.4% 76.6 m 10.4 m | |||
INFO 16:52:45,420 TraversalEngine - chr19:37240574 1.71e+08 66.7 m 23.4 s 87.4% 76.3 m 9.6 m | |||
INFO 16:53:15,438 TraversalEngine - chr19:44099263 1.73e+08 67.2 m 23.3 s 88.2% 76.2 m 9.0 m | |||
INFO 16:53:45,501 TraversalEngine - chr19:52497000 1.75e+08 67.7 m 23.2 s 89.4% 75.7 m 8.1 m | |||
INFO 16:54:15,518 TraversalEngine - chr19:56466272 1.76e+08 68.2 m 23.2 s 89.9% 75.8 m 7.7 m | |||
INFO 16:54:45,558 TraversalEngine - chr20:5922631 1.77e+08 68.7 m 23.2 s 90.6% 75.8 m 7.1 m | |||
INFO 16:55:15,579 TraversalEngine - chr20:34090619 1.79e+08 69.2 m 23.2 s 91.4% 75.7 m 6.5 m | |||
INFO 16:55:45,612 TraversalEngine - chr20:51871726 1.80e+08 69.7 m 23.2 s 92.2% 75.6 m 5.9 m | |||
INFO 16:56:15,615 TraversalEngine - chr21:34030098 1.82e+08 70.2 m 23.1 s 93.0% 75.4 m 5.3 m | |||
INFO 16:56:45,671 TraversalEngine - chr22:18081065 1.84e+08 70.7 m 23.1 s 93.9% 75.3 m 4.6 m | |||
INFO 16:57:15,726 TraversalEngine - chr22:31859828 1.85e+08 71.2 m 23.0 s 94.8% 75.1 m 3.9 m | |||
INFO 16:57:45,732 TraversalEngine - chr22:46804945 1.87e+08 71.7 m 23.0 s 95.7% 74.9 m 3.2 m | |||
INFO 16:58:15,748 TraversalEngine - chrX:23018579 1.88e+08 72.2 m 23.0 s 96.5% 74.8 m 2.6 m | |||
INFO 16:58:45,753 TraversalEngine - chrX:48979166 1.89e+08 72.7 m 23.0 s 97.1% 74.8 m 2.1 m | |||
INFO 16:59:15,801 TraversalEngine - chrX:69424814 1.91e+08 73.2 m 23.0 s 97.6% 74.9 m 105.7 s | |||
INFO 16:59:45,908 TraversalEngine - chrX:100615069 1.92e+08 73.7 m 23.1 s 98.2% 75.1 m 82.0 s | |||
INFO 17:00:16,016 TraversalEngine - chrX:119206743 1.92e+08 74.2 m 23.2 s 98.7% 75.2 m 58.4 s | |||
INFO 17:00:46,123 TraversalEngine - chrX:140995052 1.93e+08 74.7 m 23.2 s 99.2% 75.3 m 36.4 s | |||
INFO 17:01:16,288 DepthOfCoverageWalker - Printing summary info | |||
INFO 17:01:16,294 TraversalEngine - Total runtime 4511.74 secs, 75.20 min, 1.25 hours | |||
INFO 17:01:16,295 TraversalEngine - 3113436 reads were filtered out during traversal out of 392820507 total (0.79%) | |||
INFO 17:01:16,295 TraversalEngine - -> 3113436 reads (0.79% of total) failing UnmappedReadFilter </pre> | |||
==Knime4bio== | ==Knime4bio== |
Revision as of 09:04, 5 March 2012
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DailyProject RPTransfert BAM to server: XXXX1.fastq.gz 100% 58GB 32.6MB/s 30:29 XXXX2.fastq.gz 100% 58GB 32.7MB/s 30:21 XXXXsorted.bam 100% 97GB 30.8MB/s 53:36 XXXXsorted.bam.bai 100% 8595KB 8.4MB/s 00:01 XXXX1.fastq.gz 100% 53GB 28.8MB/s 31:36 XXXX2.fastq.gz 100% 53GB 33.1MB/s 27:29 XXXXsorted.bam 100% 78GB 33.1MB/s 40:21 XXXXsorted.bam.bai 100% 8565KB 8.4MB/s 00:01 XXXX1.fastq.gz 100% 51GB 33.0MB/s 26:34 XXXX2.fastq.gz 100% 51GB 33.1MB/s 26:22 XXXXsorted.bam 100% 80GB 33.1MB/s 41:13 XXXXsorted.bam.bai 100% 8608KB 8.4MB/s 00:00 XXXX1.fastq.gz 100% 52GB 33.1MB/s 26:37 XXXX2.fastq.gz 100% 52GB 33.1MB/s 26:37 XXXXsorted.bam 100% 83GB 33.1MB/s 42:49 XXXXsorted.bam.bai 100% 8607KB 8.4MB/s 00:00 XXXX1.fastq.gz 100% 57GB 33.1MB/s 29:34 XXXX2.fastq.gz 100% 57GB 33.1MB/s 29:38 XXXXsorted.bam 100% 92GB 33.1MB/s 47:34 XXXXsorted.bam.bai 100% 8619KB 8.4MB/s 00:00 Test mpileup$ samtools mpileup -D -u -f hg19.fa DataHD20120302/*/*.bam | bcftools view -bvcg - | bcftools view - | grep -v "##" | head -n 3 | verticalize [mpileup] 5 samples in 5 input files <mpileup> Set max per-file depth to 1600 >>> 2 $1 #CHROM chr1 $2 POS 9997 $3 ID . $4 REF N $5 ALT A $6 QUAL 3.55 $7 FILTER . $8 INFO DP=1;AF1=1;AC1=10;DP4=0,0,1,0;MQ=60;FQ=-25.5 $9 FORMAT GT:PL:DP:GQ $10 DataHD20120302/CD5121/CD5121_sorted.bam 0/1:31,3,0:1:5 $11 DataHD20120302/CD8260/CD8260_sorted.bam 0/0:0,0,0:0:3 $12 DataHD20120302/CD8262/CD8262_sorted.bam 0/0:0,0,0:0:3 $13 DataHD20120302/CD8289/CD8289_sorted.bam 0/0:0,0,0:0:3 $14 DataHD20120302/S0529/S0529_sorted.bam 0/0:0,0,0:0:3 <<< 2 >>> 3 $1 #CHROM chr1 $2 POS 9998 $3 ID . $4 REF N $5 ALT C $6 QUAL 29 $7 FILTER . $8 INFO DP=2;AF1=1;AC1=10;DP4=0,0,2,0;MQ=60;FQ=-27.4 $9 FORMAT GT:PL:DP:GQ $10 DataHD20120302/CD5121/CD5121_sorted.bam 1/1:31,3,0:1:6 $11 DataHD20120302/CD8260/CD8260_sorted.bam 1/1:0,0,0:0:3 $12 DataHD20120302/CD8262/CD8262_sorted.bam 1/1:0,0,0:0:3 $13 DataHD20120302/CD8289/CD8289_sorted.bam 1/1:0,0,0:0:3 $14 DataHD20120302/S0529/S0529_sorted.bam 1/1:31,3,0:1:6 <<< 3 vs only one sample: $ samtools mpileup -D -u -f hg19.fa DataHD20120302/CD5121/CD5121_sorted.bam | bcftools view -bvcg - | bcftools view - | grep -v "##" | head -n 3 | verticalize [mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 >>> 2 $1 #CHROM chr1 $2 POS 9997 $3 ID . $4 REF N $5 ALT A $6 QUAL 3.55 $7 FILTER . $8 INFO DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 $9 FORMAT GT:PL:DP:GQ $10 DataHD20120302/CD5121/CD5121_sorted.bam 0/1:31,3,0:1:4 <<< 2 >>> 3 $1 #CHROM chr1 $2 POS 9998 $3 ID . $4 REF N $5 ALT C $6 QUAL 3.55 $7 FILTER . $8 INFO DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 $9 FORMAT GT:PL:DP:GQ $10 DataHD20120302/CD5121/CD5121_sorted.bam 0/1:31,3,0:1:4 <<< 3 exomeCNVreceived message from author "Thank you for your email. I fixed the problem and the script should be functional now. Please let me know if you notice anything else not working or if you have any question about ExomeCNV."
updated GATK $ java -jar /usr/local/package/gatk/GenomeAnalysisTK-1.4-37-g0b29d54/GenomeAnalysisTK.jar -T DepthOfCoverage -omitBaseOutput -omitLocusTable -R /GENOTYPAGE/data/pubdb/ucsc/hg19/chromosomes/hg19.fa -I _jeter.bam -L PCCR.hg19.bed -o _jeter.coverage INFO 15:46:02,567 RodBindingArgumentTypeDescriptor - Dynamically determined type of PCCR.hg19.bed to be BED INFO 15:46:02,604 HelpFormatter - --------------------------------------------------------------------------------- INFO 15:46:02,604 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.4-37-g0b29d54, Compiled 2012/02/27 19:56:39 INFO 15:46:02,605 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 15:46:02,605 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 15:46:02,605 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 15:46:02,606 HelpFormatter - Program Args: -T DepthOfCoverage -omitBaseOutput -omitLocusTable -R /GENOTYPAGE/data/pubdb/ucsc/hg19/chromosomes/hg19.fa -I _jeter.bam -L PCCR.hg19.bed -o _jeter.coverage INFO 15:46:02,606 HelpFormatter - Date/Time: 2012/03/05 15:46:02 INFO 15:46:02,606 HelpFormatter - --------------------------------------------------------------------------------- INFO 15:46:02,607 HelpFormatter - --------------------------------------------------------------------------------- INFO 15:46:02,624 GenomeAnalysisEngine - Strictness is SILENT INFO 15:46:02,675 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 15:46:02,693 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 15:46:04,550 DepthOfCoverageWalker - Per-Locus Depth of Coverage output was omitted INFO 15:46:04,799 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] INFO 15:46:04,799 TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining INFO 15:46:34,838 TraversalEngine - chr1:12953045 2.30e+06 30.3 s 13.2 s 0.9% 55.3 m 54.8 m INFO 15:47:04,826 TraversalEngine - chr1:22902927 3.82e+06 60.3 s 15.8 s 1.6% 63.5 m 62.5 m INFO 15:47:34,906 TraversalEngine - chr1:38006313 5.82e+06 90.4 s 15.5 s 2.5% 59.5 m 57.9 m INFO 15:48:04,919 TraversalEngine - chr1:50310781 7.74e+06 2.0 m 15.6 s 3.3% 60.7 m 58.7 m INFO 15:48:34,943 TraversalEngine - chr1:74940943 8.77e+06 2.5 m 17.1 s 4.0% 63.0 m 60.5 m INFO 15:49:04,949 TraversalEngine - chr1:95363394 9.61e+06 3.0 m 18.8 s 4.5% 66.2 m 63.2 m INFO 15:49:35,001 TraversalEngine - chr1:114133136 1.07e+07 3.5 m 19.7 s 5.1% 68.9 m 65.4 m INFO 15:50:05,230 TraversalEngine - chr1:145293475 1.15e+07 4.0 m 21.0 s 5.5% 73.1 m 69.0 m INFO 15:50:35,254 TraversalEngine - chr1:148756537 1.22e+07 4.5 m 22.1 s 5.7% 78.7 m 74.1 m INFO 15:51:05,429 TraversalEngine - chr1:152382718 1.31e+07 5.0 m 22.9 s 6.1% 81.9 m 76.9 m INFO 15:51:35,432 TraversalEngine - chr1:159557688 1.53e+07 5.5 m 21.7 s 6.9% 79.9 m 74.4 m INFO 15:52:05,535 TraversalEngine - chr1:174957825 1.64e+07 6.0 m 22.0 s 7.6% 79.6 m 73.6 m INFO 15:52:35,564 TraversalEngine - chr1:197112474 1.75e+07 6.5 m 22.4 s 8.2% 79.7 m 73.2 m INFO 15:53:05,669 TraversalEngine - chr1:212241541 1.89e+07 7.0 m 22.3 s 8.9% 78.7 m 71.7 m INFO 15:53:35,779 TraversalEngine - chr1:232650196 2.02e+07 7.5 m 22.4 s 9.7% 77.8 m 70.3 m INFO 15:54:05,817 TraversalEngine - chr1:248512195 2.08e+07 8.0 m 23.1 s 10.2% 78.8 m 70.8 m INFO 15:54:35,820 TraversalEngine - chr2:26541793 2.18e+07 8.5 m 23.4 s 10.8% 78.7 m 70.2 m INFO 15:55:05,939 TraversalEngine - chr2:42979334 2.34e+07 9.0 m 23.2 s 11.5% 78.4 m 69.4 m INFO 15:55:35,999 TraversalEngine - chr2:69098212 2.43e+07 9.5 m 23.5 s 12.1% 78.5 m 69.0 m INFO 15:56:06,064 TraversalEngine - chr2:87420612 2.56e+07 10.0 m 23.5 s 12.8% 78.5 m 68.5 m INFO 15:56:36,166 TraversalEngine - chr2:102501806 2.66e+07 10.5 m 23.8 s 13.3% 79.4 m 68.9 m INFO 15:57:06,795 TraversalEngine - chr2:113147040 2.71e+07 11.0 m 24.4 s 13.6% 81.3 m 70.3 m INFO 15:57:36,818 TraversalEngine - chr2:135965129 2.80e+07 11.5 m 24.7 s 14.1% 81.8 m 70.2 m INFO 15:58:06,997 TraversalEngine - chr2:162226669 2.87e+07 12.0 m 25.1 s 14.6% 82.4 m 70.4 m INFO 15:58:37,012 TraversalEngine - chr2:178364420 2.96e+07 12.5 m 25.4 s 15.2% 82.6 m 70.0 m INFO 15:59:07,028 TraversalEngine - chr2:179621063 3.09e+07 13.0 m 25.3 s 15.5% 84.3 m 71.3 m INFO 15:59:37,041 TraversalEngine - chr2:201534345 3.19e+07 13.5 m 25.5 s 16.0% 84.5 m 71.0 m INFO 16:00:07,080 TraversalEngine - chr2:216299504 3.27e+07 14.0 m 25.7 s 16.5% 84.9 m 70.8 m INFO 16:00:37,101 TraversalEngine - chr2:234181617 3.47e+07 14.5 m 25.2 s 17.3% 83.9 m 69.4 m INFO 16:01:07,160 TraversalEngine - chr3:11851189 3.61e+07 15.0 m 25.0 s 18.1% 83.0 m 68.0 m INFO 16:01:37,222 TraversalEngine - chr3:38607966 3.72e+07 15.5 m 25.1 s 18.8% 82.8 m 67.2 m INFO 16:02:07,274 TraversalEngine - chr3:49201365 3.95e+07 16.0 m 24.4 s 19.6% 82.0 m 65.9 m INFO 16:02:37,347 TraversalEngine - chr3:63638404 4.18e+07 16.5 m 23.8 s 20.4% 81.1 m 64.6 m INFO 16:03:07,389 TraversalEngine - chr3:107778305 4.24e+07 17.0 m 24.1 s 20.9% 81.6 m 64.6 m INFO 16:03:37,411 TraversalEngine - chr3:124437796 4.32e+07 17.5 m 24.4 s 21.5% 81.7 m 64.2 m INFO 16:04:07,468 TraversalEngine - chr3:142525004 4.43e+07 18.0 m 24.4 s 22.2% 81.4 m 63.4 m INFO 16:04:37,947 TraversalEngine - chr3:172163093 4.51e+07 18.6 m 24.7 s 22.7% 81.6 m 63.1 m INFO 16:05:08,080 TraversalEngine - chr3:195511758 4.64e+07 19.1 m 24.6 s 23.4% 81.5 m 62.4 m INFO 16:05:38,311 TraversalEngine - chr4:9401016 4.76e+07 19.6 m 24.7 s 24.1% 81.3 m 61.7 m INFO 16:06:08,424 TraversalEngine - chr4:44691249 4.83e+07 20.1 m 24.9 s 24.6% 81.5 m 61.5 m INFO 16:06:38,570 TraversalEngine - chr4:73968224 4.91e+07 20.6 m 25.1 s 25.1% 81.8 m 61.2 m INFO 16:07:08,644 TraversalEngine - chr4:95561441 4.99e+07 21.1 m 25.4 s 25.7% 81.9 m 60.9 m INFO 16:07:38,669 TraversalEngine - chr4:123857249 5.07e+07 21.6 m 25.5 s 26.3% 82.0 m 60.4 m INFO 16:08:08,739 TraversalEngine - chr4:159136361 5.14e+07 22.1 m 25.8 s 26.9% 82.1 m 60.1 m INFO 16:08:39,042 TraversalEngine - chr4:190981641 5.21e+07 22.6 m 26.0 s 27.4% 82.5 m 59.9 m INFO 16:09:09,130 TraversalEngine - chr5:37183807 5.31e+07 23.1 m 26.1 s 28.0% 82.3 m 59.2 m INFO 16:09:39,133 TraversalEngine - chr5:67589577 5.39e+07 23.6 m 26.2 s 28.6% 82.4 m 58.9 m INFO 16:10:09,165 TraversalEngine - chr5:80762868 5.46e+07 24.1 m 26.5 s 29.1% 82.8 m 58.7 m INFO 16:10:39,166 TraversalEngine - chr5:118835178 5.53e+07 24.6 m 26.6 s 29.6% 83.0 m 58.4 m INFO 16:11:09,216 TraversalEngine - chr5:140050925 5.65e+07 25.1 m 26.6 s 30.3% 82.8 m 57.8 m INFO 16:11:39,294 TraversalEngine - chr5:151125893 5.76e+07 25.6 m 26.6 s 30.9% 82.7 m 57.1 m INFO 16:12:09,341 TraversalEngine - chr5:179013366 5.88e+07 26.1 m 26.6 s 31.7% 82.4 m 56.3 m INFO 16:12:39,407 TraversalEngine - chr6:25779329 5.98e+07 26.6 m 26.7 s 32.3% 82.3 m 55.7 m INFO 16:13:09,494 TraversalEngine - chr6:31970082 6.17e+07 27.1 m 26.4 s 33.0% 82.1 m 55.0 m INFO 16:13:39,517 TraversalEngine - chr6:43271871 6.43e+07 27.6 m 25.7 s 33.9% 81.4 m 53.8 m INFO 16:14:09,679 TraversalEngine - chr6:62442650 6.54e+07 28.1 m 25.8 s 34.4% 81.6 m 53.5 m INFO 16:14:39,746 TraversalEngine - chr6:91233448 6.63e+07 28.6 m 25.9 s 35.0% 81.6 m 53.0 m INFO 16:15:09,785 TraversalEngine - chr6:123658853 6.72e+07 29.1 m 26.0 s 35.6% 81.6 m 52.5 m INFO 16:15:39,789 TraversalEngine - chr6:147042690 6.79e+07 29.6 m 26.1 s 36.2% 81.7 m 52.1 m INFO 16:16:09,839 TraversalEngine - chr6:167570907 6.88e+07 30.1 m 26.3 s 36.8% 81.8 m 51.7 m INFO 16:16:40,040 TraversalEngine - chr7:20687564 7.00e+07 30.6 m 26.2 s 37.5% 81.6 m 51.0 m INFO 16:17:10,069 TraversalEngine - chr7:44294228 7.09e+07 31.1 m 26.3 s 38.1% 81.6 m 50.5 m INFO 16:17:40,277 TraversalEngine - chr7:74943797 7.19e+07 31.6 m 26.4 s 38.7% 81.6 m 50.0 m INFO 16:18:10,352 TraversalEngine - chr7:93518466 7.26e+07 32.1 m 26.5 s 39.3% 81.8 m 49.7 m INFO 16:18:40,483 TraversalEngine - chr7:100676544 7.40e+07 32.6 m 26.4 s 39.8% 81.9 m 49.3 m INFO 16:19:10,512 TraversalEngine - chr7:116960804 7.49e+07 33.1 m 26.5 s 40.3% 82.1 m 49.0 m INFO 16:19:40,584 TraversalEngine - chr7:140373233 7.60e+07 33.6 m 26.5 s 41.0% 82.0 m 48.4 m INFO 16:20:10,634 TraversalEngine - chr7:154774881 7.74e+07 34.1 m 26.4 s 41.6% 81.9 m 47.8 m INFO 16:20:40,686 TraversalEngine - chr8:15519796 7.80e+07 34.6 m 26.6 s 42.1% 82.2 m 47.6 m INFO 16:21:10,741 TraversalEngine - chr8:38034692 7.91e+07 35.1 m 26.6 s 42.8% 82.1 m 47.0 m INFO 16:21:40,826 TraversalEngine - chr8:70488386 8.00e+07 35.6 m 26.7 s 43.4% 82.1 m 46.5 m INFO 16:22:10,877 TraversalEngine - chr8:103281349 8.07e+07 36.1 m 26.8 s 44.0% 82.1 m 46.0 m INFO 16:22:40,886 TraversalEngine - chr8:134145808 8.15e+07 36.6 m 26.9 s 44.5% 82.2 m 45.6 m INFO 16:23:10,963 TraversalEngine - chr9:18661968 8.35e+07 37.1 m 26.7 s 45.4% 81.7 m 44.5 m INFO 16:23:41,037 TraversalEngine - chr9:37442427 8.49e+07 37.6 m 26.6 s 46.0% 81.7 m 44.1 m INFO 16:24:11,114 TraversalEngine - chr9:70871874 8.52e+07 38.1 m 26.8 s 46.3% 82.3 m 44.2 m INFO 16:24:41,129 TraversalEngine - chr9:95418779 8.59e+07 38.6 m 27.0 s 46.9% 82.4 m 43.8 m INFO 16:25:11,139 TraversalEngine - chr9:114151910 8.68e+07 39.1 m 27.0 s 47.5% 82.3 m 43.2 m INFO 16:25:41,161 TraversalEngine - chr9:131343216 8.83e+07 39.6 m 26.9 s 48.3% 82.0 m 42.4 m INFO 16:26:11,278 TraversalEngine - chr10:5789958 9.13e+07 40.1 m 26.4 s 49.4% 81.2 m 41.1 m INFO 16:26:41,348 TraversalEngine - chr10:29169105 9.22e+07 40.6 m 26.4 s 50.0% 81.1 m 40.5 m INFO 16:27:11,402 TraversalEngine - chr10:50599255 9.28e+07 41.1 m 26.6 s 50.5% 81.4 m 40.2 m INFO 16:27:41,436 TraversalEngine - chr10:73892870 9.38e+07 41.6 m 26.6 s 51.1% 81.4 m 39.8 m INFO 16:28:11,443 TraversalEngine - chr10:95069838 9.49e+07 42.1 m 26.6 s 51.8% 81.4 m 39.2 m INFO 16:28:41,461 TraversalEngine - chr10:105947244 9.66e+07 42.6 m 26.5 s 52.5% 81.1 m 38.5 m INFO 16:29:11,528 TraversalEngine - chr10:127797216 9.76e+07 43.1 m 26.5 s 53.2% 81.1 m 38.0 m INFO 16:29:41,638 TraversalEngine - chr11:5718554 9.99e+07 43.6 m 26.2 s 54.0% 80.8 m 37.1 m INFO 16:30:11,704 TraversalEngine - chr11:18420934 1.01e+08 44.1 m 26.2 s 54.7% 80.7 m 36.6 m INFO 16:30:41,725 TraversalEngine - chr11:48131654 1.02e+08 44.6 m 26.1 s 55.4% 80.6 m 35.9 m INFO 16:31:11,837 TraversalEngine - chr11:59829988 1.03e+08 45.1 m 26.3 s 55.8% 80.9 m 35.8 m INFO 16:31:41,883 TraversalEngine - chr11:67258295 1.06e+08 45.6 m 25.8 s 56.8% 80.3 m 34.7 m INFO 16:32:12,167 TraversalEngine - chr11:89534773 1.07e+08 46.1 m 25.8 s 57.6% 80.1 m 33.9 m INFO 16:32:42,291 TraversalEngine - chr11:108382050 1.08e+08 46.6 m 25.9 s 58.1% 80.3 m 33.7 m INFO 16:33:12,561 TraversalEngine - chr11:124056341 1.10e+08 47.1 m 25.8 s 58.8% 80.2 m 33.0 m INFO 16:33:42,578 TraversalEngine - chr12:7060801 1.11e+08 47.6 m 25.7 s 59.6% 80.0 m 32.4 m INFO 16:34:12,625 TraversalEngine - chr12:21422680 1.12e+08 48.1 m 25.7 s 60.1% 80.1 m 32.0 m INFO 16:34:42,737 TraversalEngine - chr12:46231482 1.13e+08 48.6 m 25.8 s 60.7% 80.2 m 31.5 m INFO 16:35:12,768 TraversalEngine - chr12:54967139 1.15e+08 49.1 m 25.5 s 61.5% 79.9 m 30.8 m INFO 16:35:42,823 TraversalEngine - chr12:68052355 1.17e+08 49.6 m 25.4 s 62.1% 79.9 m 30.2 m INFO 16:36:12,878 TraversalEngine - chr12:97337512 1.18e+08 50.1 m 25.4 s 62.7% 79.9 m 29.8 m INFO 16:36:42,898 TraversalEngine - chr12:112669451 1.19e+08 50.6 m 25.4 s 63.4% 79.9 m 29.3 m INFO 16:37:12,953 TraversalEngine - chr12:131649715 1.21e+08 51.1 m 25.4 s 64.2% 79.7 m 28.5 m INFO 16:37:42,954 TraversalEngine - chr13:34410256 1.22e+08 51.6 m 25.4 s 64.8% 79.6 m 28.0 m INFO 16:38:13,028 TraversalEngine - chr13:57743317 1.23e+08 52.1 m 25.5 s 65.4% 79.7 m 27.6 m INFO 16:38:43,037 TraversalEngine - chr13:114164602 1.24e+08 52.6 m 25.5 s 66.1% 79.6 m 27.0 m INFO 16:39:13,074 TraversalEngine - chr14:31070929 1.26e+08 53.1 m 25.4 s 66.8% 79.6 m 26.5 m INFO 16:39:43,174 TraversalEngine - chr14:58471784 1.27e+08 53.6 m 25.4 s 67.4% 79.6 m 25.9 m INFO 16:40:13,260 TraversalEngine - chr14:75276076 1.28e+08 54.1 m 25.4 s 68.1% 79.5 m 25.4 m INFO 16:40:43,295 TraversalEngine - chr14:101370029 1.29e+08 54.6 m 25.4 s 68.8% 79.4 m 24.7 m INFO 16:41:13,352 TraversalEngine - chr15:31198095 1.30e+08 55.1 m 25.4 s 69.5% 79.4 m 24.2 m INFO 16:41:43,378 TraversalEngine - chr15:43328716 1.32e+08 55.6 m 25.3 s 70.1% 79.3 m 23.7 m INFO 16:42:13,415 TraversalEngine - chr15:52903468 1.33e+08 56.1 m 25.3 s 70.7% 79.4 m 23.3 m INFO 16:42:44,145 TraversalEngine - chr15:69011163 1.34e+08 56.7 m 25.3 s 71.3% 79.4 m 22.8 m INFO 16:43:14,184 TraversalEngine - chr15:84657398 1.35e+08 57.2 m 25.3 s 72.1% 79.3 m 22.2 m INFO 16:43:44,195 TraversalEngine - chr16:789692 1.37e+08 57.7 m 25.2 s 72.8% 79.2 m 21.5 m INFO 16:44:14,225 TraversalEngine - chr16:15931975 1.40e+08 58.2 m 24.9 s 73.8% 78.8 m 20.6 m INFO 16:44:44,456 TraversalEngine - chr16:22530534 1.41e+08 58.7 m 25.0 s 74.2% 79.1 m 20.4 m INFO 16:45:14,472 TraversalEngine - chr16:47292530 1.43e+08 59.2 m 24.9 s 75.0% 78.9 m 19.7 m INFO 16:45:44,571 TraversalEngine - chr16:69143290 1.45e+08 59.7 m 24.7 s 75.9% 78.6 m 19.0 m INFO 16:46:14,592 TraversalEngine - chr16:84228835 1.46e+08 60.2 m 24.7 s 76.5% 78.6 m 18.5 m INFO 16:46:44,605 TraversalEngine - chr17:7160372 1.49e+08 60.7 m 24.5 s 77.5% 78.2 m 17.6 m INFO 16:47:14,708 TraversalEngine - chr17:16635202 1.51e+08 61.2 m 24.4 s 78.3% 78.2 m 17.0 m INFO 16:47:44,740 TraversalEngine - chr17:30202424 1.53e+08 61.7 m 24.3 s 79.0% 78.0 m 16.4 m INFO 16:48:14,838 TraversalEngine - chr17:39086206 1.54e+08 62.2 m 24.2 s 79.7% 78.0 m 15.9 m INFO 16:48:45,028 TraversalEngine - chr17:45198290 1.56e+08 62.7 m 24.1 s 80.4% 78.0 m 15.3 m INFO 16:49:15,072 TraversalEngine - chr17:60683461 1.57e+08 63.2 m 24.1 s 81.1% 77.9 m 14.7 m INFO 16:49:45,126 TraversalEngine - chr17:74570515 1.60e+08 63.7 m 23.9 s 82.0% 77.7 m 14.0 m INFO 16:50:15,153 TraversalEngine - chr18:13741552 1.62e+08 64.2 m 23.8 s 82.9% 77.4 m 13.2 m INFO 16:50:45,254 TraversalEngine - chr18:44549376 1.63e+08 64.7 m 23.9 s 83.5% 77.5 m 12.8 m INFO 16:51:15,260 TraversalEngine - chr19:2189732 1.64e+08 65.2 m 23.8 s 84.4% 77.2 m 12.0 m INFO 16:51:45,325 TraversalEngine - chr19:9868613 1.66e+08 65.7 m 23.7 s 85.4% 76.9 m 11.3 m INFO 16:52:15,331 TraversalEngine - chr19:17394596 1.69e+08 66.2 m 23.5 s 86.4% 76.6 m 10.4 m INFO 16:52:45,420 TraversalEngine - chr19:37240574 1.71e+08 66.7 m 23.4 s 87.4% 76.3 m 9.6 m INFO 16:53:15,438 TraversalEngine - chr19:44099263 1.73e+08 67.2 m 23.3 s 88.2% 76.2 m 9.0 m INFO 16:53:45,501 TraversalEngine - chr19:52497000 1.75e+08 67.7 m 23.2 s 89.4% 75.7 m 8.1 m INFO 16:54:15,518 TraversalEngine - chr19:56466272 1.76e+08 68.2 m 23.2 s 89.9% 75.8 m 7.7 m INFO 16:54:45,558 TraversalEngine - chr20:5922631 1.77e+08 68.7 m 23.2 s 90.6% 75.8 m 7.1 m INFO 16:55:15,579 TraversalEngine - chr20:34090619 1.79e+08 69.2 m 23.2 s 91.4% 75.7 m 6.5 m INFO 16:55:45,612 TraversalEngine - chr20:51871726 1.80e+08 69.7 m 23.2 s 92.2% 75.6 m 5.9 m INFO 16:56:15,615 TraversalEngine - chr21:34030098 1.82e+08 70.2 m 23.1 s 93.0% 75.4 m 5.3 m INFO 16:56:45,671 TraversalEngine - chr22:18081065 1.84e+08 70.7 m 23.1 s 93.9% 75.3 m 4.6 m INFO 16:57:15,726 TraversalEngine - chr22:31859828 1.85e+08 71.2 m 23.0 s 94.8% 75.1 m 3.9 m INFO 16:57:45,732 TraversalEngine - chr22:46804945 1.87e+08 71.7 m 23.0 s 95.7% 74.9 m 3.2 m INFO 16:58:15,748 TraversalEngine - chrX:23018579 1.88e+08 72.2 m 23.0 s 96.5% 74.8 m 2.6 m INFO 16:58:45,753 TraversalEngine - chrX:48979166 1.89e+08 72.7 m 23.0 s 97.1% 74.8 m 2.1 m INFO 16:59:15,801 TraversalEngine - chrX:69424814 1.91e+08 73.2 m 23.0 s 97.6% 74.9 m 105.7 s INFO 16:59:45,908 TraversalEngine - chrX:100615069 1.92e+08 73.7 m 23.1 s 98.2% 75.1 m 82.0 s INFO 17:00:16,016 TraversalEngine - chrX:119206743 1.92e+08 74.2 m 23.2 s 98.7% 75.2 m 58.4 s INFO 17:00:46,123 TraversalEngine - chrX:140995052 1.93e+08 74.7 m 23.2 s 99.2% 75.3 m 36.4 s INFO 17:01:16,288 DepthOfCoverageWalker - Printing summary info INFO 17:01:16,294 TraversalEngine - Total runtime 4511.74 secs, 75.20 min, 1.25 hours INFO 17:01:16,295 TraversalEngine - 3113436 reads were filtered out during traversal out of 392820507 total (0.79%) INFO 17:01:16,295 TraversalEngine - -> 3113436 reads (0.79% of total) failing UnmappedReadFilter Knime4bioadded two nodes for Knime4bio: read mpileup and smart numeric filtering: http://code.google.com/p/knime4bio/source/detail?r=220 |