2011-05-19 15:51:18,920 - INFO - Generating QC metrics for BAM File ['WTCHG_11733.bam']
2011-05-19 15:51:18,920 - INFO - Output will go to WTCHG_11733.qc.txt.tmp
2011-05-19 15:51:18,921 - INFO - Reading GC Map from file /data/Genomes/gcMap/Mouse37.gcMap.gz
2011-05-19 15:54:05,243 - INFO - Finished reading GC Map
2011-05-19 15:54:05,243 - INFO - Reading CDS from exon definition file /data/Genomes/annotation/Mouse37.refGene.txt.gz
2011-05-19 15:54:08,251 - INFO - Read 382138 exons (33804740 nucleotides) for 32 chromosomes
2011-05-19 15:54:08,252 - INFO - Computing coverage cut-off
2011-05-19 15:54:08,252 - INFO - Retrieving BAM file coverage info from samtools pileup
2011-05-19 15:54:13,790 - INFO - Processed 1000000 pile-up sites
2011-05-19 15:54:19,349 - INFO - Processed 2000000 pile-up sites
2011-05-19 15:54:24,662 - INFO - Processed 3000000 pile-up sites
2011-05-19 15:54:29,249 - INFO - Processed 4000000 pile-up sites
2011-05-19 15:54:34,508 - INFO - Processed 5000000 pile-up sites
2011-05-19 15:54:39,363 - INFO - Processed 6000000 pile-up sites
2011-05-19 15:54:44,155 - INFO - Processed 7000000 pile-up sites
2011-05-19 15:54:48,737 - INFO - Processed 8000000 pile-up sites
2011-05-19 15:54:53,781 - INFO - Processed 9000000 pile-up sites
2011-05-19 15:54:58,852 - INFO - Processed 10000000 pile-up sites
2011-05-19 15:55:01,187 - INFO - Processed 11000000 pile-up sites
2011-05-19 15:55:03,507 - INFO - Processed 12000000 pile-up sites
2011-05-19 15:55:06,236 - INFO - Processed 13000000 pile-up sites
2011-05-19 15:55:08,559 - INFO - Processed 14000000 pile-up sites
2011-05-19 15:55:12,244 - INFO - Processed 15000000 pile-up sites
2011-05-19 15:55:14,683 - INFO - Processed 16000000 pile-up sites
2011-05-19 15:55:19,750 - INFO - Processed 17000000 pile-up sites
2011-05-19 15:55:24,820 - INFO - Processed 18000000 pile-up sites
2011-05-19 15:55:29,489 - INFO - Processed 19000000 pile-up sites
2011-05-19 15:55:34,496 - INFO - Processed 20000000 pile-up sites
2011-05-19 15:55:40,584 - INFO - Processed 21000000 pile-up sites
2011-05-19 15:55:45,816 - INFO - Processed 22000000 pile-up sites
2011-05-19 15:55:51,253 - INFO - Processed 23000000 pile-up sites
2011-05-19 15:55:58,324 - INFO - Processed 24000000 pile-up sites
2011-05-19 15:56:05,157 - INFO - Processed 25000000 pile-up sites
2011-05-19 15:56:10,229 - INFO - Processed 26000000 pile-up sites
2011-05-19 15:56:16,514 - INFO - Processed 27000000 pile-up sites
2011-05-19 15:56:22,874 - INFO - Processed 28000000 pile-up sites
2011-05-19 15:56:27,744 - INFO - Processed 29000000 pile-up sites
2011-05-19 15:56:32,919 - INFO - Processed 30000000 pile-up sites
2011-05-19 15:56:37,880 - INFO - Processed 31000000 pile-up sites
2011-05-19 15:56:42,550 - INFO - Processed 32000000 pile-up sites
2011-05-19 15:56:49,026 - INFO - Processed 33000000 pile-up sites
2011-05-19 15:56:54,840 - INFO - Processed 34000000 pile-up sites
2011-05-19 15:56:59,208 - INFO - Finished processing pile-up on 34924873 sites (200000001 nucleotides)
2011-05-19 15:56:59,208 - INFO - Coverage cut-off value is 20
2011-05-19 15:56:59,208 - INFO - Loading data into QC data manager
2011-05-19 15:56:59,373 - WARNING - Found RG tag 'SM' (value: 234) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,373 - WARNING - Found RG tag 'ID' (value: WTCHG_11733) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,373 - WARNING - Found RG tag 'SM' (value: 234) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,373 - WARNING - Found RG tag 'ID' (value: WTCHG_11733) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,374 - WARNING - Found RG tag 'SM' (value: 234) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,374 - WARNING - Found RG tag 'ID' (value: WTCHG_11733) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,374 - WARNING - Found RG tag 'SM' (value: 234) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,374 - WARNING - Found RG tag 'ID' (value: WTCHG_11733) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,425 - WARNING - Found RG tag 'SM' (value: 234) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,425 - WARNING - Found RG tag 'ID' (value: WTCHG_11733) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,425 - WARNING - Found RG tag 'SM' (value: 234) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,425 - WARNING - Found RG tag 'ID' (value: WTCHG_11733) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,425 - WARNING - Found RG tag 'SM' (value: 234) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,425 - WARNING - Found RG tag 'ID' (value: WTCHG_11733) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,426 - WARNING - Found RG tag 'SM' (value: 234) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,426 - WARNING - Found RG tag 'ID' (value: WTCHG_11733) duplicated in CO field (value: 4625/10) -- ignoring CO value
2011-05-19 15:56:59,434 - INFO - Reading data from BAM file WTCHG_11733.bam. All reads in file will be read
2011-05-19 15:56:59,475 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:2990002-23010002
2011-05-19 15:57:10,466 - INFO - Processed 100000 reads so far
2011-05-19 15:57:21,775 - INFO - Processed 200000 reads so far
2011-05-19 15:57:32,842 - INFO - Processed 300000 reads so far
2011-05-19 15:57:43,922 - INFO - Processed 400000 reads so far
2011-05-19 15:57:54,684 - INFO - Processed 500000 reads so far
2011-05-19 15:58:05,925 - INFO - Processed 600000 reads so far
2011-05-19 15:58:17,066 - INFO - Processed 700000 reads so far
2011-05-19 15:58:28,205 - INFO - Processed 800000 reads so far
2011-05-19 15:58:39,138 - INFO - Processed 900000 reads so far
2011-05-19 15:58:50,267 - INFO - Processed 1000000 reads so far
2011-05-19 15:59:01,341 - INFO - Processed 1100000 reads so far
2011-05-19 15:59:04,323 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:22990006-43010006
2011-05-19 15:59:12,839 - INFO - Processed 1200000 reads so far
2011-05-19 15:59:23,907 - INFO - Processed 1300000 reads so far
2011-05-19 15:59:34,491 - INFO - Processed 1400000 reads so far
2011-05-19 15:59:44,154 - INFO - Processed 1500000 reads so far
2011-05-19 15:59:54,623 - INFO - Processed 1600000 reads so far
2011-05-19 16:00:05,214 - INFO - Processed 1700000 reads so far
2011-05-19 16:00:15,789 - INFO - Processed 1800000 reads so far
2011-05-19 16:00:26,576 - INFO - Processed 1900000 reads so far
2011-05-19 16:00:37,109 - INFO - Processed 2000000 reads so far
2011-05-19 16:00:47,504 - INFO - Processed 2100000 reads so far
2011-05-19 16:00:58,879 - INFO - Processed 2200000 reads so far
2011-05-19 16:01:04,140 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:42990079-63010079
2011-05-19 16:01:11,690 - INFO - Processed 2300000 reads so far
2011-05-19 16:01:25,276 - INFO - Processed 2400000 reads so far
2011-05-19 16:01:39,177 - INFO - Processed 2500000 reads so far
2011-05-19 16:01:50,495 - INFO - Processed 2600000 reads so far
2011-05-19 16:02:02,424 - INFO - Processed 2700000 reads so far
2011-05-19 16:02:13,490 - INFO - Processed 2800000 reads so far
2011-05-19 16:02:24,646 - INFO - Processed 2900000 reads so far
2011-05-19 16:02:33,901 - INFO - Processed 3000000 reads so far
2011-05-19 16:02:44,185 - INFO - Processed 3100000 reads so far
2011-05-19 16:02:52,988 - INFO - Processed 3200000 reads so far
2011-05-19 16:03:04,541 - INFO - Processed 3300000 reads so far
2011-05-19 16:03:08,443 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:62990088-83010088
2011-05-19 16:03:16,170 - INFO - Processed 3400000 reads so far
2011-05-19 16:03:27,470 - INFO - Processed 3500000 reads so far
2011-05-19 16:03:36,819 - INFO - Processed 3600000 reads so far
2011-05-19 16:03:46,655 - INFO - Processed 3700000 reads so far
2011-05-19 16:03:56,548 - INFO - Processed 3800000 reads so far
2011-05-19 16:04:08,602 - INFO - Processed 3900000 reads so far
2011-05-19 16:04:20,141 - INFO - Processed 4000000 reads so far
2011-05-19 16:04:33,481 - INFO - Processed 4100000 reads so far
2011-05-19 16:04:47,612 - INFO - Processed 4200000 reads so far
2011-05-19 16:04:58,552 - INFO - Processed 4300000 reads so far
2011-05-19 16:05:09,154 - INFO - Processed 4400000 reads so far
2011-05-19 16:05:12,339 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:82990111-103010111
2011-05-19 16:05:21,410 - INFO - Processed 4500000 reads so far
2011-05-19 16:05:32,963 - INFO - Processed 4600000 reads so far
2011-05-19 16:05:45,707 - INFO - Processed 4700000 reads so far
2011-05-19 16:05:59,369 - INFO - Processed 4800000 reads so far
2011-05-19 16:06:10,085 - INFO - Processed 4900000 reads so far
2011-05-19 16:06:20,704 - INFO - Processed 5000000 reads so far
2011-05-19 16:06:31,476 - INFO - Processed 5100000 reads so far
2011-05-19 16:06:43,021 - INFO - Processed 5200000 reads so far
2011-05-19 16:06:54,407 - INFO - Processed 5300000 reads so far
2011-05-19 16:07:04,982 - INFO - Processed 5400000 reads so far
2011-05-19 16:07:16,057 - INFO - Processed 5500000 reads so far
2011-05-19 16:07:22,656 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:102990127-123010127
2011-05-19 16:07:27,174 - INFO - Processed 5600000 reads so far
2011-05-19 16:07:37,905 - INFO - Processed 5700000 reads so far
2011-05-19 16:07:51,173 - INFO - Processed 5800000 reads so far
2011-05-19 16:08:04,815 - INFO - Processed 5900000 reads so far
2011-05-19 16:08:17,247 - INFO - Processed 6000000 reads so far
2011-05-19 16:08:32,474 - INFO - Processed 6100000 reads so far
2011-05-19 16:09:04,943 - INFO - Processed 6200000 reads so far
2011-05-19 16:09:16,855 - INFO - Processed 6300000 reads so far
2011-05-19 16:09:28,588 - INFO - Processed 6400000 reads so far
2011-05-19 16:09:40,004 - INFO - Processed 6500000 reads so far
2011-05-19 16:09:51,094 - INFO - Processed 6600000 reads so far
2011-05-19 16:09:58,274 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:122990146-143010146
2011-05-19 16:10:01,920 - INFO - Processed 6700000 reads so far
2011-05-19 16:10:12,386 - INFO - Processed 6800000 reads so far
2011-05-19 16:10:23,785 - INFO - Processed 6900000 reads so far
2011-05-19 16:10:35,507 - INFO - Processed 7000000 reads so far
2011-05-19 16:10:40,956 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:2990003-23010003
2011-05-19 16:10:46,318 - INFO - Processed 7100000 reads so far
2011-05-19 16:10:56,289 - INFO - Processed 7200000 reads so far
2011-05-19 16:11:06,504 - INFO - Processed 7300000 reads so far
2011-05-19 16:11:16,359 - INFO - Processed 7400000 reads so far
2011-05-19 16:11:29,384 - INFO - Processed 7500000 reads so far
2011-05-19 16:11:39,824 - INFO - Processed 7600000 reads so far
2011-05-19 16:11:51,511 - INFO - Processed 7700000 reads so far
2011-05-19 16:12:02,744 - INFO - Processed 7800000 reads so far
2011-05-19 16:12:13,783 - INFO - Processed 7900000 reads so far
2011-05-19 16:12:25,816 - INFO - Processed 8000000 reads so far
2011-05-19 16:12:37,865 - INFO - Processed 8100000 reads so far
2011-05-19 16:12:49,784 - INFO - Processed 8200000 reads so far
2011-05-19 16:13:05,584 - INFO - Processed 8300000 reads so far
2011-05-19 16:13:12,717 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:22990008-43010008
2011-05-19 16:13:16,183 - INFO - Processed 8400000 reads so far
2011-05-19 16:13:26,793 - INFO - Processed 8500000 reads so far
2011-05-19 16:13:37,745 - INFO - Processed 8600000 reads so far
2011-05-19 16:13:49,228 - INFO - Processed 8700000 reads so far
2011-05-19 16:14:00,600 - INFO - Processed 8800000 reads so far
2011-05-19 16:14:12,562 - INFO - Processed 8900000 reads so far
2011-05-19 16:14:22,772 - INFO - Processed 9000000 reads so far
2011-05-19 16:14:35,627 - INFO - Processed 9100000 reads so far
2011-05-19 16:14:46,635 - INFO - Processed 9200000 reads so far
2011-05-19 16:14:55,951 - INFO - Processed 9300000 reads so far
2011-05-19 16:15:06,744 - INFO - Processed 9400000 reads so far
2011-05-19 16:15:14,617 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:42990014-63010014
2011-05-19 16:15:16,818 - INFO - Processed 9500000 reads so far
2011-05-19 16:15:27,413 - INFO - Processed 9600000 reads so far
2011-05-19 16:15:38,104 - INFO - Processed 9700000 reads so far
2011-05-19 16:15:51,315 - INFO - Processed 9800000 reads so far
2011-05-19 16:16:02,618 - INFO - Processed 9900000 reads so far
2011-05-19 16:16:14,906 - INFO - Processed 10000000 reads so far
2011-05-19 16:16:27,098 - INFO - Processed 10100000 reads so far
2011-05-19 16:16:38,639 - INFO - Processed 10200000 reads so far
2011-05-19 16:17:16,356 - INFO - Processed 10300000 reads so far
2011-05-19 16:17:28,020 - INFO - Processed 10400000 reads so far
2011-05-19 16:17:39,757 - INFO - Processed 10500000 reads so far
2011-05-19 16:17:53,415 - INFO - Processed 10600000 reads so far
2011-05-19 16:17:55,040 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:62990026-83010026
2011-05-19 16:18:04,663 - INFO - Processed 10700000 reads so far
2011-05-19 16:18:15,541 - INFO - Processed 10800000 reads so far
2011-05-19 16:18:26,322 - INFO - Processed 10900000 reads so far
2011-05-19 16:18:37,969 - INFO - Processed 11000000 reads so far
2011-05-19 16:18:53,201 - INFO - Processed 11100000 reads so far
2011-05-19 16:19:03,729 - INFO - Processed 11200000 reads so far
2011-05-19 16:19:15,078 - INFO - Processed 11300000 reads so far
2011-05-19 16:19:28,596 - INFO - Processed 11400000 reads so far
2011-05-19 16:19:43,290 - INFO - Processed 11500000 reads so far
2011-05-19 16:19:54,914 - INFO - Processed 11600000 reads so far
2011-05-19 16:20:07,015 - INFO - Processed 11700000 reads so far
2011-05-19 16:20:11,831 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:82990037-103010037
2011-05-19 16:20:19,475 - INFO - Processed 11800000 reads so far
2011-05-19 16:20:33,153 - INFO - Processed 11900000 reads so far
2011-05-19 16:20:46,053 - INFO - Processed 12000000 reads so far
2011-05-19 16:20:59,888 - INFO - Processed 12100000 reads so far
2011-05-19 16:21:14,463 - INFO - Processed 12200000 reads so far
2011-05-19 16:21:24,932 - INFO - Processed 12300000 reads so far
2011-05-19 16:21:38,309 - INFO - Processed 12400000 reads so far
2011-05-19 16:21:48,948 - INFO - Processed 12500000 reads so far
2011-05-19 16:22:00,484 - INFO - Processed 12600000 reads so far
2011-05-19 16:22:12,547 - INFO - Processed 12700000 reads so far
2011-05-19 16:22:25,582 - INFO - Processed 12800000 reads so far
2011-05-19 16:22:28,934 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:102990093-123010093
2011-05-19 16:22:37,907 - INFO - Processed 12900000 reads so far
2011-05-19 16:22:50,255 - INFO - Processed 13000000 reads so far
2011-05-19 16:23:02,425 - INFO - Processed 13100000 reads so far
2011-05-19 16:23:13,800 - INFO - Processed 13200000 reads so far
2011-05-19 16:23:25,123 - INFO - Processed 13300000 reads so far
2011-05-19 16:23:35,964 - INFO - Processed 13400000 reads so far
2011-05-19 16:23:46,652 - INFO - Processed 13500000 reads so far
2011-05-19 16:23:56,407 - INFO - Processed 13600000 reads so far
2011-05-19 16:24:08,969 - INFO - Processed 13700000 reads so far
2011-05-19 16:24:21,853 - INFO - Processed 13800000 reads so far
2011-05-19 16:24:30,154 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:2990033-23010033
2011-05-19 16:24:32,516 - INFO - Processed 13900000 reads so far
2011-05-19 16:24:40,960 - INFO - Processed 14000000 reads so far
2011-05-19 16:24:50,372 - INFO - Processed 14100000 reads so far
2011-05-19 16:25:00,447 - INFO - Processed 14200000 reads so far
2011-05-19 16:25:12,854 - INFO - Processed 14300000 reads so far
2011-05-19 16:25:25,409 - INFO - Processed 14400000 reads so far
2011-05-19 16:25:36,552 - INFO - Processed 14500000 reads so far
2011-05-19 16:25:47,922 - INFO - Processed 14600000 reads so far
2011-05-19 16:26:00,757 - INFO - Processed 14700000 reads so far
2011-05-19 16:26:11,966 - INFO - Processed 14800000 reads so far
2011-05-19 16:26:24,422 - INFO - Processed 14900000 reads so far
2011-05-19 16:26:35,496 - INFO - Processed 15000000 reads so far
2011-05-19 16:26:46,290 - INFO - Processed 15100000 reads so far
2011-05-19 16:26:58,422 - INFO - Processed 15200000 reads so far
2011-05-19 16:27:03,033 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:22990070-43010070
2011-05-19 16:27:09,247 - INFO - Processed 15300000 reads so far
2011-05-19 16:27:21,367 - INFO - Processed 15400000 reads so far
2011-05-19 16:27:35,277 - INFO - Processed 15500000 reads so far
2011-05-19 16:27:49,334 - INFO - Processed 15600000 reads so far
2011-05-19 16:28:03,135 - INFO - Processed 15700000 reads so far
2011-05-19 16:28:17,078 - INFO - Processed 15800000 reads so far
2011-05-19 16:28:31,783 - INFO - Processed 15900000 reads so far
2011-05-19 16:28:50,126 - INFO - Processed 16000000 reads so far
2011-05-19 16:29:02,941 - INFO - Processed 16100000 reads so far
2011-05-19 16:29:16,046 - INFO - Processed 16200000 reads so far
2011-05-19 16:29:33,411 - INFO - Processed 16300000 reads so far
2011-05-19 16:29:36,346 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:42990078-63010078
2011-05-19 16:29:48,741 - INFO - Processed 16400000 reads so far
2011-05-19 16:30:00,375 - INFO - Processed 16500000 reads so far
2011-05-19 16:30:13,526 - INFO - Processed 16600000 reads so far
2011-05-19 16:30:26,613 - INFO - Processed 16700000 reads so far
2011-05-19 16:30:39,631 - INFO - Processed 16800000 reads so far
2011-05-19 16:30:53,297 - INFO - Processed 16900000 reads so far
2011-05-19 16:31:06,780 - INFO - Processed 17000000 reads so far
2011-05-19 16:31:18,744 - INFO - Processed 17100000 reads so far
2011-05-19 16:31:41,789 - INFO - Processed 17200000 reads so far
2011-05-19 16:31:57,953 - INFO - Processed 17300000 reads so far
2011-05-19 16:32:12,117 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:62990082-83010082
2011-05-19 16:32:13,056 - INFO - Processed 17400000 reads so far
2011-05-19 16:32:27,951 - INFO - Processed 17500000 reads so far
2011-05-19 16:32:42,356 - INFO - Processed 17600000 reads so far
2011-05-19 16:32:55,609 - INFO - Processed 17700000 reads so far
2011-05-19 16:33:07,786 - INFO - Processed 17800000 reads so far
2011-05-19 16:33:19,670 - INFO - Processed 17900000 reads so far
2011-05-19 16:33:33,722 - INFO - Processed 18000000 reads so far
2011-05-19 16:33:45,244 - INFO - Processed 18100000 reads so far
2011-05-19 16:33:56,836 - INFO - Processed 18200000 reads so far
2011-05-19 16:34:16,660 - INFO - Processed 18300000 reads so far
2011-05-19 16:34:30,998 - INFO - Processed 18400000 reads so far
2011-05-19 16:34:43,614 - INFO - Processed 18500000 reads so far
2011-05-19 16:34:43,731 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:82990161-103010161
2011-05-19 16:34:57,492 - INFO - Processed 18600000 reads so far
2011-05-19 16:35:09,607 - INFO - Processed 18700000 reads so far
2011-05-19 16:35:20,144 - INFO - Processed 18800000 reads so far
2011-05-19 16:35:31,955 - INFO - Processed 18900000 reads so far
2011-05-19 16:35:43,033 - INFO - Processed 19000000 reads so far
2011-05-19 16:35:52,658 - INFO - Processed 19100000 reads so far
2011-05-19 16:36:04,281 - INFO - Processed 19200000 reads so far
2011-05-19 16:36:16,672 - INFO - Processed 19300000 reads so far
2011-05-19 16:36:29,864 - INFO - Processed 19400000 reads so far
2011-05-19 16:36:41,186 - INFO - Processed 19500000 reads so far
2011-05-19 16:36:52,553 - INFO - Processed 19600000 reads so far
2011-05-19 16:36:54,235 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:102990162-123010162
2011-05-19 16:37:04,416 - INFO - Processed 19700000 reads so far
2011-05-19 16:37:15,912 - INFO - Processed 19800000 reads so far
2011-05-19 16:37:30,323 - INFO - Processed 19900000 reads so far
2011-05-19 16:37:40,810 - INFO - Processed 20000000 reads so far
2011-05-19 16:37:52,682 - INFO - Processed 20100000 reads so far
2011-05-19 16:38:06,764 - INFO - Processed 20200000 reads so far
2011-05-19 16:38:22,229 - INFO - Processed 20300000 reads so far
2011-05-19 16:38:32,509 - INFO - Processed 20400000 reads so far
2011-05-19 16:40:15,006 - INFO - Processed 20500000 reads so far
2011-05-19 16:40:25,985 - INFO - Processed 20600000 reads so far
2011-05-19 16:40:38,117 - INFO - Processed 20700000 reads so far
2011-05-19 16:40:38,482 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:2990053-23010053
2011-05-19 16:40:52,004 - INFO - Processed 20800000 reads so far
2011-05-19 16:41:03,522 - INFO - Processed 20900000 reads so far
2011-05-19 16:41:17,135 - INFO - Processed 21000000 reads so far
2011-05-19 16:41:27,263 - INFO - Processed 21100000 reads so far
2011-05-19 16:41:38,199 - INFO - Processed 21200000 reads so far
2011-05-19 16:41:48,942 - INFO - Processed 21300000 reads so far
2011-05-19 16:42:00,935 - INFO - Processed 21400000 reads so far
2011-05-19 16:42:12,406 - INFO - Processed 21500000 reads so far
2011-05-19 16:42:25,540 - INFO - Processed 21600000 reads so far
2011-05-19 16:42:37,087 - INFO - Processed 21700000 reads so far
2011-05-19 16:42:47,674 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:22990089-43010089
2011-05-19 16:42:48,485 - INFO - Processed 21800000 reads so far
2011-05-19 16:43:02,146 - INFO - Processed 21900000 reads so far
2011-05-19 16:43:14,248 - INFO - Processed 22000000 reads so far
2011-05-19 16:43:29,925 - INFO - Processed 22100000 reads so far
2011-05-19 16:43:43,006 - INFO - Processed 22200000 reads so far
2011-05-19 16:43:54,816 - INFO - Processed 22300000 reads so far
2011-05-19 16:44:09,114 - INFO - Processed 22400000 reads so far
2011-05-19 16:44:21,438 - INFO - Processed 22500000 reads so far
2011-05-19 16:44:35,114 - INFO - Processed 22600000 reads so far
2011-05-19 16:44:48,201 - INFO - Processed 22700000 reads so far
2011-05-19 16:45:05,049 - INFO - Processed 22800000 reads so far
2011-05-19 16:45:19,732 - INFO - Processed 22900000 reads so far
2011-05-19 16:45:26,770 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:42990095-63010095
2011-05-19 16:45:33,443 - INFO - Processed 23000000 reads so far
2011-05-19 16:45:43,152 - INFO - Processed 23100000 reads so far
2011-05-19 16:45:56,152 - INFO - Processed 23200000 reads so far
2011-05-19 16:46:09,848 - INFO - Processed 23300000 reads so far
2011-05-19 16:46:26,920 - INFO - Processed 23400000 reads so far
2011-05-19 16:46:40,046 - INFO - Processed 23500000 reads so far
2011-05-19 16:46:51,505 - INFO - Processed 23600000 reads so far
2011-05-19 16:47:03,365 - INFO - Processed 23700000 reads so far
2011-05-19 16:47:15,250 - INFO - Processed 23800000 reads so far
2011-05-19 16:47:27,117 - INFO - Processed 23900000 reads so far
2011-05-19 16:47:40,100 - INFO - Processed 24000000 reads so far
2011-05-19 16:47:53,871 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:62990142-83010142
2011-05-19 16:47:54,031 - INFO - Processed 24100000 reads so far
2011-05-19 16:48:10,988 - INFO - Processed 24200000 reads so far
2011-05-19 16:48:26,817 - INFO - Processed 24300000 reads so far
2011-05-19 16:48:38,381 - INFO - Processed 24400000 reads so far
2011-05-19 16:48:50,396 - INFO - Processed 24500000 reads so far
2011-05-19 16:49:01,795 - INFO - Processed 24600000 reads so far
2011-05-19 16:49:18,274 - INFO - Processed 24700000 reads so far
2011-05-19 16:49:31,308 - INFO - Processed 24800000 reads so far
2011-05-19 16:49:42,755 - INFO - Processed 24900000 reads so far
2011-05-19 16:49:54,264 - INFO - Processed 25000000 reads so far
2011-05-19 16:50:06,188 - INFO - Processed 25100000 reads so far
2011-05-19 16:50:19,037 - INFO - Processed 25200000 reads so far
2011-05-19 16:50:25,739 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:82990154-103010154
2011-05-19 16:50:33,919 - INFO - Processed 25300000 reads so far
2011-05-19 16:50:46,141 - INFO - Processed 25400000 reads so far
2011-05-19 16:50:59,145 - INFO - Processed 25500000 reads so far
2011-05-19 16:51:10,688 - INFO - Processed 25600000 reads so far
2011-05-19 16:51:23,355 - INFO - Processed 25700000 reads so far
2011-05-19 16:51:35,393 - INFO - Processed 25800000 reads so far
2011-05-19 16:51:47,684 - INFO - Processed 25900000 reads so far
2011-05-19 16:52:02,058 - INFO - Processed 26000000 reads so far
2011-05-19 16:52:13,565 - INFO - Processed 26100000 reads so far
2011-05-19 16:52:28,326 - INFO - Processed 26200000 reads so far
2011-05-19 16:52:44,733 - INFO - Processed 26300000 reads so far
2011-05-19 16:52:46,594 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:102990167-123010167
2011-05-19 16:53:01,814 - INFO - Processed 26400000 reads so far
2011-05-19 16:53:12,558 - INFO - Processed 26500000 reads so far
2011-05-19 16:53:23,729 - INFO - Processed 26600000 reads so far
2011-05-19 16:53:40,662 - INFO - Processed 26700000 reads so far
2011-05-19 16:53:52,876 - INFO - Processed 26800000 reads so far
2011-05-19 16:54:10,385 - INFO - Processed 26900000 reads so far
2011-05-19 16:54:22,005 - INFO - Processed 27000000 reads so far
2011-05-19 16:54:31,701 - INFO - Processed 27100000 reads so far
2011-05-19 16:54:42,274 - INFO - Processed 27200000 reads so far
2011-05-19 16:54:56,001 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13_random:0-20010000
2011-05-19 16:54:57,372 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:2990000-23010000
2011-05-19 16:54:58,393 - INFO - Processed 27300000 reads so far
2011-05-19 16:55:10,329 - INFO - Processed 27400000 reads so far
2011-05-19 16:55:21,584 - INFO - Processed 27500000 reads so far
2011-05-19 16:55:32,724 - INFO - Processed 27600000 reads so far
2011-05-19 16:55:43,289 - INFO - Processed 27700000 reads so far
2011-05-19 16:55:53,171 - INFO - Processed 27800000 reads so far
2011-05-19 16:56:04,171 - INFO - Processed 27900000 reads so far
2011-05-19 16:56:18,547 - INFO - Processed 28000000 reads so far
2011-05-19 16:56:31,948 - INFO - Processed 28100000 reads so far
2011-05-19 16:56:46,061 - INFO - Processed 28200000 reads so far
2011-05-19 16:56:57,201 - INFO - Processed 28300000 reads so far
2011-05-19 16:57:07,833 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:22990023-43010023
2011-05-19 16:57:11,594 - INFO - Processed 28400000 reads so far
2011-05-19 16:57:24,900 - INFO - Processed 28500000 reads so far
2011-05-19 16:57:37,085 - INFO - Processed 28600000 reads so far
2011-05-19 16:57:51,641 - INFO - Processed 28700000 reads so far
2011-05-19 16:58:04,151 - INFO - Processed 28800000 reads so far
2011-05-19 16:58:15,632 - INFO - Processed 28900000 reads so far
2011-05-19 16:58:27,890 - INFO - Processed 29000000 reads so far
2011-05-19 16:58:39,747 - INFO - Processed 29100000 reads so far
2011-05-19 16:58:53,506 - INFO - Processed 29200000 reads so far
2011-05-19 16:59:05,165 - INFO - Processed 29300000 reads so far
2011-05-19 16:59:16,656 - INFO - Processed 29400000 reads so far
2011-05-19 16:59:29,671 - INFO - Processed 29500000 reads so far
2011-05-19 16:59:35,011 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:42990048-63010048
2011-05-19 16:59:41,336 - INFO - Processed 29600000 reads so far
2011-05-19 16:59:51,759 - INFO - Processed 29700000 reads so far
2011-05-19 17:00:05,586 - INFO - Processed 29800000 reads so far
2011-05-19 17:00:17,864 - INFO - Processed 29900000 reads so far
2011-05-19 17:00:29,779 - INFO - Processed 30000000 reads so far
2011-05-19 17:00:43,581 - INFO - Processed 30100000 reads so far
2011-05-19 17:00:57,139 - INFO - Processed 30200000 reads so far
2011-05-19 17:01:12,960 - INFO - Processed 30300000 reads so far
2011-05-19 17:01:31,387 - INFO - Processed 30400000 reads so far
2011-05-19 17:01:43,478 - INFO - Processed 30500000 reads so far
2011-05-19 17:01:57,280 - INFO - Processed 30600000 reads so far
2011-05-19 17:02:09,801 - INFO - Processed 30700000 reads so far
2011-05-19 17:02:16,537 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:62990055-83010055
2011-05-19 17:02:21,821 - INFO - Processed 30800000 reads so far
2011-05-19 17:02:33,861 - INFO - Processed 30900000 reads so far
2011-05-19 17:02:45,930 - INFO - Processed 31000000 reads so far
2011-05-19 17:02:57,429 - INFO - Processed 31100000 reads so far
2011-05-19 17:03:08,668 - INFO - Processed 31200000 reads so far
2011-05-19 17:03:21,803 - INFO - Processed 31300000 reads so far
2011-05-19 17:03:35,645 - INFO - Processed 31400000 reads so far
2011-05-19 17:03:52,155 - INFO - Processed 31500000 reads so far
2011-05-19 17:04:06,501 - INFO - Processed 31600000 reads so far
2011-05-19 17:04:17,914 - INFO - Processed 31700000 reads so far
2011-05-19 17:04:29,556 - INFO - Processed 31800000 reads so far
2011-05-19 17:04:40,748 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:82990077-103010077
2011-05-19 17:04:41,252 - INFO - Processed 31900000 reads so far
2011-05-19 17:04:56,784 - INFO - Processed 32000000 reads so far
2011-05-19 17:05:09,832 - INFO - Processed 32100000 reads so far
2011-05-19 17:05:21,133 - INFO - Processed 32200000 reads so far
2011-05-19 17:05:33,569 - INFO - Processed 32300000 reads so far
2011-05-19 17:05:48,391 - INFO - Processed 32400000 reads so far
2011-05-19 17:06:00,480 - INFO - Processed 32500000 reads so far
2011-05-19 17:06:16,395 - INFO - Processed 32600000 reads so far
2011-05-19 17:06:29,733 - INFO - Processed 32700000 reads so far
2011-05-19 17:06:40,074 - INFO - Processed 32800000 reads so far
2011-05-19 17:06:52,750 - INFO - Processed 32900000 reads so far
2011-05-19 17:06:54,009 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:102990086-123010086
2011-05-19 17:07:08,480 - INFO - Processed 33000000 reads so far
2011-05-19 17:07:21,862 - INFO - Processed 33100000 reads so far
2011-05-19 17:07:35,629 - INFO - Processed 33200000 reads so far
2011-05-19 17:07:52,478 - INFO - Processed 33300000 reads so far
2011-05-19 17:08:03,524 - INFO - Processed 33400000 reads so far
2011-05-19 17:08:15,662 - INFO - Processed 33500000 reads so far
2011-05-19 17:08:25,142 - INFO - Processed 33600000 reads so far
2011-05-19 17:08:36,699 - INFO - Processed 33700000 reads so far
2011-05-19 17:08:48,808 - INFO - Processed 33800000 reads so far
2011-05-19 17:08:59,731 - INFO - Processed 33900000 reads so far
2011-05-19 17:09:08,129 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:122990130-143010130
2011-05-19 17:09:09,617 - INFO - Processed 34000000 reads so far
2011-05-19 17:09:22,667 - INFO - Processed 34100000 reads so far
2011-05-19 17:09:23,159 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:2990008-23010008
2011-05-19 17:09:32,401 - INFO - Processed 34200000 reads so far
2011-05-19 17:09:43,237 - INFO - Processed 34300000 reads so far
2011-05-19 17:09:55,505 - INFO - Processed 34400000 reads so far
2011-05-19 17:10:05,191 - INFO - Processed 34500000 reads so far
2011-05-19 17:10:17,504 - INFO - Processed 34600000 reads so far
2011-05-19 17:10:27,716 - INFO - Processed 34700000 reads so far
2011-05-19 17:10:38,962 - INFO - Processed 34800000 reads so far
2011-05-19 17:10:49,767 - INFO - Processed 34900000 reads so far
2011-05-19 17:10:58,728 - INFO - Processed 35000000 reads so far
2011-05-19 17:11:11,065 - INFO - Processed 35100000 reads so far
2011-05-19 17:11:19,557 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:22990010-43010010
2011-05-19 17:11:22,422 - INFO - Processed 35200000 reads so far
2011-05-19 17:11:35,143 - INFO - Processed 35300000 reads so far
2011-05-19 17:11:44,422 - INFO - Processed 35400000 reads so far
2011-05-19 17:11:56,864 - INFO - Processed 35500000 reads so far
2011-05-19 17:12:09,988 - INFO - Processed 35600000 reads so far
2011-05-19 17:12:22,308 - INFO - Processed 35700000 reads so far
2011-05-19 17:12:35,816 - INFO - Processed 35800000 reads so far
2011-05-19 17:12:47,377 - INFO - Processed 35900000 reads so far
2011-05-19 17:13:01,422 - INFO - Processed 36000000 reads so far
2011-05-19 17:13:14,135 - INFO - Processed 36100000 reads so far
2011-05-19 17:13:27,437 - INFO - Processed 36200000 reads so far
2011-05-19 17:13:40,178 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:42990028-63010028
2011-05-19 17:13:40,282 - INFO - Processed 36300000 reads so far
2011-05-19 17:13:54,986 - INFO - Processed 36400000 reads so far
2011-05-19 17:14:07,727 - INFO - Processed 36500000 reads so far
2011-05-19 17:14:22,052 - INFO - Processed 36600000 reads so far
2011-05-19 17:14:35,656 - INFO - Processed 36700000 reads so far
2011-05-19 17:14:47,673 - INFO - Processed 36800000 reads so far
2011-05-19 17:15:01,056 - INFO - Processed 36900000 reads so far
2011-05-19 17:15:12,614 - INFO - Processed 37000000 reads so far
2011-05-19 17:15:24,789 - INFO - Processed 37100000 reads so far
2011-05-19 17:15:36,844 - INFO - Processed 37200000 reads so far
2011-05-19 17:15:47,863 - INFO - Processed 37300000 reads so far
2011-05-19 17:15:55,292 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:62990079-83010079
2011-05-19 17:15:56,213 - INFO - Processed 37400000 reads so far
2011-05-19 17:16:05,097 - INFO - Processed 37500000 reads so far
2011-05-19 17:16:15,555 - INFO - Processed 37600000 reads so far
2011-05-19 17:16:30,571 - INFO - Processed 37700000 reads so far
2011-05-19 17:16:45,228 - INFO - Processed 37800000 reads so far
2011-05-19 17:16:56,014 - INFO - Processed 37900000 reads so far
2011-05-19 17:17:09,025 - INFO - Processed 38000000 reads so far
2011-05-19 17:17:20,016 - INFO - Processed 38100000 reads so far
2011-05-19 17:17:31,893 - INFO - Processed 38200000 reads so far
2011-05-19 17:17:45,435 - INFO - Processed 38300000 reads so far
2011-05-19 17:17:58,106 - INFO - Processed 38400000 reads so far
2011-05-19 17:18:14,729 - INFO - Processed 38500000 reads so far
2011-05-19 17:18:18,168 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:82990161-103010161
2011-05-19 17:18:26,788 - INFO - Processed 38600000 reads so far
2011-05-19 17:18:39,588 - INFO - Processed 38700000 reads so far
2011-05-19 17:18:53,111 - INFO - Processed 38800000 reads so far
2011-05-19 17:19:05,897 - INFO - Processed 38900000 reads so far
2011-05-19 17:19:21,082 - INFO - Processed 39000000 reads so far
2011-05-19 17:19:33,030 - INFO - Processed 39100000 reads so far
2011-05-19 17:19:45,447 - INFO - Processed 39200000 reads so far
2011-05-19 17:19:58,138 - INFO - Processed 39300000 reads so far
2011-05-19 17:20:09,023 - INFO - Processed 39400000 reads so far
2011-05-19 17:20:18,160 - INFO - Processed 39500000 reads so far
2011-05-19 17:20:33,459 - INFO - Processed 39600000 reads so far
2011-05-19 17:20:39,763 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:102990190-123010190
2011-05-19 17:20:44,187 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:2990004-23010004
2011-05-19 17:20:46,308 - INFO - Processed 39700000 reads so far
2011-05-19 17:20:57,693 - INFO - Processed 39800000 reads so far
2011-05-19 17:21:11,676 - INFO - Processed 39900000 reads so far
2011-05-19 17:21:23,795 - INFO - Processed 40000000 reads so far
2011-05-19 17:21:36,169 - INFO - Processed 40100000 reads so far
2011-05-19 17:21:49,714 - INFO - Processed 40200000 reads so far
2011-05-19 17:22:03,967 - INFO - Processed 40300000 reads so far
2011-05-19 17:22:17,779 - INFO - Processed 40400000 reads so far
2011-05-19 17:22:26,864 - INFO - Processed 40500000 reads so far
2011-05-19 17:22:39,532 - INFO - Processed 40600000 reads so far
2011-05-19 17:22:51,537 - INFO - Processed 40700000 reads so far
2011-05-19 17:23:05,138 - INFO - Processed 40800000 reads so far
2011-05-19 17:23:16,616 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:22990016-43010016
2011-05-19 17:23:20,519 - INFO - Processed 40900000 reads so far
2011-05-19 17:23:34,596 - INFO - Processed 41000000 reads so far
2011-05-19 17:23:47,852 - INFO - Processed 41100000 reads so far
2011-05-19 17:24:03,351 - INFO - Processed 41200000 reads so far
2011-05-19 17:24:15,078 - INFO - Processed 41300000 reads so far
2011-05-19 17:24:27,177 - INFO - Processed 41400000 reads so far
2011-05-19 17:24:41,382 - INFO - Processed 41500000 reads so far
2011-05-19 17:24:52,681 - INFO - Processed 41600000 reads so far
2011-05-19 17:25:06,829 - INFO - Processed 41700000 reads so far
2011-05-19 17:25:19,162 - INFO - Processed 41800000 reads so far
2011-05-19 17:25:32,950 - INFO - Processed 41900000 reads so far
2011-05-19 17:25:47,691 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:42990018-63010018
2011-05-19 17:25:49,174 - INFO - Processed 42000000 reads so far
2011-05-19 17:26:04,000 - INFO - Processed 42100000 reads so far
2011-05-19 17:26:16,508 - INFO - Processed 42200000 reads so far
2011-05-19 17:26:29,701 - INFO - Processed 42300000 reads so far
2011-05-19 17:26:42,536 - INFO - Processed 42400000 reads so far
2011-05-19 17:26:54,526 - INFO - Processed 42500000 reads so far
2011-05-19 17:27:07,884 - INFO - Processed 42600000 reads so far
2011-05-19 17:27:19,422 - INFO - Processed 42700000 reads so far
2011-05-19 17:27:29,819 - INFO - Processed 42800000 reads so far
2011-05-19 17:27:40,463 - INFO - Processed 42900000 reads so far
2011-05-19 17:27:51,350 - INFO - Processed 43000000 reads so far
2011-05-19 17:27:59,188 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:62990035-83010035
2011-05-19 17:28:01,129 - INFO - Processed 43100000 reads so far
2011-05-19 17:28:11,991 - INFO - Processed 43200000 reads so far
2011-05-19 17:28:22,378 - INFO - Processed 43300000 reads so far
2011-05-19 17:28:34,489 - INFO - Processed 43400000 reads so far
2011-05-19 17:28:46,357 - INFO - Processed 43500000 reads so far
2011-05-19 17:28:57,545 - INFO - Processed 43600000 reads so far
2011-05-19 17:29:10,130 - INFO - Processed 43700000 reads so far
2011-05-19 17:29:24,465 - INFO - Processed 43800000 reads so far
2011-05-19 17:29:35,617 - INFO - Processed 43900000 reads so far
2011-05-19 17:29:46,221 - INFO - Processed 44000000 reads so far
2011-05-19 17:29:59,960 - INFO - Processed 44100000 reads so far
2011-05-19 17:30:01,908 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:82990124-103010124
2011-05-19 17:30:09,425 - INFO - Processed 44200000 reads so far
2011-05-19 17:30:20,769 - INFO - Processed 44300000 reads so far
2011-05-19 17:30:34,693 - INFO - Processed 44400000 reads so far
2011-05-19 17:30:45,420 - INFO - Processed 44500000 reads so far
2011-05-19 17:30:57,371 - INFO - Processed 44600000 reads so far
2011-05-19 17:31:11,228 - INFO - Processed 44700000 reads so far
2011-05-19 17:31:23,668 - INFO - Processed 44800000 reads so far
2011-05-19 17:31:39,585 - INFO - Processed 44900000 reads so far
2011-05-19 17:31:48,563 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16_random:0-20010099
2011-05-19 17:31:48,603 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:2989979-23009979
2011-05-19 17:31:50,796 - INFO - Processed 45000000 reads so far
2011-05-19 17:32:02,072 - INFO - Processed 45100000 reads so far
2011-05-19 17:32:15,044 - INFO - Processed 45200000 reads so far
2011-05-19 17:32:27,923 - INFO - Processed 45300000 reads so far
2011-05-19 17:32:42,381 - INFO - Processed 45400000 reads so far
2011-05-19 17:32:55,976 - INFO - Processed 45500000 reads so far
2011-05-19 17:33:07,085 - INFO - Processed 45600000 reads so far
2011-05-19 17:33:20,025 - INFO - Processed 45700000 reads so far
2011-05-19 17:33:31,516 - INFO - Processed 45800000 reads so far
2011-05-19 17:33:43,251 - INFO - Processed 45900000 reads so far
2011-05-19 17:33:57,063 - INFO - Processed 46000000 reads so far
2011-05-19 17:34:09,831 - INFO - Processed 46100000 reads so far
2011-05-19 17:34:14,440 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:22990038-43010038
2011-05-19 17:34:25,139 - INFO - Processed 46200000 reads so far
2011-05-19 17:34:37,226 - INFO - Processed 46300000 reads so far
2011-05-19 17:34:50,408 - INFO - Processed 46400000 reads so far
2011-05-19 17:35:03,685 - INFO - Processed 46500000 reads so far
2011-05-19 17:35:16,012 - INFO - Processed 46600000 reads so far
2011-05-19 17:35:26,895 - INFO - Processed 46700000 reads so far
2011-05-19 17:35:40,739 - INFO - Processed 46800000 reads so far
2011-05-19 17:35:53,104 - INFO - Processed 46900000 reads so far
2011-05-19 17:36:04,910 - INFO - Processed 47000000 reads so far
2011-05-19 17:36:18,506 - INFO - Processed 47100000 reads so far
2011-05-19 17:36:28,317 - INFO - Processed 47200000 reads so far
2011-05-19 17:36:36,317 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:42990047-63010047
2011-05-19 17:36:37,658 - INFO - Processed 47300000 reads so far
2011-05-19 17:36:46,452 - INFO - Processed 47400000 reads so far
2011-05-19 17:36:56,439 - INFO - Processed 47500000 reads so far
2011-05-19 17:37:10,270 - INFO - Processed 47600000 reads so far
2011-05-19 17:37:20,710 - INFO - Processed 47700000 reads so far
2011-05-19 17:37:33,565 - INFO - Processed 47800000 reads so far
2011-05-19 17:37:45,989 - INFO - Processed 47900000 reads so far
2011-05-19 17:37:55,528 - INFO - Processed 48000000 reads so far
2011-05-19 17:38:09,948 - INFO - Processed 48100000 reads so far
2011-05-19 17:38:24,921 - INFO - Processed 48200000 reads so far
2011-05-19 17:38:41,333 - INFO - Processed 48300000 reads so far
2011-05-19 17:38:50,486 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:62990050-83010050
2011-05-19 17:38:55,326 - INFO - Processed 48400000 reads so far
2011-05-19 17:39:10,183 - INFO - Processed 48500000 reads so far
2011-05-19 17:39:23,261 - INFO - Processed 48600000 reads so far
2011-05-19 17:39:35,126 - INFO - Processed 48700000 reads so far
2011-05-19 17:39:48,330 - INFO - Processed 48800000 reads so far
2011-05-19 17:39:59,370 - INFO - Processed 48900000 reads so far
2011-05-19 17:40:10,510 - INFO - Processed 49000000 reads so far
2011-05-19 17:40:22,174 - INFO - Processed 49100000 reads so far
2011-05-19 17:40:35,006 - INFO - Processed 49200000 reads so far
2011-05-19 17:40:45,830 - INFO - Processed 49300000 reads so far
2011-05-19 17:40:59,171 - INFO - Processed 49400000 reads so far
2011-05-19 17:41:09,504 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:82990134-103010134
2011-05-19 17:41:10,563 - INFO - Processed 49500000 reads so far
2011-05-19 17:41:24,087 - INFO - Processed 49600000 reads so far
2011-05-19 17:41:36,757 - INFO - Processed 49700000 reads so far
2011-05-19 17:41:46,225 - INFO - Processed 49800000 reads so far
2011-05-19 17:41:55,274 - INFO - Processed 49900000 reads so far
2011-05-19 17:42:06,537 - INFO - Processed 50000000 reads so far
2011-05-19 17:42:18,653 - INFO - Processed 50100000 reads so far
2011-05-19 17:42:27,403 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17_random:0-20010045
2011-05-19 17:42:29,276 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:2990013-23010013
2011-05-19 17:42:30,980 - INFO - Processed 50200000 reads so far
2011-05-19 17:42:46,074 - INFO - Processed 50300000 reads so far
2011-05-19 17:42:58,582 - INFO - Processed 50400000 reads so far
2011-05-19 17:43:12,284 - INFO - Processed 50500000 reads so far
2011-05-19 17:43:27,499 - INFO - Processed 50600000 reads so far
2011-05-19 17:43:39,614 - INFO - Processed 50700000 reads so far
2011-05-19 17:43:51,301 - INFO - Processed 50800000 reads so far
2011-05-19 17:44:04,487 - INFO - Processed 50900000 reads so far
2011-05-19 17:44:17,480 - INFO - Processed 51000000 reads so far
2011-05-19 17:44:29,680 - INFO - Processed 51100000 reads so far
2011-05-19 17:44:40,656 - INFO - Processed 51200000 reads so far
2011-05-19 17:44:51,847 - INFO - Processed 51300000 reads so far
2011-05-19 17:44:57,334 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:22990015-43010015
2011-05-19 17:45:01,789 - INFO - Processed 51400000 reads so far
2011-05-19 17:45:12,215 - INFO - Processed 51500000 reads so far
2011-05-19 17:45:24,002 - INFO - Processed 51600000 reads so far
2011-05-19 17:45:35,503 - INFO - Processed 51700000 reads so far
2011-05-19 17:45:47,480 - INFO - Processed 51800000 reads so far
2011-05-19 17:45:59,176 - INFO - Processed 51900000 reads so far
2011-05-19 17:46:10,956 - INFO - Processed 52000000 reads so far
2011-05-19 17:46:24,015 - INFO - Processed 52100000 reads so far
2011-05-19 17:46:38,232 - INFO - Processed 52200000 reads so far
2011-05-19 17:46:49,203 - INFO - Processed 52300000 reads so far
2011-05-19 17:47:00,970 - INFO - Processed 52400000 reads so far
2011-05-19 17:47:11,725 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:42990069-63010069
2011-05-19 17:47:13,848 - INFO - Processed 52500000 reads so far
2011-05-19 17:47:25,304 - INFO - Processed 52600000 reads so far
2011-05-19 17:47:40,231 - INFO - Processed 52700000 reads so far
2011-05-19 17:47:52,672 - INFO - Processed 52800000 reads so far
2011-05-19 17:48:04,015 - INFO - Processed 52900000 reads so far
2011-05-19 17:48:16,776 - INFO - Processed 53000000 reads so far
2011-05-19 17:48:27,413 - INFO - Processed 53100000 reads so far
2011-05-19 17:48:38,733 - INFO - Processed 53200000 reads so far
2011-05-19 17:48:52,008 - INFO - Processed 53300000 reads so far
2011-05-19 17:49:01,611 - INFO - Processed 53400000 reads so far
2011-05-19 17:49:13,044 - INFO - Processed 53500000 reads so far
2011-05-19 17:49:24,881 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:62990076-83010076
2011-05-19 17:49:25,055 - INFO - Processed 53600000 reads so far
2011-05-19 17:49:35,738 - INFO - Processed 53700000 reads so far
2011-05-19 17:49:48,505 - INFO - Processed 53800000 reads so far
2011-05-19 17:50:01,652 - INFO - Processed 53900000 reads so far
2011-05-19 17:50:13,382 - INFO - Processed 54000000 reads so far
2011-05-19 17:50:27,723 - INFO - Processed 54100000 reads so far
2011-05-19 17:50:39,183 - INFO - Processed 54200000 reads so far
2011-05-19 17:50:50,500 - INFO - Processed 54300000 reads so far
2011-05-19 17:51:00,999 - INFO - Processed 54400000 reads so far
2011-05-19 17:51:13,889 - INFO - Processed 54500000 reads so far
2011-05-19 17:51:22,894 - INFO - Processed 54600000 reads so far
2011-05-19 17:51:32,094 - INFO - Processed 54700000 reads so far
2011-05-19 17:51:34,505 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:82990081-103010081
2011-05-19 17:51:43,046 - INFO - Processed 54800000 reads so far
2011-05-19 17:51:51,603 - INFO - Processed 54900000 reads so far
2011-05-19 17:52:04,094 - INFO - Processed 55000000 reads so far
2011-05-19 17:52:15,373 - INFO - Processed 55100000 reads so far
2011-05-19 17:52:22,037 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:2990241-23010241
2011-05-19 17:52:27,795 - INFO - Processed 55200000 reads so far
2011-05-19 17:52:41,745 - INFO - Processed 55300000 reads so far
2011-05-19 17:52:54,487 - INFO - Processed 55400000 reads so far
2011-05-19 17:53:08,423 - INFO - Processed 55500000 reads so far
2011-05-19 17:53:19,965 - INFO - Processed 55600000 reads so far
2011-05-19 17:53:31,125 - INFO - Processed 55700000 reads so far
2011-05-19 17:53:44,209 - INFO - Processed 55800000 reads so far
2011-05-19 17:53:56,635 - INFO - Processed 55900000 reads so far
2011-05-19 17:54:07,902 - INFO - Processed 56000000 reads so far
2011-05-19 17:54:21,277 - INFO - Processed 56100000 reads so far
2011-05-19 17:54:35,586 - INFO - Processed 56200000 reads so far
2011-05-19 17:54:42,223 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:22990242-43010242
2011-05-19 17:54:50,004 - INFO - Processed 56300000 reads so far
2011-05-19 17:55:01,744 - INFO - Processed 56400000 reads so far
2011-05-19 17:55:12,971 - INFO - Processed 56500000 reads so far
2011-05-19 17:55:26,136 - INFO - Processed 56600000 reads so far
2011-05-19 17:55:37,870 - INFO - Processed 56700000 reads so far
2011-05-19 17:55:50,298 - INFO - Processed 56800000 reads so far
2011-05-19 17:56:01,492 - INFO - Processed 56900000 reads so far
2011-05-19 17:56:14,449 - INFO - Processed 57000000 reads so far
2011-05-19 17:56:28,455 - INFO - Processed 57100000 reads so far
2011-05-19 17:56:39,696 - INFO - Processed 57200000 reads so far
2011-05-19 17:56:51,558 - INFO - Processed 57300000 reads so far
2011-05-19 17:56:59,439 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:42990248-63010248
2011-05-19 17:57:02,107 - INFO - Processed 57400000 reads so far
2011-05-19 17:57:13,324 - INFO - Processed 57500000 reads so far
2011-05-19 17:57:24,331 - INFO - Processed 57600000 reads so far
2011-05-19 17:57:34,552 - INFO - Processed 57700000 reads so far
2011-05-19 17:57:42,084 - INFO - Processed 57800000 reads so far
2011-05-19 17:57:50,779 - INFO - Processed 57900000 reads so far
2011-05-19 17:57:59,207 - INFO - Processed 58000000 reads so far
2011-05-19 17:58:09,874 - INFO - Processed 58100000 reads so far
2011-05-19 17:58:18,805 - INFO - Processed 58200000 reads so far
2011-05-19 17:58:28,896 - INFO - Processed 58300000 reads so far
2011-05-19 17:58:37,267 - INFO - Processed 58400000 reads so far
2011-05-19 17:58:39,890 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:2989987-23009987
2011-05-19 17:58:47,520 - INFO - Processed 58500000 reads so far
2011-05-19 17:58:57,983 - INFO - Processed 58600000 reads so far
2011-05-19 17:59:09,606 - INFO - Processed 58700000 reads so far
2011-05-19 17:59:22,812 - INFO - Processed 58800000 reads so far
2011-05-19 17:59:32,020 - INFO - Processed 58900000 reads so far
2011-05-19 17:59:43,247 - INFO - Processed 59000000 reads so far
2011-05-19 17:59:52,999 - INFO - Processed 59100000 reads so far
2011-05-19 18:00:01,301 - INFO - Processed 59200000 reads so far
2011-05-19 18:00:10,668 - INFO - Processed 59300000 reads so far
2011-05-19 18:00:18,954 - INFO - Processed 59400000 reads so far
2011-05-19 18:00:27,142 - INFO - Processed 59500000 reads so far
2011-05-19 18:00:28,701 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:22990160-43010160
2011-05-19 18:00:37,342 - INFO - Processed 59600000 reads so far
2011-05-19 18:00:48,053 - INFO - Processed 59700000 reads so far
2011-05-19 18:00:55,338 - INFO - Processed 59800000 reads so far
2011-05-19 18:01:06,931 - INFO - Processed 59900000 reads so far
2011-05-19 18:01:15,312 - INFO - Processed 60000000 reads so far
2011-05-19 18:01:24,071 - INFO - Processed 60100000 reads so far
2011-05-19 18:01:33,816 - INFO - Processed 60200000 reads so far
2011-05-19 18:01:42,602 - INFO - Processed 60300000 reads so far
2011-05-19 18:01:52,051 - INFO - Processed 60400000 reads so far
2011-05-19 18:02:02,368 - INFO - Processed 60500000 reads so far
2011-05-19 18:02:15,594 - INFO - Processed 60600000 reads so far
2011-05-19 18:02:19,288 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:42990164-63010164
2011-05-19 18:02:24,470 - INFO - Processed 60700000 reads so far
2011-05-19 18:02:33,308 - INFO - Processed 60800000 reads so far
2011-05-19 18:02:41,751 - INFO - Processed 60900000 reads so far
2011-05-19 18:02:51,128 - INFO - Processed 61000000 reads so far
2011-05-19 18:02:59,330 - INFO - Processed 61100000 reads so far
2011-05-19 18:03:08,289 - INFO - Processed 61200000 reads so far
2011-05-19 18:03:17,083 - INFO - Processed 61300000 reads so far
2011-05-19 18:03:28,635 - INFO - Processed 61400000 reads so far
2011-05-19 18:03:39,292 - INFO - Processed 61500000 reads so far
2011-05-19 18:03:50,133 - INFO - Processed 61600000 reads so far
2011-05-19 18:04:00,964 - INFO - Processed 61700000 reads so far
2011-05-19 18:04:05,589 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:62990168-83010168
2011-05-19 18:04:12,394 - INFO - Processed 61800000 reads so far
2011-05-19 18:04:30,594 - INFO - Processed 61900000 reads so far
2011-05-19 18:04:39,746 - INFO - Processed 62000000 reads so far
2011-05-19 18:04:54,342 - INFO - Processed 62100000 reads so far
2011-05-19 18:05:04,988 - INFO - Processed 62200000 reads so far
2011-05-19 18:05:14,866 - INFO - Processed 62300000 reads so far
2011-05-19 18:05:26,095 - INFO - Processed 62400000 reads so far
2011-05-19 18:05:36,600 - INFO - Processed 62500000 reads so far
2011-05-19 18:05:48,844 - INFO - Processed 62600000 reads so far
2011-05-19 18:05:58,892 - INFO - Processed 62700000 reads so far
2011-05-19 18:06:09,926 - INFO - Processed 62800000 reads so far
2011-05-19 18:06:15,387 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:82990176-103010176
2011-05-19 18:06:19,814 - INFO - Processed 62900000 reads so far
2011-05-19 18:06:29,603 - INFO - Processed 63000000 reads so far
2011-05-19 18:06:43,032 - INFO - Processed 63100000 reads so far
2011-05-19 18:06:52,546 - INFO - Processed 63200000 reads so far
2011-05-19 18:07:02,842 - INFO - Processed 63300000 reads so far
2011-05-19 18:07:11,797 - INFO - Processed 63400000 reads so far
2011-05-19 18:07:21,698 - INFO - Processed 63500000 reads so far
2011-05-19 18:07:31,727 - INFO - Processed 63600000 reads so far
2011-05-19 18:07:40,562 - INFO - Processed 63700000 reads so far
2011-05-19 18:07:51,978 - INFO - Processed 63800000 reads so far
2011-05-19 18:08:01,486 - INFO - Processed 63900000 reads so far
2011-05-19 18:08:07,502 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:102990187-123010187
2011-05-19 18:08:11,051 - INFO - Processed 64000000 reads so far
2011-05-19 18:08:20,992 - INFO - Processed 64100000 reads so far
2011-05-19 18:08:33,852 - INFO - Processed 64200000 reads so far
2011-05-19 18:08:42,466 - INFO - Processed 64300000 reads so far
2011-05-19 18:08:54,512 - INFO - Processed 64400000 reads so far
2011-05-19 18:09:05,480 - INFO - Processed 64500000 reads so far
2011-05-19 18:09:15,393 - INFO - Processed 64600000 reads so far
2011-05-19 18:09:27,173 - INFO - Processed 64700000 reads so far
2011-05-19 18:09:36,143 - INFO - Processed 64800000 reads so far
2011-05-19 18:09:47,764 - INFO - Processed 64900000 reads so far
2011-05-19 18:09:57,539 - INFO - Processed 65000000 reads so far
2011-05-19 18:10:01,935 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:122990234-143010234
2011-05-19 18:10:07,709 - INFO - Processed 65100000 reads so far
2011-05-19 18:10:20,909 - INFO - Processed 65200000 reads so far
2011-05-19 18:10:30,129 - INFO - Processed 65300000 reads so far
2011-05-19 18:10:38,769 - INFO - Processed 65400000 reads so far
2011-05-19 18:10:47,761 - INFO - Processed 65500000 reads so far
2011-05-19 18:11:01,932 - INFO - Processed 65600000 reads so far
2011-05-19 18:11:13,921 - INFO - Processed 65700000 reads so far
2011-05-19 18:11:26,519 - INFO - Processed 65800000 reads so far
2011-05-19 18:11:40,559 - INFO - Processed 65900000 reads so far
2011-05-19 18:11:51,636 - INFO - Processed 66000000 reads so far
2011-05-19 18:12:01,718 - INFO - Processed 66100000 reads so far
2011-05-19 18:12:09,603 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:142990246-163010246
2011-05-19 18:12:12,679 - INFO - Processed 66200000 reads so far
2011-05-19 18:12:23,966 - INFO - Processed 66300000 reads so far
2011-05-19 18:12:36,374 - INFO - Processed 66400000 reads so far
2011-05-19 18:12:51,789 - INFO - Processed 66500000 reads so far
2011-05-19 18:13:03,493 - INFO - Processed 66600000 reads so far
2011-05-19 18:13:17,608 - INFO - Processed 66700000 reads so far
2011-05-19 18:13:30,081 - INFO - Processed 66800000 reads so far
2011-05-19 18:13:43,284 - INFO - Processed 66900000 reads so far
2011-05-19 18:13:57,543 - INFO - Processed 67000000 reads so far
2011-05-19 18:14:08,235 - INFO - Processed 67100000 reads so far
2011-05-19 18:14:19,128 - INFO - Processed 67200000 reads so far
2011-05-19 18:14:23,996 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:162990328-183010328
2011-05-19 18:14:32,206 - INFO - Processed 67300000 reads so far
2011-05-19 18:14:43,177 - INFO - Processed 67400000 reads so far
2011-05-19 18:14:54,111 - INFO - Processed 67500000 reads so far
2011-05-19 18:15:04,686 - INFO - Processed 67600000 reads so far
2011-05-19 18:15:16,269 - INFO - Processed 67700000 reads so far
2011-05-19 18:15:28,591 - INFO - Processed 67800000 reads so far
2011-05-19 18:15:36,815 - INFO - Processed 67900000 reads so far
2011-05-19 18:15:45,634 - INFO - Processed 68000000 reads so far
2011-05-19 18:15:56,009 - INFO - Processed 68100000 reads so far
2011-05-19 18:16:07,231 - INFO - Processed 68200000 reads so far
2011-05-19 18:16:17,688 - INFO - Processed 68300000 reads so far
2011-05-19 18:16:30,384 - INFO - Processed 68400000 reads so far
2011-05-19 18:16:30,530 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:182990346-203010346
2011-05-19 18:16:41,590 - INFO - Processed 68500000 reads so far
2011-05-19 18:16:51,365 - INFO - Processed 68600000 reads so far
2011-05-19 18:17:01,012 - INFO - Processed 68700000 reads so far
2011-05-19 18:17:15,261 - INFO - Processed 68800000 reads so far
2011-05-19 18:17:30,391 - INFO - Processed 68900000 reads so far
2011-05-19 18:17:42,233 - INFO - Processed 69000000 reads so far
2011-05-19 18:17:54,939 - INFO - Processed 69100000 reads so far
2011-05-19 18:18:04,959 - INFO - Processed 69200000 reads so far
2011-05-19 18:18:05,821 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1_random:0-20010000
2011-05-19 18:24:14,460 - INFO - Processed 69300000 reads so far
2011-05-19 18:24:17,917 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:2990030-23010030
2011-05-19 18:24:26,147 - INFO - Processed 69400000 reads so far
2011-05-19 18:24:37,551 - INFO - Processed 69500000 reads so far
2011-05-19 18:24:50,641 - INFO - Processed 69600000 reads so far
2011-05-19 18:25:04,155 - INFO - Processed 69700000 reads so far
2011-05-19 18:25:15,605 - INFO - Processed 69800000 reads so far
2011-05-19 18:25:27,422 - INFO - Processed 69900000 reads so far
2011-05-19 18:25:38,737 - INFO - Processed 70000000 reads so far
2011-05-19 18:25:50,708 - INFO - Processed 70100000 reads so far
2011-05-19 18:26:02,063 - INFO - Processed 70200000 reads so far
2011-05-19 18:26:13,344 - INFO - Processed 70300000 reads so far
2011-05-19 18:26:25,236 - INFO - Processed 70400000 reads so far
2011-05-19 18:26:32,569 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:22990037-43010037
2011-05-19 18:26:34,910 - INFO - Processed 70500000 reads so far
2011-05-19 18:26:46,376 - INFO - Processed 70600000 reads so far
2011-05-19 18:26:58,675 - INFO - Processed 70700000 reads so far
2011-05-19 18:27:12,698 - INFO - Processed 70800000 reads so far
2011-05-19 18:27:26,715 - INFO - Processed 70900000 reads so far
2011-05-19 18:27:38,341 - INFO - Processed 71000000 reads so far
2011-05-19 18:27:48,366 - INFO - Processed 71100000 reads so far
2011-05-19 18:27:58,378 - INFO - Processed 71200000 reads so far
2011-05-19 18:28:06,828 - INFO - Processed 71300000 reads so far
2011-05-19 18:28:15,099 - INFO - Processed 71400000 reads so far
2011-05-19 18:28:22,944 - INFO - Processed 71500000 reads so far
2011-05-19 18:28:30,049 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:42990045-63010045
2011-05-19 18:28:33,534 - INFO - Processed 71600000 reads so far
2011-05-19 18:28:44,773 - INFO - Processed 71700000 reads so far
2011-05-19 18:28:57,106 - INFO - Processed 71800000 reads so far
2011-05-19 18:29:10,945 - INFO - Processed 71900000 reads so far
2011-05-19 18:29:22,155 - INFO - Processed 72000000 reads so far
2011-05-19 18:29:36,643 - INFO - Processed 72100000 reads so far
2011-05-19 18:29:45,898 - INFO - Processed 72200000 reads so far
2011-05-19 18:29:57,640 - INFO - Processed 72300000 reads so far
2011-05-19 18:30:09,260 - INFO - Processed 72400000 reads so far
2011-05-19 18:30:21,953 - INFO - Processed 72500000 reads so far
2011-05-19 18:30:35,255 - INFO - Processed 72600000 reads so far
2011-05-19 18:30:42,592 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:62990074-83010074
2011-05-19 18:30:48,098 - INFO - Processed 72700000 reads so far
2011-05-19 18:30:59,382 - INFO - Processed 72800000 reads so far
2011-05-19 18:31:10,653 - INFO - Processed 72900000 reads so far
2011-05-19 18:31:25,524 - INFO - Processed 73000000 reads so far
2011-05-19 18:31:38,621 - INFO - Processed 73100000 reads so far
2011-05-19 18:31:52,654 - INFO - Processed 73200000 reads so far
2011-05-19 18:32:03,953 - INFO - Processed 73300000 reads so far
2011-05-19 18:32:17,479 - INFO - Processed 73400000 reads so far
2011-05-19 18:32:28,622 - INFO - Processed 73500000 reads so far
2011-05-19 18:32:38,241 - INFO - Processed 73600000 reads so far
2011-05-19 18:32:48,995 - INFO - Processed 73700000 reads so far
2011-05-19 18:33:01,107 - INFO - Processed 73800000 reads so far
2011-05-19 18:33:12,998 - INFO - Processed 73900000 reads so far
2011-05-19 18:33:15,292 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:82990081-103010081
2011-05-19 18:33:24,180 - INFO - Processed 74000000 reads so far
2011-05-19 18:33:39,049 - INFO - Processed 74100000 reads so far
2011-05-19 18:33:50,941 - INFO - Processed 74200000 reads so far
2011-05-19 18:34:05,441 - INFO - Processed 74300000 reads so far
2011-05-19 18:34:19,727 - INFO - Processed 74400000 reads so far
2011-05-19 18:34:31,614 - INFO - Processed 74500000 reads so far
2011-05-19 18:34:47,094 - INFO - Processed 74600000 reads so far
2011-05-19 18:34:56,729 - INFO - Processed 74700000 reads so far
2011-05-19 18:35:06,949 - INFO - Processed 74800000 reads so far
2011-05-19 18:35:16,375 - INFO - Processed 74900000 reads so far
2011-05-19 18:35:26,268 - INFO - Processed 75000000 reads so far
2011-05-19 18:35:35,033 - INFO - Processed 75100000 reads so far
2011-05-19 18:35:44,335 - INFO - Processed 75200000 reads so far
2011-05-19 18:35:56,601 - INFO - Processed 75300000 reads so far
2011-05-19 18:36:07,986 - INFO - Processed 75400000 reads so far
2011-05-19 18:36:18,458 - INFO - Processed 75500000 reads so far
2011-05-19 18:36:34,196 - INFO - Processed 75600000 reads so far
2011-05-19 18:36:43,396 - INFO - Processed 75700000 reads so far
2011-05-19 18:36:52,193 - INFO - Processed 75800000 reads so far
2011-05-19 18:37:01,353 - INFO - Processed 75900000 reads so far
2011-05-19 18:37:11,860 - INFO - Processed 76000000 reads so far
2011-05-19 18:37:21,948 - INFO - Processed 76100000 reads so far
2011-05-19 18:37:33,738 - INFO - Processed 76200000 reads so far
2011-05-19 18:37:43,522 - INFO - Processed 76300000 reads so far
2011-05-19 18:37:53,266 - INFO - Processed 76400000 reads so far
2011-05-19 18:38:02,790 - INFO - Processed 76500000 reads so far
2011-05-19 18:38:12,285 - INFO - Processed 76600000 reads so far
2011-05-19 18:38:23,316 - INFO - Processed 76700000 reads so far
2011-05-19 18:38:32,611 - INFO - Processed 76800000 reads so far
2011-05-19 18:38:41,930 - INFO - Processed 76900000 reads so far
2011-05-19 18:38:55,452 - INFO - Processed 77000000 reads so far
2011-05-19 18:39:04,922 - INFO - Processed 77100000 reads so far
2011-05-19 18:39:16,379 - INFO - Processed 77200000 reads so far
2011-05-19 18:39:28,922 - INFO - Processed 77300000 reads so far
2011-05-19 18:39:37,644 - INFO - Processed 77400000 reads so far
2011-05-19 18:39:47,006 - INFO - Processed 77500000 reads so far
2011-05-19 18:39:56,018 - INFO - Processed 77600000 reads so far
2011-05-19 18:40:06,314 - INFO - Processed 77700000 reads so far
2011-05-19 18:40:15,104 - INFO - Processed 77800000 reads so far
2011-05-19 18:40:23,981 - INFO - Processed 77900000 reads so far
2011-05-19 18:40:34,182 - INFO - Processed 78000000 reads so far
2011-05-19 18:40:43,700 - INFO - Processed 78100000 reads so far
2011-05-19 18:40:53,147 - INFO - Processed 78200000 reads so far
2011-05-19 18:41:02,257 - INFO - Processed 78300000 reads so far
2011-05-19 18:41:15,610 - INFO - Processed 78400000 reads so far
2011-05-19 18:41:25,337 - INFO - Processed 78500000 reads so far
2011-05-19 18:41:33,963 - INFO - Processed 78600000 reads so far
2011-05-19 18:41:43,755 - INFO - Processed 78700000 reads so far
2011-05-19 18:41:50,824 - INFO - Processed 78800000 reads so far
2011-05-19 18:41:57,528 - INFO - Processed 78900000 reads so far
2011-05-19 18:42:05,961 - INFO - Processed 79000000 reads so far
2011-05-19 18:42:14,245 - INFO - Processed 79100000 reads so far
2011-05-19 18:42:25,196 - INFO - Processed 79200000 reads so far
2011-05-19 18:42:34,442 - INFO - Processed 79300000 reads so far
2011-05-19 18:42:43,414 - INFO - Processed 79400000 reads so far
2011-05-19 18:42:51,491 - INFO - Processed 79500000 reads so far
2011-05-19 18:43:00,934 - INFO - Processed 79600000 reads so far
2011-05-19 18:43:09,218 - INFO - Processed 79700000 reads so far
2011-05-19 18:43:17,754 - INFO - Processed 79800000 reads so far
2011-05-19 18:43:27,004 - INFO - Processed 79900000 reads so far
2011-05-19 18:43:37,648 - INFO - Processed 80000000 reads so far
2011-05-19 18:43:45,179 - INFO - Processed 80100000 reads so far
2011-05-19 18:43:55,362 - INFO - Processed 80200000 reads so far
2011-05-19 18:44:08,269 - INFO - Processed 80300000 reads so far
2011-05-19 18:44:18,391 - INFO - Processed 80400000 reads so far
2011-05-19 18:44:27,775 - INFO - Processed 80500000 reads so far
2011-05-19 18:44:36,992 - INFO - Processed 80600000 reads so far
2011-05-19 18:44:50,202 - INFO - Processed 80700000 reads so far
2011-05-19 18:45:00,877 - INFO - Processed 80800000 reads so far
2011-05-19 18:45:09,909 - INFO - Processed 80900000 reads so far
2011-05-19 18:45:21,342 - INFO - Processed 81000000 reads so far
2011-05-19 18:45:31,072 - INFO - Processed 81100000 reads so far
2011-05-19 18:45:40,869 - INFO - Processed 81200000 reads so far
2011-05-19 18:45:51,519 - INFO - Processed 81300000 reads so far
2011-05-19 18:46:01,998 - INFO - Processed 81400000 reads so far
2011-05-19 18:46:09,352 - INFO - Processed 81500000 reads so far
2011-05-19 18:46:16,277 - INFO - Processed 81600000 reads so far
2011-05-19 18:46:27,724 - INFO - Processed 81700000 reads so far
2011-05-19 18:46:38,779 - INFO - Processed 81800000 reads so far
2011-05-19 18:46:47,215 - INFO - Processed 81900000 reads so far
2011-05-19 18:46:55,383 - INFO - Processed 82000000 reads so far
2011-05-19 18:47:04,900 - INFO - Processed 82100000 reads so far
2011-05-19 18:47:12,721 - INFO - Processed 82200000 reads so far
2011-05-19 18:47:20,577 - INFO - Processed 82300000 reads so far
2011-05-19 18:47:28,260 - INFO - Processed 82400000 reads so far
2011-05-19 18:47:35,940 - INFO - Processed 82500000 reads so far
2011-05-19 18:47:44,971 - INFO - Processed 82600000 reads so far
2011-05-19 18:47:52,038 - INFO - Processed 82700000 reads so far
2011-05-19 18:47:59,247 - INFO - Processed 82800000 reads so far
2011-05-19 18:48:09,290 - INFO - Processed 82900000 reads so far
2011-05-19 18:48:20,340 - INFO - Processed 83000000 reads so far
2011-05-19 18:48:29,524 - INFO - Processed 83100000 reads so far
2011-05-19 18:48:39,875 - INFO - Processed 83200000 reads so far
2011-05-19 18:48:49,158 - INFO - Processed 83300000 reads so far
2011-05-19 18:48:58,152 - INFO - Processed 83400000 reads so far
2011-05-19 18:49:08,170 - INFO - Processed 83500000 reads so far
2011-05-19 18:49:16,054 - INFO - Processed 83600000 reads so far
2011-05-19 18:49:26,153 - INFO - Processed 83700000 reads so far
2011-05-19 18:49:33,102 - INFO - Processed 83800000 reads so far
2011-05-19 18:49:43,800 - INFO - Processed 83900000 reads so far
2011-05-19 18:49:54,842 - INFO - Processed 84000000 reads so far
2011-05-19 18:50:05,247 - INFO - Processed 84100000 reads so far
2011-05-19 18:50:15,032 - INFO - Processed 84200000 reads so far
2011-05-19 18:50:23,876 - INFO - Processed 84300000 reads so far
2011-05-19 18:50:35,278 - INFO - Processed 84400000 reads so far
2011-05-19 18:50:45,071 - INFO - Processed 84500000 reads so far
2011-05-19 18:50:54,961 - INFO - Processed 84600000 reads so far
2011-05-19 18:51:05,608 - INFO - Processed 84700000 reads so far
2011-05-19 18:51:15,104 - INFO - Processed 84800000 reads so far
2011-05-19 18:51:24,575 - INFO - Processed 84900000 reads so far
2011-05-19 18:51:35,065 - INFO - Processed 85000000 reads so far
2011-05-19 18:51:44,643 - INFO - Processed 85100000 reads so far
2011-05-19 18:51:56,505 - INFO - Processed 85200000 reads so far
2011-05-19 18:52:07,630 - INFO - Processed 85300000 reads so far
2011-05-19 18:52:14,459 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:102990087-123010087
2011-05-19 18:52:22,400 - INFO - Processed 85400000 reads so far
2011-05-19 18:52:34,068 - INFO - Processed 85500000 reads so far
2011-05-19 18:52:45,032 - INFO - Processed 85600000 reads so far
2011-05-19 18:52:57,533 - INFO - Processed 85700000 reads so far
2011-05-19 18:53:08,717 - INFO - Processed 85800000 reads so far
2011-05-19 18:53:20,437 - INFO - Processed 85900000 reads so far
2011-05-19 18:53:34,063 - INFO - Processed 86000000 reads so far
2011-05-19 18:53:48,689 - INFO - Processed 86100000 reads so far
2011-05-19 18:54:00,399 - INFO - Processed 86200000 reads so far
2011-05-19 18:54:10,661 - INFO - Processed 86300000 reads so far
2011-05-19 18:54:57,674 - INFO - Processed 86400000 reads so far
2011-05-19 18:55:03,420 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:122990131-143010131
2011-05-19 18:55:09,234 - INFO - Processed 86500000 reads so far
2011-05-19 18:55:20,858 - INFO - Processed 86600000 reads so far
2011-05-19 18:55:34,603 - INFO - Processed 86700000 reads so far
2011-05-19 18:55:47,225 - INFO - Processed 86800000 reads so far
2011-05-19 18:56:01,166 - INFO - Processed 86900000 reads so far
2011-05-19 18:56:12,821 - INFO - Processed 87000000 reads so far
2011-05-19 18:56:26,972 - INFO - Processed 87100000 reads so far
2011-05-19 18:56:40,826 - INFO - Processed 87200000 reads so far
2011-05-19 18:56:55,827 - INFO - Processed 87300000 reads so far
2011-05-19 18:57:08,923 - INFO - Processed 87400000 reads so far
2011-05-19 18:57:17,868 - INFO - Processed 87500000 reads so far
2011-05-19 18:57:25,447 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:142990132-163010132
2011-05-19 18:57:26,536 - INFO - Processed 87600000 reads so far
2011-05-19 18:57:38,357 - INFO - Processed 87700000 reads so far
2011-05-19 18:57:51,930 - INFO - Processed 87800000 reads so far
2011-05-19 18:58:03,052 - INFO - Processed 87900000 reads so far
2011-05-19 18:58:14,412 - INFO - Processed 88000000 reads so far
2011-05-19 18:58:26,977 - INFO - Processed 88100000 reads so far
2011-05-19 18:58:38,612 - INFO - Processed 88200000 reads so far
2011-05-19 18:58:49,852 - INFO - Processed 88300000 reads so far
2011-05-19 18:59:01,581 - INFO - Processed 88400000 reads so far
2011-05-19 18:59:15,149 - INFO - Processed 88500000 reads so far
2011-05-19 18:59:27,100 - INFO - Processed 88600000 reads so far
2011-05-19 18:59:38,911 - INFO - Processed 88700000 reads so far
2011-05-19 18:59:45,104 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:162990139-183010139
2011-05-19 18:59:51,177 - INFO - Processed 88800000 reads so far
2011-05-19 19:00:02,818 - INFO - Processed 88900000 reads so far
2011-05-19 19:00:15,518 - INFO - Processed 89000000 reads so far
2011-05-19 19:00:25,435 - INFO - Processed 89100000 reads so far
2011-05-19 19:00:35,364 - INFO - Processed 89200000 reads so far
2011-05-19 19:00:45,122 - INFO - Processed 89300000 reads so far
2011-05-19 19:00:55,517 - INFO - Processed 89400000 reads so far
2011-05-19 19:01:05,698 - INFO - Processed 89500000 reads so far
2011-05-19 19:01:18,064 - INFO - Processed 89600000 reads so far
2011-05-19 19:01:28,563 - INFO - Processed 89700000 reads so far
2011-05-19 19:01:40,549 - INFO - Processed 89800000 reads so far
2011-05-19 19:01:46,657 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:2989991-23009991
2011-05-19 19:01:48,801 - INFO - Processed 89900000 reads so far
2011-05-19 19:01:59,707 - INFO - Processed 90000000 reads so far
2011-05-19 19:02:13,585 - INFO - Processed 90100000 reads so far
2011-05-19 19:02:24,255 - INFO - Processed 90200000 reads so far
2011-05-19 19:02:34,636 - INFO - Processed 90300000 reads so far
2011-05-19 19:02:44,999 - INFO - Processed 90400000 reads so far
2011-05-19 19:02:55,694 - INFO - Processed 90500000 reads so far
2011-05-19 19:03:08,271 - INFO - Processed 90600000 reads so far
2011-05-19 19:03:17,810 - INFO - Processed 90700000 reads so far
2011-05-19 19:03:28,400 - INFO - Processed 90800000 reads so far
2011-05-19 19:03:39,880 - INFO - Processed 90900000 reads so far
2011-05-19 19:03:48,332 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:22990006-43010006
2011-05-19 19:03:50,543 - INFO - Processed 91000000 reads so far
2011-05-19 19:04:00,029 - INFO - Processed 91100000 reads so far
2011-05-19 19:04:09,643 - INFO - Processed 91200000 reads so far
2011-05-19 19:04:19,854 - INFO - Processed 91300000 reads so far
2011-05-19 19:04:29,814 - INFO - Processed 91400000 reads so far
2011-05-19 19:04:41,710 - INFO - Processed 91500000 reads so far
2011-05-19 19:04:53,046 - INFO - Processed 91600000 reads so far
2011-05-19 19:05:03,995 - INFO - Processed 91700000 reads so far
2011-05-19 19:05:16,185 - INFO - Processed 91800000 reads so far
2011-05-19 19:05:29,418 - INFO - Processed 91900000 reads so far
2011-05-19 19:05:39,320 - INFO - Processed 92000000 reads so far
2011-05-19 19:05:49,110 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:42990038-63010038
2011-05-19 19:05:49,610 - INFO - Processed 92100000 reads so far
2011-05-19 19:06:01,126 - INFO - Processed 92200000 reads so far
2011-05-19 19:06:10,428 - INFO - Processed 92300000 reads so far
2011-05-19 19:06:20,738 - INFO - Processed 92400000 reads so far
2011-05-19 19:06:33,778 - INFO - Processed 92500000 reads so far
2011-05-19 19:06:42,012 - INFO - Processed 92600000 reads so far
2011-05-19 19:06:50,488 - INFO - Processed 92700000 reads so far
2011-05-19 19:07:00,166 - INFO - Processed 92800000 reads so far
2011-05-19 19:07:09,960 - INFO - Processed 92900000 reads so far
2011-05-19 19:07:20,489 - INFO - Processed 93000000 reads so far
2011-05-19 19:07:29,489 - INFO - Processed 93100000 reads so far
2011-05-19 19:07:38,883 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:62990137-83010137
2011-05-19 19:07:42,101 - INFO - Processed 93200000 reads so far
2011-05-19 19:07:53,950 - INFO - Processed 93300000 reads so far
2011-05-19 19:08:07,730 - INFO - Processed 93400000 reads so far
2011-05-19 19:08:19,291 - INFO - Processed 93500000 reads so far
2011-05-19 19:08:31,009 - INFO - Processed 93600000 reads so far
2011-05-19 19:08:41,354 - INFO - Processed 93700000 reads so far
2011-05-19 19:08:54,415 - INFO - Processed 93800000 reads so far
2011-05-19 19:09:04,250 - INFO - Processed 93900000 reads so far
2011-05-19 19:09:13,728 - INFO - Processed 94000000 reads so far
2011-05-19 19:09:23,859 - INFO - Processed 94100000 reads so far
2011-05-19 19:09:34,171 - INFO - Processed 94200000 reads so far
2011-05-19 19:09:38,410 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:82990138-103010138
2011-05-19 19:09:43,977 - INFO - Processed 94300000 reads so far
2011-05-19 19:09:52,560 - INFO - Processed 94400000 reads so far
2011-05-19 19:10:02,719 - INFO - Processed 94500000 reads so far
2011-05-19 19:10:11,874 - INFO - Processed 94600000 reads so far
2011-05-19 19:10:52,650 - INFO - Processed 94700000 reads so far
2011-05-19 19:11:29,582 - INFO - Processed 94800000 reads so far
2011-05-19 19:11:46,348 - INFO - Processed 94900000 reads so far
2011-05-19 19:12:02,729 - INFO - Processed 95000000 reads so far
2011-05-19 19:12:13,021 - INFO - Processed 95100000 reads so far
2011-05-19 19:12:24,439 - INFO - Processed 95200000 reads so far
2011-05-19 19:12:32,406 - INFO - Processed 95300000 reads so far
2011-05-19 19:12:38,234 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:102990148-123010148
2011-05-19 19:12:41,689 - INFO - Processed 95400000 reads so far
2011-05-19 19:12:52,033 - INFO - Processed 95500000 reads so far
2011-05-19 19:13:01,392 - INFO - Processed 95600000 reads so far
2011-05-19 19:13:11,570 - INFO - Processed 95700000 reads so far
2011-05-19 19:13:20,879 - INFO - Processed 95800000 reads so far
2011-05-19 19:13:31,476 - INFO - Processed 95900000 reads so far
2011-05-19 19:13:44,038 - INFO - Processed 96000000 reads so far
2011-05-19 19:13:57,241 - INFO - Processed 96100000 reads so far
2011-05-19 19:14:06,234 - INFO - Processed 96200000 reads so far
2011-05-19 19:14:14,408 - INFO - Processed 96300000 reads so far
2011-05-19 19:14:24,088 - INFO - Processed 96400000 reads so far
2011-05-19 19:14:32,336 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:122990166-143010166
2011-05-19 19:14:35,268 - INFO - Processed 96500000 reads so far
2011-05-19 19:14:46,568 - INFO - Processed 96600000 reads so far
2011-05-19 19:14:58,952 - INFO - Processed 96700000 reads so far
2011-05-19 19:15:09,886 - INFO - Processed 96800000 reads so far
2011-05-19 19:15:21,660 - INFO - Processed 96900000 reads so far
2011-05-19 19:15:32,758 - INFO - Processed 97000000 reads so far
2011-05-19 19:15:47,217 - INFO - Processed 97100000 reads so far
2011-05-19 19:15:58,706 - INFO - Processed 97200000 reads so far
2011-05-19 19:16:11,531 - INFO - Processed 97300000 reads so far
2011-05-19 19:16:25,298 - INFO - Processed 97400000 reads so far
2011-05-19 19:16:39,377 - INFO - Processed 97500000 reads so far
2011-05-19 19:16:50,034 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:142990178-163010178
2011-05-19 19:16:51,504 - INFO - Processed 97600000 reads so far
2011-05-19 19:17:02,558 - INFO - Processed 97700000 reads so far
2011-05-19 19:17:14,842 - INFO - Processed 97800000 reads so far
2011-05-19 19:17:27,670 - INFO - Processed 97900000 reads so far
2011-05-19 19:17:38,899 - INFO - Processed 98000000 reads so far
2011-05-19 19:17:50,117 - INFO - Processed 98100000 reads so far
2011-05-19 19:18:00,118 - INFO - Processed 98200000 reads so far
2011-05-19 19:18:08,413 - INFO - Processed 98300000 reads so far
2011-05-19 19:18:18,119 - INFO - Processed 98400000 reads so far
2011-05-19 19:18:27,639 - INFO - Processed 98500000 reads so far
2011-05-19 19:18:31,479 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3_random:0-20010101
2011-05-19 19:18:31,569 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:2989992-23009992
2011-05-19 19:18:37,031 - INFO - Processed 98600000 reads so far
2011-05-19 19:18:45,211 - INFO - Processed 98700000 reads so far
2011-05-19 19:18:53,343 - INFO - Processed 98800000 reads so far
2011-05-19 19:19:01,350 - INFO - Processed 98900000 reads so far
2011-05-19 19:19:11,759 - INFO - Processed 99000000 reads so far
2011-05-19 19:19:20,607 - INFO - Processed 99100000 reads so far
2011-05-19 19:19:28,617 - INFO - Processed 99200000 reads so far
2011-05-19 19:19:42,336 - INFO - Processed 99300000 reads so far
2011-05-19 19:19:52,106 - INFO - Processed 99400000 reads so far
2011-05-19 19:20:03,159 - INFO - Processed 99500000 reads so far
2011-05-19 19:20:11,445 - INFO - Processed 99600000 reads so far
2011-05-19 19:20:18,084 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:22990025-43010025
2011-05-19 19:20:20,917 - INFO - Processed 99700000 reads so far
2011-05-19 19:20:30,272 - INFO - Processed 99800000 reads so far
2011-05-19 19:20:41,454 - INFO - Processed 99900000 reads so far
2011-05-19 19:20:53,980 - INFO - Processed 100000000 reads so far
2011-05-19 19:21:02,718 - INFO - Processed 100100000 reads so far
2011-05-19 19:21:11,122 - INFO - Processed 100200000 reads so far
2011-05-19 19:21:20,076 - INFO - Processed 100300000 reads so far
2011-05-19 19:21:28,802 - INFO - Processed 100400000 reads so far
2011-05-19 19:21:39,293 - INFO - Processed 100500000 reads so far
2011-05-19 19:21:50,145 - INFO - Processed 100600000 reads so far
2011-05-19 19:22:02,997 - INFO - Processed 100700000 reads so far
2011-05-19 19:22:04,861 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:42990039-63010039
2011-05-19 19:22:14,430 - INFO - Processed 100800000 reads so far
2011-05-19 19:22:25,296 - INFO - Processed 100900000 reads so far
2011-05-19 19:22:37,334 - INFO - Processed 101000000 reads so far
2011-05-19 19:22:48,318 - INFO - Processed 101100000 reads so far
2011-05-19 19:23:00,314 - INFO - Processed 101200000 reads so far
2011-05-19 19:23:12,180 - INFO - Processed 101300000 reads so far
2011-05-19 19:23:25,007 - INFO - Processed 101400000 reads so far
2011-05-19 19:23:35,297 - INFO - Processed 101500000 reads so far
2011-05-19 19:23:44,125 - INFO - Processed 101600000 reads so far
2011-05-19 19:23:54,299 - INFO - Processed 101700000 reads so far
2011-05-19 19:24:03,502 - INFO - Processed 101800000 reads so far
2011-05-19 19:24:06,862 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:62990040-83010040
2011-05-19 19:24:13,324 - INFO - Processed 101900000 reads so far
2011-05-19 19:24:24,636 - INFO - Processed 102000000 reads so far
2011-05-19 19:24:36,327 - INFO - Processed 102100000 reads so far
2011-05-19 19:24:46,040 - INFO - Processed 102200000 reads so far
2011-05-19 19:24:55,420 - INFO - Processed 102300000 reads so far
2011-05-19 19:25:04,934 - INFO - Processed 102400000 reads so far
2011-05-19 19:25:15,907 - INFO - Processed 102500000 reads so far
2011-05-19 19:25:25,985 - INFO - Processed 102600000 reads so far
2011-05-19 19:25:38,650 - INFO - Processed 102700000 reads so far
2011-05-19 19:25:53,288 - INFO - Processed 102800000 reads so far
2011-05-19 19:26:03,126 - INFO - Processed 102900000 reads so far
2011-05-19 19:26:07,615 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:82990081-103010081
2011-05-19 19:26:15,491 - INFO - Processed 103000000 reads so far
2011-05-19 19:26:26,636 - INFO - Processed 103100000 reads so far
2011-05-19 19:26:36,907 - INFO - Processed 103200000 reads so far
2011-05-19 19:26:46,481 - INFO - Processed 103300000 reads so far
2011-05-19 19:26:59,421 - INFO - Processed 103400000 reads so far
2011-05-19 19:27:10,652 - INFO - Processed 103500000 reads so far
2011-05-19 19:27:22,491 - INFO - Processed 103600000 reads so far
2011-05-19 19:27:35,064 - INFO - Processed 103700000 reads so far
2011-05-19 19:27:45,923 - INFO - Processed 103800000 reads so far
2011-05-19 19:27:58,179 - INFO - Processed 103900000 reads so far
2011-05-19 19:28:13,100 - INFO - Processed 104000000 reads so far
2011-05-19 19:28:21,995 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:102990114-123010114
2011-05-19 19:28:26,716 - INFO - Processed 104100000 reads so far
2011-05-19 19:28:39,483 - INFO - Processed 104200000 reads so far
2011-05-19 19:28:50,300 - INFO - Processed 104300000 reads so far
2011-05-19 19:29:01,200 - INFO - Processed 104400000 reads so far
2011-05-19 19:29:14,806 - INFO - Processed 104500000 reads so far
2011-05-19 19:29:26,325 - INFO - Processed 104600000 reads so far
2011-05-19 19:29:37,039 - INFO - Processed 104700000 reads so far
2011-05-19 19:29:49,437 - INFO - Processed 104800000 reads so far
2011-05-19 19:30:02,084 - INFO - Processed 104900000 reads so far
2011-05-19 19:30:10,611 - INFO - Processed 105000000 reads so far
2011-05-19 19:30:23,352 - INFO - Processed 105100000 reads so far
2011-05-19 19:30:28,991 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:122990171-143010171
2011-05-19 19:30:34,925 - INFO - Processed 105200000 reads so far
2011-05-19 19:30:46,727 - INFO - Processed 105300000 reads so far
2011-05-19 19:30:59,739 - INFO - Processed 105400000 reads so far
2011-05-19 19:31:11,088 - INFO - Processed 105500000 reads so far
2011-05-19 19:31:21,329 - INFO - Processed 105600000 reads so far
2011-05-19 19:31:37,700 - INFO - Processed 105700000 reads so far
2011-05-19 19:31:50,530 - INFO - Processed 105800000 reads so far
2011-05-19 19:32:02,752 - INFO - Processed 105900000 reads so far
2011-05-19 19:32:19,590 - INFO - Processed 106000000 reads so far
2011-05-19 19:32:32,995 - INFO - Processed 106100000 reads so far
2011-05-19 19:32:50,119 - INFO - Processed 106200000 reads so far
2011-05-19 19:32:52,921 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:142990187-163010187
2011-05-19 19:33:01,253 - INFO - Processed 106300000 reads so far
2011-05-19 19:33:09,363 - INFO - Processed 106400000 reads so far
2011-05-19 19:33:18,760 - INFO - Processed 106500000 reads so far
2011-05-19 19:33:28,874 - INFO - Processed 106600000 reads so far
2011-05-19 19:33:37,622 - INFO - Processed 106700000 reads so far
2011-05-19 19:33:46,272 - INFO - Processed 106800000 reads so far
2011-05-19 19:33:55,298 - INFO - Processed 106900000 reads so far
2011-05-19 19:34:05,062 - INFO - Processed 107000000 reads so far
2011-05-19 19:34:06,609 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4_random:0-20010033
2011-05-19 19:34:07,275 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:2990000-23010000
2011-05-19 19:34:13,389 - INFO - Processed 107100000 reads so far
2011-05-19 19:34:22,882 - INFO - Processed 107200000 reads so far
2011-05-19 19:34:32,452 - INFO - Processed 107300000 reads so far
2011-05-19 19:34:42,650 - INFO - Processed 107400000 reads so far
2011-05-19 19:34:51,525 - INFO - Processed 107500000 reads so far
2011-05-19 19:35:01,212 - INFO - Processed 107600000 reads so far
2011-05-19 19:35:11,564 - INFO - Processed 107700000 reads so far
2011-05-19 19:35:21,869 - INFO - Processed 107800000 reads so far
2011-05-19 19:35:33,217 - INFO - Processed 107900000 reads so far
2011-05-19 19:35:43,350 - INFO - Processed 108000000 reads so far
2011-05-19 19:35:53,409 - INFO - Processed 108100000 reads so far
2011-05-19 19:35:57,059 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:22990005-43010005
2011-05-19 19:36:04,682 - INFO - Processed 108200000 reads so far
2011-05-19 19:36:14,533 - INFO - Processed 108300000 reads so far
2011-05-19 19:36:26,180 - INFO - Processed 108400000 reads so far
2011-05-19 19:36:37,578 - INFO - Processed 108500000 reads so far
2011-05-19 19:36:47,387 - INFO - Processed 108600000 reads so far
2011-05-19 19:36:55,971 - INFO - Processed 108700000 reads so far
2011-05-19 19:37:07,090 - INFO - Processed 108800000 reads so far
2011-05-19 19:37:17,747 - INFO - Processed 108900000 reads so far
2011-05-19 19:37:28,576 - INFO - Processed 109000000 reads so far
2011-05-19 19:37:39,980 - INFO - Processed 109100000 reads so far
2011-05-19 19:37:51,065 - INFO - Processed 109200000 reads so far
2011-05-19 19:37:58,377 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:42990007-63010007
2011-05-19 19:38:02,933 - INFO - Processed 109300000 reads so far
2011-05-19 19:38:15,201 - INFO - Processed 109400000 reads so far
2011-05-19 19:38:23,416 - INFO - Processed 109500000 reads so far
2011-05-19 19:38:34,912 - INFO - Processed 109600000 reads so far
2011-05-19 19:38:45,632 - INFO - Processed 109700000 reads so far
2011-05-19 19:38:54,392 - INFO - Processed 109800000 reads so far
2011-05-19 19:39:03,141 - INFO - Processed 109900000 reads so far
2011-05-19 19:39:13,538 - INFO - Processed 110000000 reads so far
2011-05-19 19:39:24,639 - INFO - Processed 110100000 reads so far
2011-05-19 19:39:34,263 - INFO - Processed 110200000 reads so far
2011-05-19 19:39:43,975 - INFO - Processed 110300000 reads so far
2011-05-19 19:39:47,928 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:62990028-83010028
2011-05-19 19:39:53,313 - INFO - Processed 110400000 reads so far
2011-05-19 19:40:31,714 - INFO - Processed 110500000 reads so far
2011-05-19 19:40:42,786 - INFO - Processed 110600000 reads so far
2011-05-19 19:40:54,017 - INFO - Processed 110700000 reads so far
2011-05-19 19:41:02,774 - INFO - Processed 110800000 reads so far
2011-05-19 19:41:12,273 - INFO - Processed 110900000 reads so far
2011-05-19 19:41:22,842 - INFO - Processed 111000000 reads so far
2011-05-19 19:41:32,863 - INFO - Processed 111100000 reads so far
2011-05-19 19:41:44,277 - INFO - Processed 111200000 reads so far
2011-05-19 19:41:54,072 - INFO - Processed 111300000 reads so far
2011-05-19 19:42:03,105 - INFO - Processed 111400000 reads so far
2011-05-19 19:42:05,407 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:82990037-103010037
2011-05-19 19:42:14,636 - INFO - Processed 111500000 reads so far
2011-05-19 19:42:27,995 - INFO - Processed 111600000 reads so far
2011-05-19 19:42:40,374 - INFO - Processed 111700000 reads so far
2011-05-19 19:42:56,610 - INFO - Processed 111800000 reads so far
2011-05-19 19:43:08,303 - INFO - Processed 111900000 reads so far
2011-05-19 19:43:21,140 - INFO - Processed 112000000 reads so far
2011-05-19 19:43:32,754 - INFO - Processed 112100000 reads so far
2011-05-19 19:43:43,658 - INFO - Processed 112200000 reads so far
2011-05-19 19:43:58,595 - INFO - Processed 112300000 reads so far
2011-05-19 19:44:12,675 - INFO - Processed 112400000 reads so far
2011-05-19 19:44:21,257 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:102990071-123010071
2011-05-19 19:44:23,546 - INFO - Processed 112500000 reads so far
2011-05-19 19:44:35,614 - INFO - Processed 112600000 reads so far
2011-05-19 19:44:48,393 - INFO - Processed 112700000 reads so far
2011-05-19 19:44:59,852 - INFO - Processed 112800000 reads so far
2011-05-19 19:45:15,536 - INFO - Processed 112900000 reads so far
2011-05-19 19:45:27,059 - INFO - Processed 113000000 reads so far
2011-05-19 19:45:39,758 - INFO - Processed 113100000 reads so far
2011-05-19 19:45:53,406 - INFO - Processed 113200000 reads so far
2011-05-19 19:46:04,438 - INFO - Processed 113300000 reads so far
2011-05-19 19:46:16,450 - INFO - Processed 113400000 reads so far
2011-05-19 19:46:30,298 - INFO - Processed 113500000 reads so far
2011-05-19 19:46:41,961 - INFO - Processed 113600000 reads so far
2011-05-19 19:46:42,221 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:122990115-143010115
2011-05-19 19:46:53,856 - INFO - Processed 113700000 reads so far
2011-05-19 19:47:02,980 - INFO - Processed 113800000 reads so far
2011-05-19 19:47:10,580 - INFO - Processed 113900000 reads so far
2011-05-19 19:47:22,786 - INFO - Processed 114000000 reads so far
2011-05-19 19:47:31,566 - INFO - Processed 114100000 reads so far
2011-05-19 19:47:41,992 - INFO - Processed 114200000 reads so far
2011-05-19 19:47:50,563 - INFO - Processed 114300000 reads so far
2011-05-19 19:48:01,605 - INFO - Processed 114400000 reads so far
2011-05-19 19:48:13,337 - INFO - Processed 114500000 reads so far
2011-05-19 19:48:24,853 - INFO - Processed 114600000 reads so far
2011-05-19 19:48:36,072 - INFO - Processed 114700000 reads so far
2011-05-19 19:48:37,109 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:142990116-163010116
2011-05-19 19:48:46,271 - INFO - Processed 114800000 reads so far
2011-05-19 19:48:56,488 - INFO - Processed 114900000 reads so far
2011-05-19 19:49:04,811 - INFO - Processed 115000000 reads so far
2011-05-19 19:49:15,673 - INFO - Processed 115100000 reads so far
2011-05-19 19:49:22,803 - INFO - Processed 115200000 reads so far
2011-05-19 19:49:28,049 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5_random:0-20010000
2011-05-19 19:49:28,621 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:2989979-23009979
2011-05-19 19:49:33,312 - INFO - Processed 115300000 reads so far
2011-05-19 19:49:46,071 - INFO - Processed 115400000 reads so far
2011-05-19 19:49:57,553 - INFO - Processed 115500000 reads so far
2011-05-19 19:50:08,891 - INFO - Processed 115600000 reads so far
2011-05-19 19:50:19,815 - INFO - Processed 115700000 reads so far
2011-05-19 19:50:28,505 - INFO - Processed 115800000 reads so far
2011-05-19 19:50:37,901 - INFO - Processed 115900000 reads so far
2011-05-19 19:50:47,206 - INFO - Processed 116000000 reads so far
2011-05-19 19:50:58,254 - INFO - Processed 116100000 reads so far
2011-05-19 19:51:10,457 - INFO - Processed 116200000 reads so far
2011-05-19 19:51:19,810 - INFO - Processed 116300000 reads so far
2011-05-19 19:51:23,119 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:22990001-43010001
2011-05-19 19:51:28,847 - INFO - Processed 116400000 reads so far
2011-05-19 19:51:37,534 - INFO - Processed 116500000 reads so far
2011-05-19 19:51:49,978 - INFO - Processed 116600000 reads so far
2011-05-19 19:52:01,902 - INFO - Processed 116700000 reads so far
2011-05-19 19:52:10,104 - INFO - Processed 116800000 reads so far
2011-05-19 19:52:20,959 - INFO - Processed 116900000 reads so far
2011-05-19 19:52:32,260 - INFO - Processed 117000000 reads so far
2011-05-19 19:52:42,043 - INFO - Processed 117100000 reads so far
2011-05-19 19:52:52,424 - INFO - Processed 117200000 reads so far
2011-05-19 19:53:03,490 - INFO - Processed 117300000 reads so far
2011-05-19 19:53:17,079 - INFO - Processed 117400000 reads so far
2011-05-19 19:53:23,348 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:42990014-63010014
2011-05-19 19:53:26,854 - INFO - Processed 117500000 reads so far
2011-05-19 19:53:37,640 - INFO - Processed 117600000 reads so far
2011-05-19 19:53:49,809 - INFO - Processed 117700000 reads so far
2011-05-19 19:54:00,982 - INFO - Processed 117800000 reads so far
2011-05-19 19:54:11,267 - INFO - Processed 117900000 reads so far
2011-05-19 19:54:22,280 - INFO - Processed 118000000 reads so far
2011-05-19 19:54:32,654 - INFO - Processed 118100000 reads so far
2011-05-19 19:54:40,819 - INFO - Processed 118200000 reads so far
2011-05-19 19:54:48,598 - INFO - Processed 118300000 reads so far
2011-05-19 19:54:59,509 - INFO - Processed 118400000 reads so far
2011-05-19 19:55:09,632 - INFO - Processed 118500000 reads so far
2011-05-19 19:55:18,316 - INFO - Processed 118600000 reads so far
2011-05-19 19:55:22,413 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:62990057-83010057
2011-05-19 19:55:28,075 - INFO - Processed 118700000 reads so far
2011-05-19 19:55:39,783 - INFO - Processed 118800000 reads so far
2011-05-19 19:55:46,742 - INFO - Processed 118900000 reads so far
2011-05-19 19:55:55,319 - INFO - Processed 119000000 reads so far
2011-05-19 19:56:03,049 - INFO - Processed 119100000 reads so far
2011-05-19 19:56:15,427 - INFO - Processed 119200000 reads so far
2011-05-19 19:56:25,807 - INFO - Processed 119300000 reads so far
2011-05-19 19:56:36,438 - INFO - Processed 119400000 reads so far
2011-05-19 19:56:47,503 - INFO - Processed 119500000 reads so far
2011-05-19 19:56:58,034 - INFO - Processed 119600000 reads so far
2011-05-19 19:57:09,344 - INFO - Processed 119700000 reads so far
2011-05-19 19:57:09,837 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:82990111-103010111
2011-05-19 19:57:22,039 - INFO - Processed 119800000 reads so far
2011-05-19 19:57:30,026 - INFO - Processed 119900000 reads so far
2011-05-19 19:57:39,216 - INFO - Processed 120000000 reads so far
2011-05-19 19:57:48,639 - INFO - Processed 120100000 reads so far
2011-05-19 19:57:59,801 - INFO - Processed 120200000 reads so far
2011-05-19 19:58:11,302 - INFO - Processed 120300000 reads so far
2011-05-19 19:58:20,333 - INFO - Processed 120400000 reads so far
2011-05-19 19:58:33,579 - INFO - Processed 120500000 reads so far
2011-05-19 19:58:44,596 - INFO - Processed 120600000 reads so far
2011-05-19 19:58:56,412 - INFO - Processed 120700000 reads so far
2011-05-19 19:59:08,615 - INFO - Processed 120800000 reads so far
2011-05-19 19:59:12,369 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:102990112-123010112
2011-05-19 19:59:17,931 - INFO - Processed 120900000 reads so far
2011-05-19 19:59:24,398 - INFO - Processed 121000000 reads so far
2011-05-19 19:59:30,869 - INFO - Processed 121100000 reads so far
2011-05-19 19:59:44,379 - INFO - Processed 121200000 reads so far
2011-05-19 19:59:54,218 - INFO - Processed 121300000 reads so far
2011-05-19 20:00:04,091 - INFO - Processed 121400000 reads so far
2011-05-19 20:00:13,233 - INFO - Processed 121500000 reads so far
2011-05-19 20:00:22,971 - INFO - Processed 121600000 reads so far
2011-05-19 20:00:34,138 - INFO - Processed 121700000 reads so far
2011-05-19 20:00:41,948 - INFO - Processed 121800000 reads so far
2011-05-19 20:00:51,379 - INFO - Processed 121900000 reads so far
2011-05-19 20:00:58,279 - INFO - Processed 122000000 reads so far
2011-05-19 20:01:06,678 - INFO - Processed 122100000 reads so far
2011-05-19 20:01:15,950 - INFO - Processed 122200000 reads so far
2011-05-19 20:01:25,429 - INFO - Processed 122300000 reads so far
2011-05-19 20:01:37,849 - INFO - Processed 122400000 reads so far
2011-05-19 20:01:52,792 - INFO - Processed 122500000 reads so far
2011-05-19 20:02:05,896 - INFO - Processed 122600000 reads so far
2011-05-19 20:02:17,150 - INFO - Processed 122700000 reads so far
2011-05-19 20:02:28,509 - INFO - Processed 122800000 reads so far
2011-05-19 20:02:37,507 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:122990118-143010118
2011-05-19 20:02:42,331 - INFO - Processed 122900000 reads so far
2011-05-19 20:02:54,580 - INFO - Processed 123000000 reads so far
2011-05-19 20:03:05,204 - INFO - Processed 123100000 reads so far
2011-05-19 20:03:16,522 - INFO - Processed 123200000 reads so far
2011-05-19 20:03:28,391 - INFO - Processed 123300000 reads so far
2011-05-19 20:03:37,731 - INFO - Processed 123400000 reads so far
2011-05-19 20:03:50,192 - INFO - Processed 123500000 reads so far
2011-05-19 20:04:00,670 - INFO - Processed 123600000 reads so far
2011-05-19 20:04:08,687 - INFO - Processed 123700000 reads so far
2011-05-19 20:04:15,932 - INFO - Processed 123800000 reads so far
2011-05-19 20:04:28,887 - INFO - Processed 123900000 reads so far
2011-05-19 20:04:37,848 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:142990137-163010137
2011-05-19 20:04:39,039 - INFO - Processed 124000000 reads so far
2011-05-19 20:04:51,488 - INFO - Processed 124100000 reads so far
2011-05-19 20:05:01,470 - INFO - Processed 124200000 reads so far
2011-05-19 20:05:11,171 - INFO - Processed 124300000 reads so far
2011-05-19 20:05:16,512 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:2990035-23010035
2011-05-19 20:05:20,236 - INFO - Processed 124400000 reads so far
2011-05-19 20:05:32,879 - INFO - Processed 124500000 reads so far
2011-05-19 20:05:43,914 - INFO - Processed 124600000 reads so far
2011-05-19 20:05:57,027 - INFO - Processed 124700000 reads so far
2011-05-19 20:06:07,528 - INFO - Processed 124800000 reads so far
2011-05-19 20:06:19,001 - INFO - Processed 124900000 reads so far
2011-05-19 20:06:32,301 - INFO - Processed 125000000 reads so far
2011-05-19 20:06:43,596 - INFO - Processed 125100000 reads so far
2011-05-19 20:06:54,449 - INFO - Processed 125200000 reads so far
2011-05-19 20:07:02,321 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:22990159-43010159
2011-05-19 20:07:04,100 - INFO - Processed 125300000 reads so far
2011-05-19 20:07:12,552 - INFO - Processed 125400000 reads so far
2011-05-19 20:07:22,715 - INFO - Processed 125500000 reads so far
2011-05-19 20:07:34,392 - INFO - Processed 125600000 reads so far
2011-05-19 20:07:45,326 - INFO - Processed 125700000 reads so far
2011-05-19 20:07:56,692 - INFO - Processed 125800000 reads so far
2011-05-19 20:08:06,881 - INFO - Processed 125900000 reads so far
2011-05-19 20:08:16,171 - INFO - Processed 126000000 reads so far
2011-05-19 20:08:24,273 - INFO - Processed 126100000 reads so far
2011-05-19 20:08:29,910 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:46346334-66366334
2011-05-19 20:08:32,654 - INFO - Processed 126200000 reads so far
2011-05-19 20:08:42,288 - INFO - Processed 126300000 reads so far
2011-05-19 20:08:52,941 - INFO - Processed 126400000 reads so far
2011-05-19 20:09:03,244 - INFO - Processed 126500000 reads so far
2011-05-19 20:09:13,586 - INFO - Processed 126600000 reads so far
2011-05-19 20:09:23,745 - INFO - Processed 126700000 reads so far
2011-05-19 20:09:35,295 - INFO - Processed 126800000 reads so far
2011-05-19 20:09:46,574 - INFO - Processed 126900000 reads so far
2011-05-19 20:09:56,599 - INFO - Processed 127000000 reads so far
2011-05-19 20:10:10,000 - INFO - Processed 127100000 reads so far
2011-05-19 20:10:22,679 - INFO - Processed 127200000 reads so far
2011-05-19 20:10:32,910 - INFO - Processed 127300000 reads so far
2011-05-19 20:10:34,439 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:66346341-86366341
2011-05-19 20:10:44,901 - INFO - Processed 127400000 reads so far
2011-05-19 20:10:59,949 - INFO - Processed 127500000 reads so far
2011-05-19 20:11:10,866 - INFO - Processed 127600000 reads so far
2011-05-19 20:11:21,890 - INFO - Processed 127700000 reads so far
2011-05-19 20:11:33,145 - INFO - Processed 127800000 reads so far
2011-05-19 20:11:45,532 - INFO - Processed 127900000 reads so far
2011-05-19 20:12:00,113 - INFO - Processed 128000000 reads so far
2011-05-19 20:12:11,051 - INFO - Processed 128100000 reads so far
2011-05-19 20:12:22,014 - INFO - Processed 128200000 reads so far
2011-05-19 20:12:33,178 - INFO - Processed 128300000 reads so far
2011-05-19 20:12:45,043 - INFO - Processed 128400000 reads so far
2011-05-19 20:12:51,617 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:86346363-106366363
2011-05-19 20:12:55,902 - INFO - Processed 128500000 reads so far
2011-05-19 20:13:10,717 - INFO - Processed 128600000 reads so far
2011-05-19 20:13:21,874 - INFO - Processed 128700000 reads so far
2011-05-19 20:13:33,254 - INFO - Processed 128800000 reads so far
2011-05-19 20:13:45,981 - INFO - Processed 128900000 reads so far
2011-05-19 20:13:56,913 - INFO - Processed 129000000 reads so far
2011-05-19 20:14:08,126 - INFO - Processed 129100000 reads so far
2011-05-19 20:14:19,909 - INFO - Processed 129200000 reads so far
2011-05-19 20:14:31,399 - INFO - Processed 129300000 reads so far
2011-05-19 20:14:41,716 - INFO - Processed 129400000 reads so far
2011-05-19 20:14:50,194 - INFO - Processed 129500000 reads so far
2011-05-19 20:14:56,113 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:106346364-126366364
2011-05-19 20:14:58,445 - INFO - Processed 129600000 reads so far
2011-05-19 20:15:07,746 - INFO - Processed 129700000 reads so far
2011-05-19 20:15:19,515 - INFO - Processed 129800000 reads so far
2011-05-19 20:15:28,178 - INFO - Processed 129900000 reads so far
2011-05-19 20:15:37,029 - INFO - Processed 130000000 reads so far
2011-05-19 20:15:45,300 - INFO - Processed 130100000 reads so far
2011-05-19 20:16:01,248 - INFO - Processed 130200000 reads so far
2011-05-19 20:16:09,576 - INFO - Processed 130300000 reads so far
2011-05-19 20:16:19,243 - INFO - Processed 130400000 reads so far
2011-05-19 20:16:34,017 - INFO - Processed 130500000 reads so far
2011-05-19 20:16:45,744 - INFO - Processed 130600000 reads so far
2011-05-19 20:16:56,313 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:126346404-146366404
2011-05-19 20:16:56,914 - INFO - Processed 130700000 reads so far
2011-05-19 20:17:09,659 - INFO - Processed 130800000 reads so far
2011-05-19 20:17:17,694 - INFO - Processed 130900000 reads so far
2011-05-19 20:17:27,640 - INFO - Processed 131000000 reads so far
2011-05-19 20:17:34,901 - INFO - Processed 131100000 reads so far
2011-05-19 20:17:42,496 - INFO - Processed 131200000 reads so far
2011-05-19 20:17:53,882 - INFO - Processed 131300000 reads so far
2011-05-19 20:18:02,104 - INFO - Processed 131400000 reads so far
2011-05-19 20:18:14,362 - INFO - Processed 131500000 reads so far
2011-05-19 20:18:24,001 - INFO - Processed 131600000 reads so far
2011-05-19 20:18:33,923 - INFO - Processed 131700000 reads so far
2011-05-19 20:18:42,241 - INFO - Processed 131800000 reads so far
2011-05-19 20:18:47,135 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:146346429-166366429
2011-05-19 20:18:50,275 - INFO - Processed 131900000 reads so far
2011-05-19 20:18:59,604 - INFO - Processed 132000000 reads so far
2011-05-19 20:19:06,566 - INFO - Processed 132100000 reads so far
2011-05-19 20:19:13,915 - INFO - Processed 132200000 reads so far
2011-05-19 20:19:14,264 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7_random:0-20010010
2011-05-19 20:19:15,047 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:2990025-23010025
2011-05-19 20:19:23,406 - INFO - Processed 132300000 reads so far
2011-05-19 20:19:31,396 - INFO - Processed 132400000 reads so far
2011-05-19 20:19:38,461 - INFO - Processed 132500000 reads so far
2011-05-19 20:19:45,924 - INFO - Processed 132600000 reads so far
2011-05-19 20:19:52,781 - INFO - Processed 132700000 reads so far
2011-05-19 20:20:01,399 - INFO - Processed 132800000 reads so far
2011-05-19 20:20:09,321 - INFO - Processed 132900000 reads so far
2011-05-19 20:20:17,184 - INFO - Processed 133000000 reads so far
2011-05-19 20:20:23,967 - INFO - Processed 133100000 reads so far
2011-05-19 20:20:34,072 - INFO - Processed 133200000 reads so far
2011-05-19 20:20:43,144 - INFO - Processed 133300000 reads so far
2011-05-19 20:20:49,107 - INFO - Processed 133400000 reads so far
2011-05-19 20:20:59,078 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:22990027-43010027
2011-05-19 20:21:00,122 - INFO - Processed 133500000 reads so far
2011-05-19 20:21:17,453 - INFO - Processed 133600000 reads so far
2011-05-19 20:21:28,061 - INFO - Processed 133700000 reads so far
2011-05-19 20:21:36,603 - INFO - Processed 133800000 reads so far
2011-05-19 20:21:49,937 - INFO - Processed 133900000 reads so far
2011-05-19 20:22:01,739 - INFO - Processed 134000000 reads so far
2011-05-19 20:22:12,107 - INFO - Processed 134100000 reads so far
2011-05-19 20:22:21,537 - INFO - Processed 134200000 reads so far
2011-05-19 20:22:32,210 - INFO - Processed 134300000 reads so far
2011-05-19 20:22:40,697 - INFO - Processed 134400000 reads so far
2011-05-19 20:22:49,151 - INFO - Processed 134500000 reads so far
2011-05-19 20:23:00,936 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:42990045-63010045
2011-05-19 20:23:02,011 - INFO - Processed 134600000 reads so far
2011-05-19 20:23:13,234 - INFO - Processed 134700000 reads so far
2011-05-19 20:23:23,975 - INFO - Processed 134800000 reads so far
2011-05-19 20:23:35,075 - INFO - Processed 134900000 reads so far
2011-05-19 20:23:45,600 - INFO - Processed 135000000 reads so far
2011-05-19 20:23:55,777 - INFO - Processed 135100000 reads so far
2011-05-19 20:24:10,818 - INFO - Processed 135200000 reads so far
2011-05-19 20:24:19,386 - INFO - Processed 135300000 reads so far
2011-05-19 20:24:30,502 - INFO - Processed 135400000 reads so far
2011-05-19 20:24:44,496 - INFO - Processed 135500000 reads so far
2011-05-19 20:24:54,802 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:62990046-83010046
2011-05-19 20:24:58,958 - INFO - Processed 135600000 reads so far
2011-05-19 20:25:10,124 - INFO - Processed 135700000 reads so far
2011-05-19 20:25:25,249 - INFO - Processed 135800000 reads so far
2011-05-19 20:25:36,402 - INFO - Processed 135900000 reads so far
2011-05-19 20:25:48,195 - INFO - Processed 136000000 reads so far
2011-05-19 20:25:59,980 - INFO - Processed 136100000 reads so far
2011-05-19 20:26:13,718 - INFO - Processed 136200000 reads so far
2011-05-19 20:26:25,187 - INFO - Processed 136300000 reads so far
2011-05-19 20:26:39,181 - INFO - Processed 136400000 reads so far
2011-05-19 20:26:53,367 - INFO - Processed 136500000 reads so far
2011-05-19 20:27:04,739 - INFO - Processed 136600000 reads so far
2011-05-19 20:27:19,267 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:82990047-103010047
2011-05-19 20:27:19,844 - INFO - Processed 136700000 reads so far
2011-05-19 20:27:30,680 - INFO - Processed 136800000 reads so far
2011-05-19 20:27:43,087 - INFO - Processed 136900000 reads so far
2011-05-19 20:28:03,426 - INFO - Processed 137000000 reads so far
2011-05-19 20:28:14,685 - INFO - Processed 137100000 reads so far
2011-05-19 20:28:27,669 - INFO - Processed 137200000 reads so far
2011-05-19 20:28:40,625 - INFO - Processed 137300000 reads so far
2011-05-19 20:28:53,525 - INFO - Processed 137400000 reads so far
2011-05-19 20:29:05,485 - INFO - Processed 137500000 reads so far
2011-05-19 20:29:17,022 - INFO - Processed 137600000 reads so far
2011-05-19 20:29:28,317 - INFO - Processed 137700000 reads so far
2011-05-19 20:29:39,537 - INFO - Processed 137800000 reads so far
2011-05-19 20:29:40,252 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:102990057-123010057
2011-05-19 20:29:50,529 - INFO - Processed 137900000 reads so far
2011-05-19 20:30:01,724 - INFO - Processed 138000000 reads so far
2011-05-19 20:30:13,055 - INFO - Processed 138100000 reads so far
2011-05-19 20:30:22,994 - INFO - Processed 138200000 reads so far
2011-05-19 20:30:33,334 - INFO - Processed 138300000 reads so far
2011-05-19 20:30:43,847 - INFO - Processed 138400000 reads so far
2011-05-19 20:30:52,997 - INFO - Processed 138500000 reads so far
2011-05-19 20:31:02,567 - INFO - Processed 138600000 reads so far
2011-05-19 20:31:13,592 - INFO - Processed 138700000 reads so far
2011-05-19 20:31:23,955 - INFO - Processed 138800000 reads so far
2011-05-19 20:31:34,634 - INFO - Processed 138900000 reads so far
2011-05-19 20:31:37,457 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:122990101-143010101
2011-05-19 20:31:45,512 - INFO - Processed 139000000 reads so far
2011-05-19 20:31:59,696 - INFO - Processed 139100000 reads so far
2011-05-19 20:32:10,053 - INFO - Processed 139200000 reads so far
2011-05-19 20:32:18,268 - INFO - Processed 139300000 reads so far
2011-05-19 20:32:29,526 - INFO - Processed 139400000 reads so far
2011-05-19 20:32:32,355 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8_random:0-20010006
2011-05-19 20:32:38,086 - INFO - Processed 139500000 reads so far
2011-05-19 20:32:45,424 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:2989997-23009997
2011-05-19 20:32:46,123 - INFO - Processed 139600000 reads so far
2011-05-19 20:32:53,626 - INFO - Processed 139700000 reads so far
2011-05-19 20:33:02,091 - INFO - Processed 139800000 reads so far
2011-05-19 20:33:13,063 - INFO - Processed 139900000 reads so far
2011-05-19 20:33:21,302 - INFO - Processed 140000000 reads so far
2011-05-19 20:33:30,744 - INFO - Processed 140100000 reads so far
2011-05-19 20:33:37,641 - INFO - Processed 140200000 reads so far
2011-05-19 20:33:44,990 - INFO - Processed 140300000 reads so far
2011-05-19 20:33:55,291 - INFO - Processed 140400000 reads so far
2011-05-19 20:34:03,067 - INFO - Processed 140500000 reads so far
2011-05-19 20:34:10,392 - INFO - Processed 140600000 reads so far
2011-05-19 20:34:18,711 - INFO - Processed 140700000 reads so far
2011-05-19 20:34:27,409 - INFO - Processed 140800000 reads so far
2011-05-19 20:34:36,248 - INFO - Processed 140900000 reads so far
2011-05-19 20:34:43,917 - INFO - Processed 141000000 reads so far
2011-05-19 20:34:53,622 - INFO - Processed 141100000 reads so far
2011-05-19 20:35:00,744 - INFO - Processed 141200000 reads so far
2011-05-19 20:35:08,335 - INFO - Processed 141300000 reads so far
2011-05-19 20:35:18,375 - INFO - Processed 141400000 reads so far
2011-05-19 20:35:25,851 - INFO - Processed 141500000 reads so far
2011-05-19 20:35:34,344 - INFO - Processed 141600000 reads so far
2011-05-19 20:35:42,802 - INFO - Processed 141700000 reads so far
2011-05-19 20:35:50,976 - INFO - Processed 141800000 reads so far
2011-05-19 20:35:58,934 - INFO - Processed 141900000 reads so far
2011-05-19 20:36:05,927 - INFO - Processed 142000000 reads so far
2011-05-19 20:36:13,277 - INFO - Processed 142100000 reads so far
2011-05-19 20:36:20,306 - INFO - Processed 142200000 reads so far
2011-05-19 20:36:28,478 - INFO - Processed 142300000 reads so far
2011-05-19 20:36:37,208 - INFO - Processed 142400000 reads so far
2011-05-19 20:36:47,007 - INFO - Processed 142500000 reads so far
2011-05-19 20:36:56,479 - INFO - Processed 142600000 reads so far
2011-05-19 20:37:05,836 - INFO - Processed 142700000 reads so far
2011-05-19 20:37:15,388 - INFO - Processed 142800000 reads so far
2011-05-19 20:37:25,044 - INFO - Processed 142900000 reads so far
2011-05-19 20:37:34,863 - INFO - Processed 143000000 reads so far
2011-05-19 20:37:44,314 - INFO - Processed 143100000 reads so far
2011-05-19 20:37:53,697 - INFO - Processed 143200000 reads so far
2011-05-19 20:38:03,122 - INFO - Processed 143300000 reads so far
2011-05-19 20:38:13,248 - INFO - Processed 143400000 reads so far
2011-05-19 20:38:23,106 - INFO - Processed 143500000 reads so far
2011-05-19 20:38:34,280 - INFO - Processed 143600000 reads so far
2011-05-19 20:38:43,909 - INFO - Processed 143700000 reads so far
2011-05-19 20:38:53,347 - INFO - Processed 143800000 reads so far
2011-05-19 20:39:02,470 - INFO - Processed 143900000 reads so far
2011-05-19 20:39:13,086 - INFO - Processed 144000000 reads so far
2011-05-19 20:39:22,317 - INFO - Processed 144100000 reads so far
2011-05-19 20:39:32,252 - INFO - Processed 144200000 reads so far
2011-05-19 20:39:43,279 - INFO - Processed 144300000 reads so far
2011-05-19 20:39:52,870 - INFO - Processed 144400000 reads so far
2011-05-19 20:40:02,454 - INFO - Processed 144500000 reads so far
2011-05-19 20:40:11,851 - INFO - Processed 144600000 reads so far
2011-05-19 20:40:21,644 - INFO - Processed 144700000 reads so far
2011-05-19 20:40:31,224 - INFO - Processed 144800000 reads so far
2011-05-19 20:40:39,950 - INFO - Processed 144900000 reads so far
2011-05-19 20:40:49,164 - INFO - Processed 145000000 reads so far
2011-05-19 20:41:01,436 - INFO - Processed 145100000 reads so far
2011-05-19 20:41:10,963 - INFO - Processed 145200000 reads so far
2011-05-19 20:41:20,168 - INFO - Processed 145300000 reads so far
2011-05-19 20:41:29,602 - INFO - Processed 145400000 reads so far
2011-05-19 20:41:38,705 - INFO - Processed 145500000 reads so far
2011-05-19 20:41:48,682 - INFO - Processed 145600000 reads so far
2011-05-19 20:41:57,994 - INFO - Processed 145700000 reads so far
2011-05-19 20:42:06,995 - INFO - Processed 145800000 reads so far
2011-05-19 20:42:17,360 - INFO - Processed 145900000 reads so far
2011-05-19 20:42:27,046 - INFO - Processed 146000000 reads so far
2011-05-19 20:42:37,352 - INFO - Processed 146100000 reads so far
2011-05-19 20:42:47,552 - INFO - Processed 146200000 reads so far
2011-05-19 20:42:57,315 - INFO - Processed 146300000 reads so far
2011-05-19 20:43:06,067 - INFO - Processed 146400000 reads so far
2011-05-19 20:43:18,209 - INFO - Processed 146500000 reads so far
2011-05-19 20:43:28,429 - INFO - Processed 146600000 reads so far
2011-05-19 20:43:40,386 - INFO - Processed 146700000 reads so far
2011-05-19 20:43:54,785 - INFO - Processed 146800000 reads so far
2011-05-19 20:44:05,103 - INFO - Processed 146900000 reads so far
2011-05-19 20:44:15,187 - INFO - Processed 147000000 reads so far
2011-05-19 20:44:27,452 - INFO - Processed 147100000 reads so far
2011-05-19 20:44:38,715 - INFO - Processed 147200000 reads so far
2011-05-19 20:44:50,772 - INFO - Processed 147300000 reads so far
2011-05-19 20:45:00,045 - INFO - Processed 147400000 reads so far
2011-05-19 20:45:10,927 - INFO - Processed 147500000 reads so far
2011-05-19 20:45:21,708 - INFO - Processed 147600000 reads so far
2011-05-19 20:45:32,862 - INFO - Processed 147700000 reads so far
2011-05-19 20:45:37,991 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:22990007-43010007
2011-05-19 20:45:45,126 - INFO - Processed 147800000 reads so far
2011-05-19 20:45:55,691 - INFO - Processed 147900000 reads so far
2011-05-19 20:46:06,118 - INFO - Processed 148000000 reads so far
2011-05-19 20:46:14,619 - INFO - Processed 148100000 reads so far
2011-05-19 20:46:24,327 - INFO - Processed 148200000 reads so far
2011-05-19 20:46:35,405 - INFO - Processed 148300000 reads so far
2011-05-19 20:46:45,937 - INFO - Processed 148400000 reads so far
2011-05-19 20:46:58,522 - INFO - Processed 148500000 reads so far
2011-05-19 20:47:07,284 - INFO - Processed 148600000 reads so far
2011-05-19 20:47:18,217 - INFO - Processed 148700000 reads so far
2011-05-19 20:47:26,111 - INFO - Processed 148800000 reads so far
2011-05-19 20:47:38,049 - INFO - Processed 148900000 reads so far
2011-05-19 20:47:47,532 - INFO - Processed 149000000 reads so far
2011-05-19 20:47:50,644 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:42990014-63010014
2011-05-19 20:47:58,548 - INFO - Processed 149100000 reads so far
2011-05-19 20:48:09,506 - INFO - Processed 149200000 reads so far
2011-05-19 20:48:21,325 - INFO - Processed 149300000 reads so far
2011-05-19 20:48:33,397 - INFO - Processed 149400000 reads so far
2011-05-19 20:49:00,248 - INFO - Processed 149500000 reads so far
2011-05-19 20:49:08,986 - INFO - Processed 149600000 reads so far
2011-05-19 20:49:21,575 - INFO - Processed 149700000 reads so far
2011-05-19 20:49:33,111 - INFO - Processed 149800000 reads so far
2011-05-19 20:49:42,558 - INFO - Processed 149900000 reads so far
2011-05-19 20:49:52,208 - INFO - Processed 150000000 reads so far
2011-05-19 20:50:01,003 - INFO - Processed 150100000 reads so far
2011-05-19 20:50:06,642 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:62990015-83010015
2011-05-19 20:50:10,536 - INFO - Processed 150200000 reads so far
2011-05-19 20:50:19,635 - INFO - Processed 150300000 reads so far
2011-05-19 20:50:30,101 - INFO - Processed 150400000 reads so far
2011-05-19 20:50:40,656 - INFO - Processed 150500000 reads so far
2011-05-19 20:50:49,978 - INFO - Processed 150600000 reads so far
2011-05-19 20:50:58,055 - INFO - Processed 150700000 reads so far
2011-05-19 20:51:06,853 - INFO - Processed 150800000 reads so far
2011-05-19 20:51:16,076 - INFO - Processed 150900000 reads so far
2011-05-19 20:51:26,794 - INFO - Processed 151000000 reads so far
2011-05-19 20:51:38,373 - INFO - Processed 151100000 reads so far
2011-05-19 20:51:48,092 - INFO - Processed 151200000 reads so far
2011-05-19 20:51:55,346 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:82990040-103010040
2011-05-19 20:51:57,249 - INFO - Processed 151300000 reads so far
2011-05-19 20:52:07,144 - INFO - Processed 151400000 reads so far
2011-05-19 20:52:17,340 - INFO - Processed 151500000 reads so far
2011-05-19 20:52:24,601 - INFO - Processed 151600000 reads so far
2011-05-19 20:52:34,168 - INFO - Processed 151700000 reads so far
2011-05-19 20:52:43,295 - INFO - Processed 151800000 reads so far
2011-05-19 20:52:52,806 - INFO - Processed 151900000 reads so far
2011-05-19 20:53:00,460 - INFO - Processed 152000000 reads so far
2011-05-19 20:53:08,316 - INFO - Processed 152100000 reads so far
2011-05-19 20:53:16,550 - INFO - Processed 152200000 reads so far
2011-05-19 20:53:26,835 - INFO - Processed 152300000 reads so far
2011-05-19 20:53:36,153 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:102990041-123010041
2011-05-19 20:53:36,440 - INFO - Processed 152400000 reads so far
2011-05-19 20:53:48,068 - INFO - Processed 152500000 reads so far
2011-05-19 20:54:00,836 - INFO - Processed 152600000 reads so far
2011-05-19 20:54:11,869 - INFO - Processed 152700000 reads so far
2011-05-19 20:54:21,626 - INFO - Processed 152800000 reads so far
2011-05-19 20:54:29,421 - INFO - Processed 152900000 reads so far
2011-05-19 20:54:39,796 - INFO - Processed 153000000 reads so far
2011-05-19 20:54:48,266 - INFO - Processed 153100000 reads so far
2011-05-19 20:54:55,956 - INFO - Processed 153200000 reads so far
2011-05-19 20:55:02,849 - INFO - Processed 153300000 reads so far
2011-05-19 20:55:10,585 - INFO - Processed 153400000 reads so far
2011-05-19 20:55:18,064 - INFO - Processed 153500000 reads so far
2011-05-19 20:55:21,226 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:122990052-143010052
2011-05-19 20:55:27,281 - INFO - Processed 153600000 reads so far
2011-05-19 20:55:27,832 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9_random:0-20010020
2011-05-19 20:55:30,760 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrM:0-20010000
2011-05-19 20:55:33,664 - INFO - Processed 153700000 reads so far
2011-05-19 20:55:35,683 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrUn_random:0-20010002
2011-05-19 20:55:42,035 - INFO - Processed 153800000 reads so far
2011-05-19 20:55:50,309 - INFO - Processed 153900000 reads so far
2011-05-19 20:55:57,811 - INFO - Processed 154000000 reads so far
2011-05-19 20:56:05,926 - INFO - Processed 154100000 reads so far
2011-05-19 20:56:10,386 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:2990014-23010014
2011-05-19 20:56:13,737 - INFO - Processed 154200000 reads so far
2011-05-19 20:56:21,790 - INFO - Processed 154300000 reads so far
2011-05-19 20:56:31,187 - INFO - Processed 154400000 reads so far
2011-05-19 20:56:40,965 - INFO - Processed 154500000 reads so far
2011-05-19 20:56:52,937 - INFO - Processed 154600000 reads so far
2011-05-19 20:57:02,459 - INFO - Processed 154700000 reads so far
2011-05-19 20:57:12,925 - INFO - Processed 154800000 reads so far
2011-05-19 20:57:13,665 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:22990039-43010039
2011-05-19 20:57:25,005 - INFO - Processed 154900000 reads so far
2011-05-19 20:57:36,696 - INFO - Processed 155000000 reads so far
2011-05-19 20:57:47,623 - INFO - Processed 155100000 reads so far
2011-05-19 20:57:58,352 - INFO - Processed 155200000 reads so far
2011-05-19 20:58:10,420 - INFO - Processed 155300000 reads so far
2011-05-19 20:58:22,186 - INFO - Processed 155400000 reads so far
2011-05-19 20:58:28,226 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:42990327-63010327
2011-05-19 20:58:34,179 - INFO - Processed 155500000 reads so far
2011-05-19 20:58:46,810 - INFO - Processed 155600000 reads so far
2011-05-19 20:58:58,816 - INFO - Processed 155700000 reads so far
2011-05-19 20:59:11,640 - INFO - Processed 155800000 reads so far
2011-05-19 20:59:24,986 - INFO - Processed 155900000 reads so far
2011-05-19 20:59:38,040 - INFO - Processed 156000000 reads so far
2011-05-19 20:59:42,912 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:62990371-83010371
2011-05-19 20:59:49,917 - INFO - Processed 156100000 reads so far
2011-05-19 21:00:01,569 - INFO - Processed 156200000 reads so far
2011-05-19 21:00:16,776 - INFO - Processed 156300000 reads so far
2011-05-19 21:00:28,244 - INFO - Processed 156400000 reads so far
2011-05-19 21:00:42,391 - INFO - Processed 156500000 reads so far
2011-05-19 21:00:51,929 - INFO - Processed 156600000 reads so far
2011-05-19 21:00:53,199 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:82990398-103010398
2011-05-19 21:01:03,305 - INFO - Processed 156700000 reads so far
2011-05-19 21:01:16,774 - INFO - Processed 156800000 reads so far
2011-05-19 21:01:29,759 - INFO - Processed 156900000 reads so far
2011-05-19 21:01:44,504 - INFO - Processed 157000000 reads so far
2011-05-19 21:01:58,336 - INFO - Processed 157100000 reads so far
2011-05-19 21:02:08,436 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:102990406-123010406
2011-05-19 21:02:09,581 - INFO - Processed 157200000 reads so far
2011-05-19 21:02:21,481 - INFO - Processed 157300000 reads so far
2011-05-19 21:02:35,709 - INFO - Processed 157400000 reads so far
2011-05-19 21:02:49,107 - INFO - Processed 157500000 reads so far
2011-05-19 21:03:01,698 - INFO - Processed 157600000 reads so far
2011-05-19 21:03:14,610 - INFO - Processed 157700000 reads so far
2011-05-19 21:03:25,020 - INFO - Processed 157800000 reads so far
2011-05-19 21:03:32,384 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:122990407-143010407
2011-05-19 21:03:36,350 - INFO - Processed 157900000 reads so far
2011-05-19 21:03:49,190 - INFO - Processed 158000000 reads so far
2011-05-19 21:04:01,052 - INFO - Processed 158100000 reads so far
2011-05-19 21:04:13,500 - INFO - Processed 158200000 reads so far
2011-05-19 21:04:24,351 - INFO - Processed 158300000 reads so far
2011-05-19 21:04:35,966 - INFO - Processed 158400000 reads so far
2011-05-19 21:04:45,939 - INFO - Processed 158500000 reads so far
2011-05-19 21:04:46,066 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:142990424-163010424
2011-05-19 21:04:55,659 - INFO - Processed 158600000 reads so far
2011-05-19 21:05:05,469 - INFO - Processed 158700000 reads so far
2011-05-19 21:05:15,796 - INFO - Processed 158800000 reads so far
2011-05-19 21:05:24,573 - INFO - Processed 158900000 reads so far
2011-05-19 21:05:34,052 - INFO - Processed 159000000 reads so far
2011-05-19 21:05:39,384 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:162990472-183010472
2011-05-19 21:05:43,234 - INFO - Processed 159100000 reads so far
2011-05-19 21:05:51,474 - INFO - Processed 159200000 reads so far
2011-05-19 21:05:54,131 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX_random:0-20010085
2011-05-19 21:05:57,492 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY:0-20010021
2011-05-19 21:06:00,758 - INFO - Processed 159300000 reads so far
2011-05-19 21:06:06,697 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:0-20010368
2011-05-19 21:06:10,242 - INFO - Processed 159400000 reads so far
2011-05-19 21:06:21,003 - INFO - Processed 159500000 reads so far
2011-05-19 21:06:29,454 - INFO - Processed 159600000 reads so far
2011-05-19 21:06:38,946 - INFO - Processed 159700000 reads so far
2011-05-19 21:06:49,183 - INFO - Processed 159800000 reads so far
2011-05-19 21:06:57,746 - INFO - Processed 159900000 reads so far
2011-05-19 21:07:05,414 - INFO - Processed 160000000 reads so far
2011-05-19 21:07:13,983 - INFO - Processed 160100000 reads so far
2011-05-19 21:07:23,176 - INFO - Processed 160200000 reads so far
2011-05-19 21:07:25,070 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:19990561-40010561
2011-05-19 21:07:32,770 - INFO - Processed 160300000 reads so far
2011-05-19 21:07:42,415 - INFO - Processed 160400000 reads so far
2011-05-19 21:07:51,897 - INFO - Processed 160500000 reads so far
2011-05-19 21:08:01,965 - INFO - Processed 160600000 reads so far
2011-05-19 21:08:08,284 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:39990570-60010570
2011-05-19 21:08:09,549 - INFO - Processed 160700000 reads so far
2011-05-19 21:08:17,856 - INFO - Processed 160800000 reads so far
2011-05-19 21:08:26,462 - INFO - Processed 160900000 reads so far
2011-05-19 21:08:33,799 - INFO - Processed 161000000 reads so far
2011-05-19 21:08:43,426 - INFO - Processed 161100000 reads so far
2011-05-19 21:08:50,417 - INFO - Processed 161200000 reads so far
2011-05-19 21:08:58,307 - INFO - Processed 161300000 reads so far
2011-05-19 21:09:04,617 - INFO - Processed 161400000 reads so far
2011-05-19 21:09:09,030 - INFO - Processed 161500000 reads so far
2011-05-19 21:09:13,218 - INFO - Processed 161600000 reads so far
2011-05-19 21:09:17,079 - INFO - Processed 161700000 reads so far
2011-05-19 21:09:21,416 - INFO - Processed 161800000 reads so far
2011-05-19 21:09:25,804 - INFO - Processed 161900000 reads so far
2011-05-19 21:09:29,923 - INFO - Processed 162000000 reads so far
2011-05-19 21:09:33,657 - INFO - Processed 162100000 reads so far
2011-05-19 21:09:37,257 - INFO - Processed 162200000 reads so far
2011-05-19 21:09:44,480 - INFO - Processed 162300000 reads so far
2011-05-19 21:10:06,709 - INFO - Processed 162400000 reads so far
2011-05-19 21:10:13,013 - INFO - Processed 162500000 reads so far
2011-05-19 21:10:16,374 - INFO - Processed 162600000 reads so far
2011-05-19 21:10:27,664 - INFO - Processed 162700000 reads so far
2011-05-19 21:10:47,754 - INFO - Processed 162800000 reads so far
2011-05-19 21:10:55,577 - INFO - Processed 162900000 reads so far
2011-05-19 21:11:03,273 - INFO - Processed 163000000 reads so far
2011-05-19 21:11:13,851 - INFO - Processed 163100000 reads so far
2011-05-19 21:11:17,982 - INFO - Processed 163200000 reads so far
2011-05-19 21:11:22,134 - INFO - Processed 163300000 reads so far
2011-05-19 21:11:26,269 - INFO - Processed 163400000 reads so far
2011-05-19 21:11:30,772 - INFO - Processed 163500000 reads so far
2011-05-19 21:11:34,930 - INFO - Processed 163600000 reads so far
2011-05-19 21:11:40,805 - INFO - Processed 163700000 reads so far
2011-05-19 21:11:46,367 - INFO - Finished loading data. Outputting QC metrics
2011-05-19 21:12:08,176 - INFO - Finished outputting QC metrics
2011-05-19 21:12:08,299 - INFO - Finished generating QC metrics