2011-05-19 20:49:39,291 - INFO - Generating QC metrics for BAM File ['WTCHG_13230.bam']
2011-05-19 20:49:39,292 - INFO - Output will go to WTCHG_13230.qc.txt.tmp
2011-05-19 20:49:39,292 - INFO - Reading GC Map from file /data/Genomes/gcMap/Mouse37.gcMap.gz
2011-05-19 20:52:26,540 - INFO - Finished reading GC Map
2011-05-19 20:52:26,540 - INFO - Reading CDS from exon definition file /data/Genomes/annotation/Mouse37.refGene.txt.gz
2011-05-19 20:52:29,360 - INFO - Read 382138 exons (33804740 nucleotides) for 32 chromosomes
2011-05-19 20:52:29,361 - INFO - Computing coverage cut-off
2011-05-19 20:52:29,361 - INFO - Retrieving BAM file coverage info from samtools pileup
2011-05-19 20:52:34,263 - INFO - Processed 1000000 pile-up sites
2011-05-19 20:52:39,757 - INFO - Processed 2000000 pile-up sites
2011-05-19 20:52:44,734 - INFO - Processed 3000000 pile-up sites
2011-05-19 20:52:50,818 - INFO - Processed 4000000 pile-up sites
2011-05-19 20:52:55,846 - INFO - Processed 5000000 pile-up sites
2011-05-19 20:53:00,816 - INFO - Processed 6000000 pile-up sites
2011-05-19 20:53:05,339 - INFO - Processed 7000000 pile-up sites
2011-05-19 20:53:10,356 - INFO - Processed 8000000 pile-up sites
2011-05-19 20:53:14,944 - INFO - Processed 9000000 pile-up sites
2011-05-19 20:53:19,011 - INFO - Processed 10000000 pile-up sites
2011-05-19 20:53:24,381 - INFO - Processed 11000000 pile-up sites
2011-05-19 20:53:26,768 - INFO - Processed 12000000 pile-up sites
2011-05-19 20:53:32,015 - INFO - Processed 13000000 pile-up sites
2011-05-19 20:53:36,578 - INFO - Processed 14000000 pile-up sites
2011-05-19 20:53:42,096 - INFO - Processed 15000000 pile-up sites
2011-05-19 20:53:46,823 - INFO - Processed 16000000 pile-up sites
2011-05-19 20:53:51,479 - INFO - Processed 17000000 pile-up sites
2011-05-19 20:53:57,373 - INFO - Processed 18000000 pile-up sites
2011-05-19 20:54:02,173 - INFO - Processed 19000000 pile-up sites
2011-05-19 20:54:06,962 - INFO - Processed 20000000 pile-up sites
2011-05-19 20:54:11,550 - INFO - Processed 21000000 pile-up sites
2011-05-19 20:54:16,297 - INFO - Processed 22000000 pile-up sites
2011-05-19 20:54:20,966 - INFO - Processed 23000000 pile-up sites
2011-05-19 20:54:25,653 - INFO - Processed 24000000 pile-up sites
2011-05-19 20:54:31,341 - INFO - Processed 25000000 pile-up sites
2011-05-19 20:54:35,913 - INFO - Processed 26000000 pile-up sites
2011-05-19 20:54:40,688 - INFO - Processed 27000000 pile-up sites
2011-05-19 20:54:46,696 - INFO - Processed 28000000 pile-up sites
2011-05-19 20:54:49,936 - INFO - Processed 29000000 pile-up sites
2011-05-19 20:54:52,360 - INFO - Processed 30000000 pile-up sites
2011-05-19 20:54:54,788 - INFO - Processed 31000000 pile-up sites
2011-05-19 20:54:59,321 - INFO - Processed 32000000 pile-up sites
2011-05-19 20:55:04,049 - INFO - Processed 33000000 pile-up sites
2011-05-19 20:55:08,942 - INFO - Processed 34000000 pile-up sites
2011-05-19 20:55:13,649 - INFO - Processed 35000000 pile-up sites
2011-05-19 20:55:18,223 - INFO - Processed 36000000 pile-up sites
2011-05-19 20:55:22,998 - INFO - Processed 37000000 pile-up sites
2011-05-19 20:55:27,608 - INFO - Processed 38000000 pile-up sites
2011-05-19 20:55:31,273 - INFO - Finished processing pile-up on 38813029 sites (200000006 nucleotides)
2011-05-19 20:55:31,273 - INFO - Coverage cut-off value is 21
2011-05-19 20:55:31,273 - INFO - Loading data into QC data manager
2011-05-19 20:55:31,493 - INFO - Reading data from BAM file WTCHG_13230.bam. All reads in file will be read
2011-05-19 20:55:31,535 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:2990166-23010166
2011-05-19 20:55:44,586 - INFO - Processed 100000 reads so far
2011-05-19 20:55:56,624 - INFO - Processed 200000 reads so far
2011-05-19 20:56:08,386 - INFO - Processed 300000 reads so far
2011-05-19 20:56:18,723 - INFO - Processed 400000 reads so far
2011-05-19 20:56:30,579 - INFO - Processed 500000 reads so far
2011-05-19 20:56:42,703 - INFO - Processed 600000 reads so far
2011-05-19 20:56:54,006 - INFO - Processed 700000 reads so far
2011-05-19 20:57:06,015 - INFO - Processed 800000 reads so far
2011-05-19 20:57:17,939 - INFO - Processed 900000 reads so far
2011-05-19 20:57:29,103 - INFO - Processed 1000000 reads so far
2011-05-19 20:57:31,441 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:22990184-43010184
2011-05-19 20:57:40,899 - INFO - Processed 1100000 reads so far
2011-05-19 20:57:53,094 - INFO - Processed 1200000 reads so far
2011-05-19 20:58:04,137 - INFO - Processed 1300000 reads so far
2011-05-19 20:58:15,338 - INFO - Processed 1400000 reads so far
2011-05-19 20:58:26,646 - INFO - Processed 1500000 reads so far
2011-05-19 20:58:38,048 - INFO - Processed 1600000 reads so far
2011-05-19 20:58:45,349 - INFO - Processed 1700000 reads so far
2011-05-19 20:58:53,635 - INFO - Processed 1800000 reads so far
2011-05-19 20:59:03,883 - INFO - Processed 1900000 reads so far
2011-05-19 20:59:12,547 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:42990202-63010202
2011-05-19 20:59:12,695 - INFO - Processed 2000000 reads so far
2011-05-19 20:59:24,060 - INFO - Processed 2100000 reads so far
2011-05-19 20:59:35,880 - INFO - Processed 2200000 reads so far
2011-05-19 20:59:45,728 - INFO - Processed 2300000 reads so far
2011-05-19 20:59:56,435 - INFO - Processed 2400000 reads so far
2011-05-19 21:00:06,695 - INFO - Processed 2500000 reads so far
2011-05-19 21:00:19,771 - INFO - Processed 2600000 reads so far
2011-05-19 21:00:27,714 - INFO - Processed 2700000 reads so far
2011-05-19 21:00:39,968 - INFO - Processed 2800000 reads so far
2011-05-19 21:00:48,586 - INFO - Processed 2900000 reads so far
2011-05-19 21:00:55,580 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:62990245-83010245
2011-05-19 21:00:57,926 - INFO - Processed 3000000 reads so far
2011-05-19 21:01:06,328 - INFO - Processed 3100000 reads so far
2011-05-19 21:01:17,415 - INFO - Processed 3200000 reads so far
2011-05-19 21:01:27,789 - INFO - Processed 3300000 reads so far
2011-05-19 21:01:38,756 - INFO - Processed 3400000 reads so far
2011-05-19 21:01:49,030 - INFO - Processed 3500000 reads so far
2011-05-19 21:01:59,877 - INFO - Processed 3600000 reads so far
2011-05-19 21:02:11,593 - INFO - Processed 3700000 reads so far
2011-05-19 21:02:24,322 - INFO - Processed 3800000 reads so far
2011-05-19 21:02:39,916 - INFO - Processed 3900000 reads so far
2011-05-19 21:02:51,556 - INFO - Processed 4000000 reads so far
2011-05-19 21:02:51,598 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:82990259-103010259
2011-05-19 21:03:02,518 - INFO - Processed 4100000 reads so far
2011-05-19 21:03:13,825 - INFO - Processed 4200000 reads so far
2011-05-19 21:03:23,727 - INFO - Processed 4300000 reads so far
2011-05-19 21:03:36,126 - INFO - Processed 4400000 reads so far
2011-05-19 21:03:48,395 - INFO - Processed 4500000 reads so far
2011-05-19 21:03:58,622 - INFO - Processed 4600000 reads so far
2011-05-19 21:04:07,636 - INFO - Processed 4700000 reads so far
2011-05-19 21:04:18,119 - INFO - Processed 4800000 reads so far
2011-05-19 21:04:31,577 - INFO - Processed 4900000 reads so far
2011-05-19 21:04:43,763 - INFO - Processed 5000000 reads so far
2011-05-19 21:04:44,590 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:102990270-123010270
2011-05-19 21:04:54,895 - INFO - Processed 5100000 reads so far
2011-05-19 21:05:06,886 - INFO - Processed 5200000 reads so far
2011-05-19 21:05:19,763 - INFO - Processed 5300000 reads so far
2011-05-19 21:05:31,385 - INFO - Processed 5400000 reads so far
2011-05-19 21:05:43,278 - INFO - Processed 5500000 reads so far
2011-05-19 21:05:54,905 - INFO - Processed 5600000 reads so far
2011-05-19 21:06:05,321 - INFO - Processed 5700000 reads so far
2011-05-19 21:06:19,107 - INFO - Processed 5800000 reads so far
2011-05-19 21:06:29,962 - INFO - Processed 5900000 reads so far
2011-05-19 21:06:38,744 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:122990272-143010272
2011-05-19 21:06:41,022 - INFO - Processed 6000000 reads so far
2011-05-19 21:06:52,717 - INFO - Processed 6100000 reads so far
2011-05-19 21:07:03,893 - INFO - Processed 6200000 reads so far
2011-05-19 21:07:14,992 - INFO - Processed 6300000 reads so far
2011-05-19 21:07:18,886 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:2990003-23010003
2011-05-19 21:07:26,377 - INFO - Processed 6400000 reads so far
2011-05-19 21:07:36,554 - INFO - Processed 6500000 reads so far
2011-05-19 21:07:47,841 - INFO - Processed 6600000 reads so far
2011-05-19 21:07:58,697 - INFO - Processed 6700000 reads so far
2011-05-19 21:08:08,851 - INFO - Processed 6800000 reads so far
2011-05-19 21:08:19,299 - INFO - Processed 6900000 reads so far
2011-05-19 21:08:29,709 - INFO - Processed 7000000 reads so far
2011-05-19 21:08:40,215 - INFO - Processed 7100000 reads so far
2011-05-19 21:08:50,929 - INFO - Processed 7200000 reads so far
2011-05-19 21:09:02,566 - INFO - Processed 7300000 reads so far
2011-05-19 21:09:13,535 - INFO - Processed 7400000 reads so far
2011-05-19 21:09:25,660 - INFO - Processed 7500000 reads so far
2011-05-19 21:09:26,122 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:22990022-43010022
2011-05-19 21:09:38,055 - INFO - Processed 7600000 reads so far
2011-05-19 21:10:09,410 - INFO - Processed 7700000 reads so far
2011-05-19 21:10:32,123 - INFO - Processed 7800000 reads so far
2011-05-19 21:10:56,714 - INFO - Processed 7900000 reads so far
2011-05-19 21:11:14,736 - INFO - Processed 8000000 reads so far
2011-05-19 21:11:26,232 - INFO - Processed 8100000 reads so far
2011-05-19 21:11:40,452 - INFO - Processed 8200000 reads so far
2011-05-19 21:11:53,043 - INFO - Processed 8300000 reads so far
2011-05-19 21:12:04,537 - INFO - Processed 8400000 reads so far
2011-05-19 21:12:14,099 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:42990026-63010026
2011-05-19 21:12:15,586 - INFO - Processed 8500000 reads so far
2011-05-19 21:12:27,169 - INFO - Processed 8600000 reads so far
2011-05-19 21:12:37,905 - INFO - Processed 8700000 reads so far
2011-05-19 21:12:48,837 - INFO - Processed 8800000 reads so far
2011-05-19 21:13:04,117 - INFO - Processed 8900000 reads so far
2011-05-19 21:13:15,005 - INFO - Processed 9000000 reads so far
2011-05-19 21:13:27,603 - INFO - Processed 9100000 reads so far
2011-05-19 21:13:41,460 - INFO - Processed 9200000 reads so far
2011-05-19 21:13:53,930 - INFO - Processed 9300000 reads so far
2011-05-19 21:14:06,682 - INFO - Processed 9400000 reads so far
2011-05-19 21:14:21,158 - INFO - Processed 9500000 reads so far
2011-05-19 21:14:28,772 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:62990064-83010064
2011-05-19 21:14:34,154 - INFO - Processed 9600000 reads so far
2011-05-19 21:14:45,588 - INFO - Processed 9700000 reads so far
2011-05-19 21:14:57,748 - INFO - Processed 9800000 reads so far
2011-05-19 21:15:10,907 - INFO - Processed 9900000 reads so far
2011-05-19 21:15:23,870 - INFO - Processed 10000000 reads so far
2011-05-19 21:15:35,590 - INFO - Processed 10100000 reads so far
2011-05-19 21:15:51,009 - INFO - Processed 10200000 reads so far
2011-05-19 21:16:01,782 - INFO - Processed 10300000 reads so far
2011-05-19 21:16:14,367 - INFO - Processed 10400000 reads so far
2011-05-19 21:16:28,525 - INFO - Processed 10500000 reads so far
2011-05-19 21:16:42,746 - INFO - Processed 10600000 reads so far
2011-05-19 21:16:43,099 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:82990065-103010065
2011-05-19 21:16:52,530 - INFO - Processed 10700000 reads so far
2011-05-19 21:17:05,445 - INFO - Processed 10800000 reads so far
2011-05-19 21:17:15,891 - INFO - Processed 10900000 reads so far
2011-05-19 21:17:27,299 - INFO - Processed 11000000 reads so far
2011-05-19 21:17:40,077 - INFO - Processed 11100000 reads so far
2011-05-19 21:17:47,461 - INFO - Processed 11200000 reads so far
2011-05-19 21:17:54,903 - INFO - Processed 11300000 reads so far
2011-05-19 21:18:05,656 - INFO - Processed 11400000 reads so far
2011-05-19 21:18:13,614 - INFO - Processed 11500000 reads so far
2011-05-19 21:18:22,307 - INFO - Processed 11600000 reads so far
2011-05-19 21:18:23,454 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:102990112-123010112
2011-05-19 21:18:31,422 - INFO - Processed 11700000 reads so far
2011-05-19 21:18:40,372 - INFO - Processed 11800000 reads so far
2011-05-19 21:18:48,578 - INFO - Processed 11900000 reads so far
2011-05-19 21:18:56,049 - INFO - Processed 12000000 reads so far
2011-05-19 21:19:06,280 - INFO - Processed 12100000 reads so far
2011-05-19 21:19:17,351 - INFO - Processed 12200000 reads so far
2011-05-19 21:19:28,603 - INFO - Processed 12300000 reads so far
2011-05-19 21:19:40,341 - INFO - Processed 12400000 reads so far
2011-05-19 21:19:54,123 - INFO - Processed 12500000 reads so far
2011-05-19 21:20:05,966 - INFO - Processed 12600000 reads so far
2011-05-19 21:20:09,125 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:2990057-23010057
2011-05-19 21:20:16,063 - INFO - Processed 12700000 reads so far
2011-05-19 21:20:25,355 - INFO - Processed 12800000 reads so far
2011-05-19 21:20:40,465 - INFO - Processed 12900000 reads so far
2011-05-19 21:20:51,892 - INFO - Processed 13000000 reads so far
2011-05-19 21:21:03,550 - INFO - Processed 13100000 reads so far
2011-05-19 21:21:14,801 - INFO - Processed 13200000 reads so far
2011-05-19 21:21:27,704 - INFO - Processed 13300000 reads so far
2011-05-19 21:21:39,510 - INFO - Processed 13400000 reads so far
2011-05-19 21:21:48,694 - INFO - Processed 13500000 reads so far
2011-05-19 21:21:57,158 - INFO - Processed 13600000 reads so far
2011-05-19 21:22:08,844 - INFO - Processed 13700000 reads so far
2011-05-19 21:22:18,621 - INFO - Processed 13800000 reads so far
2011-05-19 21:22:29,661 - INFO - Processed 13900000 reads so far
2011-05-19 21:22:30,681 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:22990203-43010203
2011-05-19 21:22:42,088 - INFO - Processed 14000000 reads so far
2011-05-19 21:22:53,493 - INFO - Processed 14100000 reads so far
2011-05-19 21:23:04,127 - INFO - Processed 14200000 reads so far
2011-05-19 21:23:15,671 - INFO - Processed 14300000 reads so far
2011-05-19 21:23:28,703 - INFO - Processed 14400000 reads so far
2011-05-19 21:23:40,871 - INFO - Processed 14500000 reads so far
2011-05-19 21:23:52,348 - INFO - Processed 14600000 reads so far
2011-05-19 21:24:01,640 - INFO - Processed 14700000 reads so far
2011-05-19 21:24:13,590 - INFO - Processed 14800000 reads so far
2011-05-19 21:24:21,558 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:42990234-63010234
2011-05-19 21:24:25,380 - INFO - Processed 14900000 reads so far
2011-05-19 21:24:37,688 - INFO - Processed 15000000 reads so far
2011-05-19 21:24:49,186 - INFO - Processed 15100000 reads so far
2011-05-19 21:25:01,615 - INFO - Processed 15200000 reads so far
2011-05-19 21:25:14,473 - INFO - Processed 15300000 reads so far
2011-05-19 21:25:26,123 - INFO - Processed 15400000 reads so far
2011-05-19 21:25:39,059 - INFO - Processed 15500000 reads so far
2011-05-19 21:25:51,054 - INFO - Processed 15600000 reads so far
2011-05-19 21:26:04,377 - INFO - Processed 15700000 reads so far
2011-05-19 21:26:17,070 - INFO - Processed 15800000 reads so far
2011-05-19 21:26:18,110 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:62990243-83010243
2011-05-19 21:26:29,474 - INFO - Processed 15900000 reads so far
2011-05-19 21:26:42,622 - INFO - Processed 16000000 reads so far
2011-05-19 21:26:50,041 - INFO - Processed 16100000 reads so far
2011-05-19 21:27:01,895 - INFO - Processed 16200000 reads so far
2011-05-19 21:27:11,566 - INFO - Processed 16300000 reads so far
2011-05-19 21:27:21,699 - INFO - Processed 16400000 reads so far
2011-05-19 21:27:32,673 - INFO - Processed 16500000 reads so far
2011-05-19 21:27:43,042 - INFO - Processed 16600000 reads so far
2011-05-19 21:27:54,590 - INFO - Processed 16700000 reads so far
2011-05-19 21:28:05,731 - INFO - Processed 16800000 reads so far
2011-05-19 21:28:06,388 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:82990269-103010269
2011-05-19 21:28:17,233 - INFO - Processed 16900000 reads so far
2011-05-19 21:28:27,897 - INFO - Processed 17000000 reads so far
2011-05-19 21:28:39,549 - INFO - Processed 17100000 reads so far
2011-05-19 21:28:51,102 - INFO - Processed 17200000 reads so far
2011-05-19 21:29:04,090 - INFO - Processed 17300000 reads so far
2011-05-19 21:29:15,746 - INFO - Processed 17400000 reads so far
2011-05-19 21:29:31,286 - INFO - Processed 17500000 reads so far
2011-05-19 21:29:40,757 - INFO - Processed 17600000 reads so far
2011-05-19 21:29:53,266 - INFO - Processed 17700000 reads so far
2011-05-19 21:30:01,354 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:102990284-123010284
2011-05-19 21:30:03,334 - INFO - Processed 17800000 reads so far
2011-05-19 21:30:15,010 - INFO - Processed 17900000 reads so far
2011-05-19 21:30:26,371 - INFO - Processed 18000000 reads so far
2011-05-19 21:30:37,883 - INFO - Processed 18100000 reads so far
2011-05-19 21:30:48,883 - INFO - Processed 18200000 reads so far
2011-05-19 21:30:59,770 - INFO - Processed 18300000 reads so far
2011-05-19 21:31:13,641 - INFO - Processed 18400000 reads so far
2011-05-19 21:31:25,879 - INFO - Processed 18500000 reads so far
2011-05-19 21:31:38,274 - INFO - Processed 18600000 reads so far
2011-05-19 21:31:51,216 - INFO - Processed 18700000 reads so far
2011-05-19 21:32:00,346 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:2990027-23010027
2011-05-19 21:32:03,675 - INFO - Processed 18800000 reads so far
2011-05-19 21:32:14,101 - INFO - Processed 18900000 reads so far
2011-05-19 21:32:29,734 - INFO - Processed 19000000 reads so far
2011-05-19 21:32:41,239 - INFO - Processed 19100000 reads so far
2011-05-19 21:32:51,416 - INFO - Processed 19200000 reads so far
2011-05-19 21:33:03,068 - INFO - Processed 19300000 reads so far
2011-05-19 21:33:14,794 - INFO - Processed 19400000 reads so far
2011-05-19 21:33:28,710 - INFO - Processed 19500000 reads so far
2011-05-19 21:33:39,832 - INFO - Processed 19600000 reads so far
2011-05-19 21:33:52,215 - INFO - Processed 19700000 reads so far
2011-05-19 21:33:55,963 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:22990040-43010040
2011-05-19 21:34:05,871 - INFO - Processed 19800000 reads so far
2011-05-19 21:34:18,731 - INFO - Processed 19900000 reads so far
2011-05-19 21:34:33,847 - INFO - Processed 20000000 reads so far
2011-05-19 21:34:49,664 - INFO - Processed 20100000 reads so far
2011-05-19 21:34:58,943 - INFO - Processed 20200000 reads so far
2011-05-19 21:35:11,161 - INFO - Processed 20300000 reads so far
2011-05-19 21:35:21,315 - INFO - Processed 20400000 reads so far
2011-05-19 21:35:34,030 - INFO - Processed 20500000 reads so far
2011-05-19 21:35:46,353 - INFO - Processed 20600000 reads so far
2011-05-19 21:36:01,661 - INFO - Processed 20700000 reads so far
2011-05-19 21:36:08,980 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:42990064-63010064
2011-05-19 21:36:14,191 - INFO - Processed 20800000 reads so far
2011-05-19 21:36:25,584 - INFO - Processed 20900000 reads so far
2011-05-19 21:36:37,779 - INFO - Processed 21000000 reads so far
2011-05-19 21:36:49,315 - INFO - Processed 21100000 reads so far
2011-05-19 21:37:02,162 - INFO - Processed 21200000 reads so far
2011-05-19 21:37:15,286 - INFO - Processed 21300000 reads so far
2011-05-19 21:37:27,438 - INFO - Processed 21400000 reads so far
2011-05-19 21:37:40,455 - INFO - Processed 21500000 reads so far
2011-05-19 21:37:53,740 - INFO - Processed 21600000 reads so far
2011-05-19 21:38:04,687 - INFO - Processed 21700000 reads so far
2011-05-19 21:38:15,909 - INFO - Processed 21800000 reads so far
2011-05-19 21:38:18,819 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:62990085-83010085
2011-05-19 21:38:28,089 - INFO - Processed 21900000 reads so far
2011-05-19 21:38:39,683 - INFO - Processed 22000000 reads so far
2011-05-19 21:38:52,887 - INFO - Processed 22100000 reads so far
2011-05-19 21:39:04,507 - INFO - Processed 22200000 reads so far
2011-05-19 21:39:12,897 - INFO - Processed 22300000 reads so far
2011-05-19 21:39:24,329 - INFO - Processed 22400000 reads so far
2011-05-19 21:39:36,744 - INFO - Processed 22500000 reads so far
2011-05-19 21:39:48,246 - INFO - Processed 22600000 reads so far
2011-05-19 21:39:59,656 - INFO - Processed 22700000 reads so far
2011-05-19 21:40:09,768 - INFO - Processed 22800000 reads so far
2011-05-19 21:40:12,818 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:82990086-103010086
2011-05-19 21:40:21,427 - INFO - Processed 22900000 reads so far
2011-05-19 21:40:33,182 - INFO - Processed 23000000 reads so far
2011-05-19 21:40:45,532 - INFO - Processed 23100000 reads so far
2011-05-19 21:40:57,737 - INFO - Processed 23200000 reads so far
2011-05-19 21:41:10,592 - INFO - Processed 23300000 reads so far
2011-05-19 21:41:24,413 - INFO - Processed 23400000 reads so far
2011-05-19 21:41:36,125 - INFO - Processed 23500000 reads so far
2011-05-19 21:41:47,664 - INFO - Processed 23600000 reads so far
2011-05-19 21:41:59,193 - INFO - Processed 23700000 reads so far
2011-05-19 21:42:08,321 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:102990088-123010088
2011-05-19 21:42:10,409 - INFO - Processed 23800000 reads so far
2011-05-19 21:42:23,289 - INFO - Processed 23900000 reads so far
2011-05-19 21:42:34,456 - INFO - Processed 24000000 reads so far
2011-05-19 21:42:45,668 - INFO - Processed 24100000 reads so far
2011-05-19 21:42:55,154 - INFO - Processed 24200000 reads so far
2011-05-19 21:43:04,680 - INFO - Processed 24300000 reads so far
2011-05-19 21:43:13,985 - INFO - Processed 24400000 reads so far
2011-05-19 21:43:26,616 - INFO - Processed 24500000 reads so far
2011-05-19 21:43:38,487 - INFO - Processed 24600000 reads so far
2011-05-19 21:43:42,423 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13_random:0-20010000
2011-05-19 21:43:43,687 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:2990056-23010056
2011-05-19 21:43:51,585 - INFO - Processed 24700000 reads so far
2011-05-19 21:44:01,675 - INFO - Processed 24800000 reads so far
2011-05-19 21:44:12,920 - INFO - Processed 24900000 reads so far
2011-05-19 21:44:22,915 - INFO - Processed 25000000 reads so far
2011-05-19 21:44:33,166 - INFO - Processed 25100000 reads so far
2011-05-19 21:44:45,614 - INFO - Processed 25200000 reads so far
2011-05-19 21:44:57,221 - INFO - Processed 25300000 reads so far
2011-05-19 21:45:09,202 - INFO - Processed 25400000 reads so far
2011-05-19 21:45:22,674 - INFO - Processed 25500000 reads so far
2011-05-19 21:45:33,758 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:22990059-43010059
2011-05-19 21:45:35,318 - INFO - Processed 25600000 reads so far
2011-05-19 21:45:47,380 - INFO - Processed 25700000 reads so far
2011-05-19 21:45:59,980 - INFO - Processed 25800000 reads so far
2011-05-19 21:46:11,872 - INFO - Processed 25900000 reads so far
2011-05-19 21:46:24,081 - INFO - Processed 26000000 reads so far
2011-05-19 21:46:36,831 - INFO - Processed 26100000 reads so far
2011-05-19 21:46:45,859 - INFO - Processed 26200000 reads so far
2011-05-19 21:46:56,348 - INFO - Processed 26300000 reads so far
2011-05-19 21:47:07,660 - INFO - Processed 26400000 reads so far
2011-05-19 21:47:18,392 - INFO - Processed 26500000 reads so far
2011-05-19 21:47:25,861 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:42993206-63013206
2011-05-19 21:47:29,038 - INFO - Processed 26600000 reads so far
2011-05-19 21:47:40,730 - INFO - Processed 26700000 reads so far
2011-05-19 21:47:50,816 - INFO - Processed 26800000 reads so far
2011-05-19 21:48:00,229 - INFO - Processed 26900000 reads so far
2011-05-19 21:48:13,226 - INFO - Processed 27000000 reads so far
2011-05-19 21:48:26,279 - INFO - Processed 27100000 reads so far
2011-05-19 21:48:37,837 - INFO - Processed 27200000 reads so far
2011-05-19 21:48:49,237 - INFO - Processed 27300000 reads so far
2011-05-19 21:49:00,604 - INFO - Processed 27400000 reads so far
2011-05-19 21:49:15,231 - INFO - Processed 27500000 reads so far
2011-05-19 21:49:17,983 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:62993219-83013219
2011-05-19 21:49:26,894 - INFO - Processed 27600000 reads so far
2011-05-19 21:49:39,316 - INFO - Processed 27700000 reads so far
2011-05-19 21:49:52,565 - INFO - Processed 27800000 reads so far
2011-05-19 21:50:04,289 - INFO - Processed 27900000 reads so far
2011-05-19 21:50:14,045 - INFO - Processed 28000000 reads so far
2011-05-19 21:50:24,561 - INFO - Processed 28100000 reads so far
2011-05-19 21:50:33,644 - INFO - Processed 28200000 reads so far
2011-05-19 21:50:42,446 - INFO - Processed 28300000 reads so far
2011-05-19 21:50:52,206 - INFO - Processed 28400000 reads so far
2011-05-19 21:51:00,991 - INFO - Processed 28500000 reads so far
2011-05-19 21:51:06,407 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:82993239-103013239
2011-05-19 21:51:11,024 - INFO - Processed 28600000 reads so far
2011-05-19 21:51:20,871 - INFO - Processed 28700000 reads so far
2011-05-19 21:51:32,279 - INFO - Processed 28800000 reads so far
2011-05-19 21:51:44,666 - INFO - Processed 28900000 reads so far
2011-05-19 21:51:57,537 - INFO - Processed 29000000 reads so far
2011-05-19 21:52:09,498 - INFO - Processed 29100000 reads so far
2011-05-19 21:52:21,089 - INFO - Processed 29200000 reads so far
2011-05-19 21:52:33,983 - INFO - Processed 29300000 reads so far
2011-05-19 21:52:44,779 - INFO - Processed 29400000 reads so far
2011-05-19 21:52:48,427 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:102993292-123013292
2011-05-19 21:52:53,635 - INFO - Processed 29500000 reads so far
2011-05-19 21:53:04,148 - INFO - Processed 29600000 reads so far
2011-05-19 21:53:14,043 - INFO - Processed 29700000 reads so far
2011-05-19 21:53:22,876 - INFO - Processed 29800000 reads so far
2011-05-19 21:53:31,643 - INFO - Processed 29900000 reads so far
2011-05-19 21:53:41,127 - INFO - Processed 30000000 reads so far
2011-05-19 21:53:50,727 - INFO - Processed 30100000 reads so far
2011-05-19 21:53:59,910 - INFO - Processed 30200000 reads so far
2011-05-19 21:54:08,569 - INFO - Processed 30300000 reads so far
2011-05-19 21:54:17,371 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:122993302-143013302
2011-05-19 21:54:18,380 - INFO - Processed 30400000 reads so far
2011-05-19 21:54:28,443 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:2990152-23010152
2011-05-19 21:54:29,248 - INFO - Processed 30500000 reads so far
2011-05-19 21:54:39,553 - INFO - Processed 30600000 reads so far
2011-05-19 21:54:51,121 - INFO - Processed 30700000 reads so far
2011-05-19 21:55:01,604 - INFO - Processed 30800000 reads so far
2011-05-19 21:55:10,047 - INFO - Processed 30900000 reads so far
2011-05-19 21:55:21,916 - INFO - Processed 31000000 reads so far
2011-05-19 21:55:33,365 - INFO - Processed 31100000 reads so far
2011-05-19 21:55:44,030 - INFO - Processed 31200000 reads so far
2011-05-19 21:55:55,244 - INFO - Processed 31300000 reads so far
2011-05-19 21:56:08,294 - INFO - Processed 31400000 reads so far
2011-05-19 21:56:13,176 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:22990233-43010233
2011-05-19 21:56:19,602 - INFO - Processed 31500000 reads so far
2011-05-19 21:56:29,581 - INFO - Processed 31600000 reads so far
2011-05-19 21:56:40,662 - INFO - Processed 31700000 reads so far
2011-05-19 21:56:53,261 - INFO - Processed 31800000 reads so far
2011-05-19 21:57:02,272 - INFO - Processed 31900000 reads so far
2011-05-19 21:57:12,645 - INFO - Processed 32000000 reads so far
2011-05-19 21:57:25,785 - INFO - Processed 32100000 reads so far
2011-05-19 21:57:39,602 - INFO - Processed 32200000 reads so far
2011-05-19 21:57:54,453 - INFO - Processed 32300000 reads so far
2011-05-19 21:58:03,704 - INFO - Processed 32400000 reads so far
2011-05-19 21:58:09,514 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:42990241-63010241
2011-05-19 21:58:13,516 - INFO - Processed 32500000 reads so far
2011-05-19 21:58:24,306 - INFO - Processed 32600000 reads so far
2011-05-19 21:58:33,792 - INFO - Processed 32700000 reads so far
2011-05-19 21:58:43,726 - INFO - Processed 32800000 reads so far
2011-05-19 21:58:52,194 - INFO - Processed 32900000 reads so far
2011-05-19 21:59:02,068 - INFO - Processed 33000000 reads so far
2011-05-19 21:59:13,586 - INFO - Processed 33100000 reads so far
2011-05-19 21:59:27,060 - INFO - Processed 33200000 reads so far
2011-05-19 21:59:38,230 - INFO - Processed 33300000 reads so far
2011-05-19 21:59:49,587 - INFO - Processed 33400000 reads so far
2011-05-19 21:59:50,186 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:62990245-83010245
2011-05-19 22:00:00,977 - INFO - Processed 33500000 reads so far
2011-05-19 22:00:15,130 - INFO - Processed 33600000 reads so far
2011-05-19 22:00:28,027 - INFO - Processed 33700000 reads so far
2011-05-19 22:00:40,214 - INFO - Processed 33800000 reads so far
2011-05-19 22:00:53,777 - INFO - Processed 33900000 reads so far
2011-05-19 22:01:03,009 - INFO - Processed 34000000 reads so far
2011-05-19 22:01:11,852 - INFO - Processed 34100000 reads so far
2011-05-19 22:01:25,531 - INFO - Processed 34200000 reads so far
2011-05-19 22:01:35,555 - INFO - Processed 34300000 reads so far
2011-05-19 22:01:47,461 - INFO - Processed 34400000 reads so far
2011-05-19 22:01:58,604 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:82990255-103010255
2011-05-19 22:02:00,222 - INFO - Processed 34500000 reads so far
2011-05-19 22:02:12,082 - INFO - Processed 34600000 reads so far
2011-05-19 22:02:24,011 - INFO - Processed 34700000 reads so far
2011-05-19 22:02:34,206 - INFO - Processed 34800000 reads so far
2011-05-19 22:02:45,874 - INFO - Processed 34900000 reads so far
2011-05-19 22:02:54,349 - INFO - Processed 35000000 reads so far
2011-05-19 22:03:04,355 - INFO - Processed 35100000 reads so far
2011-05-19 22:03:14,014 - INFO - Processed 35200000 reads so far
2011-05-19 22:03:23,020 - INFO - Processed 35300000 reads so far
2011-05-19 22:03:35,221 - INFO - Processed 35400000 reads so far
2011-05-19 22:03:46,467 - INFO - Processed 35500000 reads so far
2011-05-19 22:03:52,031 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:102990272-123010272
2011-05-19 22:03:54,086 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:2990015-23010015
2011-05-19 22:03:56,891 - INFO - Processed 35600000 reads so far
2011-05-19 22:04:06,562 - INFO - Processed 35700000 reads so far
2011-05-19 22:04:17,203 - INFO - Processed 35800000 reads so far
2011-05-19 22:04:26,556 - INFO - Processed 35900000 reads so far
2011-05-19 22:04:39,146 - INFO - Processed 36000000 reads so far
2011-05-19 22:04:49,137 - INFO - Processed 36100000 reads so far
2011-05-19 22:04:57,804 - INFO - Processed 36200000 reads so far
2011-05-19 22:05:06,552 - INFO - Processed 36300000 reads so far
2011-05-19 22:05:16,355 - INFO - Processed 36400000 reads so far
2011-05-19 22:05:25,672 - INFO - Processed 36500000 reads so far
2011-05-19 22:05:34,822 - INFO - Processed 36600000 reads so far
2011-05-19 22:05:41,372 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:22990046-43010046
2011-05-19 22:05:43,408 - INFO - Processed 36700000 reads so far
2011-05-19 22:05:51,891 - INFO - Processed 36800000 reads so far
2011-05-19 22:06:03,106 - INFO - Processed 36900000 reads so far
2011-05-19 22:06:12,064 - INFO - Processed 37000000 reads so far
2011-05-19 22:06:20,690 - INFO - Processed 37100000 reads so far
2011-05-19 22:06:32,794 - INFO - Processed 37200000 reads so far
2011-05-19 22:06:42,128 - INFO - Processed 37300000 reads so far
2011-05-19 22:06:50,517 - INFO - Processed 37400000 reads so far
2011-05-19 22:07:01,738 - INFO - Processed 37500000 reads so far
2011-05-19 22:07:14,661 - INFO - Processed 37600000 reads so far
2011-05-19 22:07:24,234 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:42990064-63010064
2011-05-19 22:07:25,699 - INFO - Processed 37700000 reads so far
2011-05-19 22:07:37,093 - INFO - Processed 37800000 reads so far
2011-05-19 22:07:50,428 - INFO - Processed 37900000 reads so far
2011-05-19 22:08:01,985 - INFO - Processed 38000000 reads so far
2011-05-19 22:08:13,040 - INFO - Processed 38100000 reads so far
2011-05-19 22:08:24,973 - INFO - Processed 38200000 reads so far
2011-05-19 22:08:37,950 - INFO - Processed 38300000 reads so far
2011-05-19 22:08:49,749 - INFO - Processed 38400000 reads so far
2011-05-19 22:09:01,274 - INFO - Processed 38500000 reads so far
2011-05-19 22:09:23,148 - INFO - Processed 38600000 reads so far
2011-05-19 22:09:40,045 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:62990123-83010123
2011-05-19 22:09:48,685 - INFO - Processed 38700000 reads so far
2011-05-19 22:09:59,118 - INFO - Processed 38800000 reads so far
2011-05-19 22:10:07,948 - INFO - Processed 38900000 reads so far
2011-05-19 22:10:16,984 - INFO - Processed 39000000 reads so far
2011-05-19 22:10:25,970 - INFO - Processed 39100000 reads so far
2011-05-19 22:10:34,917 - INFO - Processed 39200000 reads so far
2011-05-19 22:10:43,973 - INFO - Processed 39300000 reads so far
2011-05-19 22:10:53,007 - INFO - Processed 39400000 reads so far
2011-05-19 22:11:01,939 - INFO - Processed 39500000 reads so far
2011-05-19 22:11:07,943 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:82990125-103010125
2011-05-19 22:11:12,262 - INFO - Processed 39600000 reads so far
2011-05-19 22:11:21,059 - INFO - Processed 39700000 reads so far
2011-05-19 22:11:30,472 - INFO - Processed 39800000 reads so far
2011-05-19 22:11:40,877 - INFO - Processed 39900000 reads so far
2011-05-19 22:11:50,468 - INFO - Processed 40000000 reads so far
2011-05-19 22:11:59,597 - INFO - Processed 40100000 reads so far
2011-05-19 22:12:08,770 - INFO - Processed 40200000 reads so far
2011-05-19 22:12:16,820 - INFO - Processed 40300000 reads so far
2011-05-19 22:12:21,823 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16_random:0-20010088
2011-05-19 22:12:21,843 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:2989982-23009982
2011-05-19 22:12:27,116 - INFO - Processed 40400000 reads so far
2011-05-19 22:12:36,409 - INFO - Processed 40500000 reads so far
2011-05-19 22:12:45,739 - INFO - Processed 40600000 reads so far
2011-05-19 22:12:54,421 - INFO - Processed 40700000 reads so far
2011-05-19 22:13:03,458 - INFO - Processed 40800000 reads so far
2011-05-19 22:13:16,199 - INFO - Processed 40900000 reads so far
2011-05-19 22:13:25,573 - INFO - Processed 41000000 reads so far
2011-05-19 22:13:34,214 - INFO - Processed 41100000 reads so far
2011-05-19 22:13:43,560 - INFO - Processed 41200000 reads so far
2011-05-19 22:13:53,837 - INFO - Processed 41300000 reads so far
2011-05-19 22:14:02,466 - INFO - Processed 41400000 reads so far
2011-05-19 22:14:08,432 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:22990011-43010011
2011-05-19 22:14:11,931 - INFO - Processed 41500000 reads so far
2011-05-19 22:14:23,354 - INFO - Processed 41600000 reads so far
2011-05-19 22:14:32,364 - INFO - Processed 41700000 reads so far
2011-05-19 22:14:43,231 - INFO - Processed 41800000 reads so far
2011-05-19 22:14:53,453 - INFO - Processed 41900000 reads so far
2011-05-19 22:15:03,234 - INFO - Processed 42000000 reads so far
2011-05-19 22:15:12,676 - INFO - Processed 42100000 reads so far
2011-05-19 22:15:22,484 - INFO - Processed 42200000 reads so far
2011-05-19 22:15:32,006 - INFO - Processed 42300000 reads so far
2011-05-19 22:15:40,452 - INFO - Processed 42400000 reads so far
2011-05-19 22:15:51,507 - INFO - Processed 42500000 reads so far
2011-05-19 22:15:53,060 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:42990018-63010018
2011-05-19 22:16:03,073 - INFO - Processed 42600000 reads so far
2011-05-19 22:16:13,406 - INFO - Processed 42700000 reads so far
2011-05-19 22:16:25,231 - INFO - Processed 42800000 reads so far
2011-05-19 22:16:34,529 - INFO - Processed 42900000 reads so far
2011-05-19 22:16:46,064 - INFO - Processed 43000000 reads so far
2011-05-19 22:16:56,488 - INFO - Processed 43100000 reads so far
2011-05-19 22:17:07,089 - INFO - Processed 43200000 reads so far
2011-05-19 22:17:16,456 - INFO - Processed 43300000 reads so far
2011-05-19 22:17:26,080 - INFO - Processed 43400000 reads so far
2011-05-19 22:17:37,232 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:62990023-83010023
2011-05-19 22:17:37,601 - INFO - Processed 43500000 reads so far
2011-05-19 22:17:47,733 - INFO - Processed 43600000 reads so far
2011-05-19 22:17:57,113 - INFO - Processed 43700000 reads so far
2011-05-19 22:18:09,214 - INFO - Processed 43800000 reads so far
2011-05-19 22:18:18,652 - INFO - Processed 43900000 reads so far
2011-05-19 22:18:28,511 - INFO - Processed 44000000 reads so far
2011-05-19 22:18:39,960 - INFO - Processed 44100000 reads so far
2011-05-19 22:18:50,200 - INFO - Processed 44200000 reads so far
2011-05-19 22:19:00,889 - INFO - Processed 44300000 reads so far
2011-05-19 22:19:11,120 - INFO - Processed 44400000 reads so far
2011-05-19 22:19:21,614 - INFO - Processed 44500000 reads so far
2011-05-19 22:19:23,128 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:82990221-103010221
2011-05-19 22:19:30,367 - INFO - Processed 44600000 reads so far
2011-05-19 22:19:41,124 - INFO - Processed 44700000 reads so far
2011-05-19 22:19:52,361 - INFO - Processed 44800000 reads so far
2011-05-19 22:20:02,334 - INFO - Processed 44900000 reads so far
2011-05-19 22:20:11,245 - INFO - Processed 45000000 reads so far
2011-05-19 22:20:20,021 - INFO - Processed 45100000 reads so far
2011-05-19 22:20:22,474 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17_random:0-20010013
2011-05-19 22:20:23,841 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:2989999-23009999
2011-05-19 22:20:29,498 - INFO - Processed 45200000 reads so far
2011-05-19 22:20:39,662 - INFO - Processed 45300000 reads so far
2011-05-19 22:20:50,024 - INFO - Processed 45400000 reads so far
2011-05-19 22:20:59,069 - INFO - Processed 45500000 reads so far
2011-05-19 22:21:10,896 - INFO - Processed 45600000 reads so far
2011-05-19 22:21:23,392 - INFO - Processed 45700000 reads so far
2011-05-19 22:21:32,912 - INFO - Processed 45800000 reads so far
2011-05-19 22:21:46,003 - INFO - Processed 45900000 reads so far
2011-05-19 22:21:57,402 - INFO - Processed 46000000 reads so far
2011-05-19 22:22:09,050 - INFO - Processed 46100000 reads so far
2011-05-19 22:22:18,833 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:22990005-43010005
2011-05-19 22:22:21,112 - INFO - Processed 46200000 reads so far
2011-05-19 22:22:31,142 - INFO - Processed 46300000 reads so far
2011-05-19 22:22:41,682 - INFO - Processed 46400000 reads so far
2011-05-19 22:22:50,234 - INFO - Processed 46500000 reads so far
2011-05-19 22:22:59,376 - INFO - Processed 46600000 reads so far
2011-05-19 22:23:10,117 - INFO - Processed 46700000 reads so far
2011-05-19 22:23:22,569 - INFO - Processed 46800000 reads so far
2011-05-19 22:23:32,398 - INFO - Processed 46900000 reads so far
2011-05-19 22:23:42,208 - INFO - Processed 47000000 reads so far
2011-05-19 22:23:52,269 - INFO - Processed 47100000 reads so far
2011-05-19 22:24:10,108 - INFO - Processed 47200000 reads so far
2011-05-19 22:24:10,281 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:42990009-63010009
2011-05-19 22:24:20,213 - INFO - Processed 47300000 reads so far
2011-05-19 22:24:31,118 - INFO - Processed 47400000 reads so far
2011-05-19 22:24:40,597 - INFO - Processed 47500000 reads so far
2011-05-19 22:24:49,797 - INFO - Processed 47600000 reads so far
2011-05-19 22:24:59,557 - INFO - Processed 47700000 reads so far
2011-05-19 22:25:08,697 - INFO - Processed 47800000 reads so far
2011-05-19 22:25:18,214 - INFO - Processed 47900000 reads so far
2011-05-19 22:25:26,951 - INFO - Processed 48000000 reads so far
2011-05-19 22:25:36,878 - INFO - Processed 48100000 reads so far
2011-05-19 22:25:44,540 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:62990010-83010010
2011-05-19 22:25:45,626 - INFO - Processed 48200000 reads so far
2011-05-19 22:25:56,396 - INFO - Processed 48300000 reads so far
2011-05-19 22:26:05,331 - INFO - Processed 48400000 reads so far
2011-05-19 22:26:14,378 - INFO - Processed 48500000 reads so far
2011-05-19 22:26:22,373 - INFO - Processed 48600000 reads so far
2011-05-19 22:26:30,554 - INFO - Processed 48700000 reads so far
2011-05-19 22:26:40,609 - INFO - Processed 48800000 reads so far
2011-05-19 22:26:51,307 - INFO - Processed 48900000 reads so far
2011-05-19 22:27:01,947 - INFO - Processed 49000000 reads so far
2011-05-19 22:27:14,927 - INFO - Processed 49100000 reads so far
2011-05-19 22:27:26,040 - INFO - Processed 49200000 reads so far
2011-05-19 22:27:28,874 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:82990074-103010074
2011-05-19 22:27:38,063 - INFO - Processed 49300000 reads so far
2011-05-19 22:27:49,795 - INFO - Processed 49400000 reads so far
2011-05-19 22:28:01,203 - INFO - Processed 49500000 reads so far
2011-05-19 22:28:13,165 - INFO - Processed 49600000 reads so far
2011-05-19 22:28:13,660 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:2990050-23010050
2011-05-19 22:28:24,616 - INFO - Processed 49700000 reads so far
2011-05-19 22:28:37,330 - INFO - Processed 49800000 reads so far
2011-05-19 22:28:49,118 - INFO - Processed 49900000 reads so far
2011-05-19 22:29:01,484 - INFO - Processed 50000000 reads so far
2011-05-19 22:29:12,394 - INFO - Processed 50100000 reads so far
2011-05-19 22:29:21,671 - INFO - Processed 50200000 reads so far
2011-05-19 22:29:32,785 - INFO - Processed 50300000 reads so far
2011-05-19 22:29:44,135 - INFO - Processed 50400000 reads so far
2011-05-19 22:29:53,919 - INFO - Processed 50500000 reads so far
2011-05-19 22:30:03,407 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:22990066-43010066
2011-05-19 22:30:03,805 - INFO - Processed 50600000 reads so far
2011-05-19 22:30:14,266 - INFO - Processed 50700000 reads so far
2011-05-19 22:30:25,309 - INFO - Processed 50800000 reads so far
2011-05-19 22:30:35,132 - INFO - Processed 50900000 reads so far
2011-05-19 22:30:45,981 - INFO - Processed 51000000 reads so far
2011-05-19 22:30:57,571 - INFO - Processed 51100000 reads so far
2011-05-19 22:31:09,627 - INFO - Processed 51200000 reads so far
2011-05-19 22:31:22,172 - INFO - Processed 51300000 reads so far
2011-05-19 22:31:32,958 - INFO - Processed 51400000 reads so far
2011-05-19 22:31:42,892 - INFO - Processed 51500000 reads so far
2011-05-19 22:31:53,643 - INFO - Processed 51600000 reads so far
2011-05-19 22:31:54,795 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:42990068-63010068
2011-05-19 22:32:02,732 - INFO - Processed 51700000 reads so far
2011-05-19 22:32:12,759 - INFO - Processed 51800000 reads so far
2011-05-19 22:32:24,718 - INFO - Processed 51900000 reads so far
2011-05-19 22:32:38,241 - INFO - Processed 52000000 reads so far
2011-05-19 22:32:47,294 - INFO - Processed 52100000 reads so far
2011-05-19 22:32:55,421 - INFO - Processed 52200000 reads so far
2011-05-19 22:33:03,289 - INFO - Processed 52300000 reads so far
2011-05-19 22:33:11,896 - INFO - Processed 52400000 reads so far
2011-05-19 22:33:21,586 - INFO - Processed 52500000 reads so far
2011-05-19 22:33:29,813 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:2989999-23009999
2011-05-19 22:33:33,484 - INFO - Processed 52600000 reads so far
2011-05-19 22:33:46,127 - INFO - Processed 52700000 reads so far
2011-05-19 22:33:59,805 - INFO - Processed 52800000 reads so far
2011-05-19 22:34:08,922 - INFO - Processed 52900000 reads so far
2011-05-19 22:34:17,050 - INFO - Processed 53000000 reads so far
2011-05-19 22:34:25,450 - INFO - Processed 53100000 reads so far
2011-05-19 22:34:35,043 - INFO - Processed 53200000 reads so far
2011-05-19 22:34:44,924 - INFO - Processed 53300000 reads so far
2011-05-19 22:34:53,713 - INFO - Processed 53400000 reads so far
2011-05-19 22:35:05,324 - INFO - Processed 53500000 reads so far
2011-05-19 22:35:08,973 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:22990035-43010035
2011-05-19 22:35:15,557 - INFO - Processed 53600000 reads so far
2011-05-19 22:35:25,013 - INFO - Processed 53700000 reads so far
2011-05-19 22:35:38,246 - INFO - Processed 53800000 reads so far
2011-05-19 22:35:47,083 - INFO - Processed 53900000 reads so far
2011-05-19 22:35:56,454 - INFO - Processed 54000000 reads so far
2011-05-19 22:36:08,696 - INFO - Processed 54100000 reads so far
2011-05-19 22:36:19,137 - INFO - Processed 54200000 reads so far
2011-05-19 22:36:28,622 - INFO - Processed 54300000 reads so far
2011-05-19 22:36:37,036 - INFO - Processed 54400000 reads so far
2011-05-19 22:36:47,981 - INFO - Processed 54500000 reads so far
2011-05-19 22:36:51,098 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:42990038-63010038
2011-05-19 22:36:58,771 - INFO - Processed 54600000 reads so far
2011-05-19 22:37:08,347 - INFO - Processed 54700000 reads so far
2011-05-19 22:37:17,118 - INFO - Processed 54800000 reads so far
2011-05-19 22:37:27,709 - INFO - Processed 54900000 reads so far
2011-05-19 22:37:37,184 - INFO - Processed 55000000 reads so far
2011-05-19 22:37:46,228 - INFO - Processed 55100000 reads so far
2011-05-19 22:37:56,085 - INFO - Processed 55200000 reads so far
2011-05-19 22:38:05,674 - INFO - Processed 55300000 reads so far
2011-05-19 22:38:20,327 - INFO - Processed 55400000 reads so far
2011-05-19 22:38:30,642 - INFO - Processed 55500000 reads so far
2011-05-19 22:38:31,662 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:62990080-83010080
2011-05-19 22:38:41,325 - INFO - Processed 55600000 reads so far
2011-05-19 22:38:54,498 - INFO - Processed 55700000 reads so far
2011-05-19 22:39:06,664 - INFO - Processed 55800000 reads so far
2011-05-19 22:39:17,629 - INFO - Processed 55900000 reads so far
2011-05-19 22:39:28,688 - INFO - Processed 56000000 reads so far
2011-05-19 22:39:37,885 - INFO - Processed 56100000 reads so far
2011-05-19 22:39:46,524 - INFO - Processed 56200000 reads so far
2011-05-19 22:39:54,104 - INFO - Processed 56300000 reads so far
2011-05-19 22:40:05,050 - INFO - Processed 56400000 reads so far
2011-05-19 22:40:17,742 - INFO - Processed 56500000 reads so far
2011-05-19 22:40:18,054 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:82990093-103010093
2011-05-19 22:40:28,735 - INFO - Processed 56600000 reads so far
2011-05-19 22:40:37,669 - INFO - Processed 56700000 reads so far
2011-05-19 22:40:49,428 - INFO - Processed 56800000 reads so far
2011-05-19 22:40:59,393 - INFO - Processed 56900000 reads so far
2011-05-19 22:41:10,503 - INFO - Processed 57000000 reads so far
2011-05-19 22:41:21,300 - INFO - Processed 57100000 reads so far
2011-05-19 22:41:32,637 - INFO - Processed 57200000 reads so far
2011-05-19 22:41:42,731 - INFO - Processed 57300000 reads so far
2011-05-19 22:41:52,573 - INFO - Processed 57400000 reads so far
2011-05-19 22:42:02,282 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:102990110-123010110
2011-05-19 22:42:02,826 - INFO - Processed 57500000 reads so far
2011-05-19 22:42:14,335 - INFO - Processed 57600000 reads so far
2011-05-19 22:42:24,718 - INFO - Processed 57700000 reads so far
2011-05-19 22:42:36,798 - INFO - Processed 57800000 reads so far
2011-05-19 22:42:48,379 - INFO - Processed 57900000 reads so far
2011-05-19 22:43:00,579 - INFO - Processed 58000000 reads so far
2011-05-19 22:43:11,895 - INFO - Processed 58100000 reads so far
2011-05-19 22:43:24,136 - INFO - Processed 58200000 reads so far
2011-05-19 22:43:35,639 - INFO - Processed 58300000 reads so far
2011-05-19 22:43:44,425 - INFO - Processed 58400000 reads so far
2011-05-19 22:43:49,192 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:122990120-143010120
2011-05-19 22:43:54,261 - INFO - Processed 58500000 reads so far
2011-05-19 22:44:05,264 - INFO - Processed 58600000 reads so far
2011-05-19 22:44:15,992 - INFO - Processed 58700000 reads so far
2011-05-19 22:44:25,865 - INFO - Processed 58800000 reads so far
2011-05-19 22:44:35,309 - INFO - Processed 58900000 reads so far
2011-05-19 22:44:43,905 - INFO - Processed 59000000 reads so far
2011-05-19 22:44:54,643 - INFO - Processed 59100000 reads so far
2011-05-19 22:45:14,586 - INFO - Processed 59200000 reads so far
2011-05-19 22:45:23,166 - INFO - Processed 59300000 reads so far
2011-05-19 22:45:34,319 - INFO - Processed 59400000 reads so far
2011-05-19 22:45:42,530 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:142990146-163010146
2011-05-19 22:45:44,993 - INFO - Processed 59500000 reads so far
2011-05-19 22:45:54,197 - INFO - Processed 59600000 reads so far
2011-05-19 22:46:01,605 - INFO - Processed 59700000 reads so far
2011-05-19 22:46:14,060 - INFO - Processed 59800000 reads so far
2011-05-19 22:46:25,066 - INFO - Processed 59900000 reads so far
2011-05-19 22:46:34,540 - INFO - Processed 60000000 reads so far
2011-05-19 22:46:46,475 - INFO - Processed 60100000 reads so far
2011-05-19 22:46:59,464 - INFO - Processed 60200000 reads so far
2011-05-19 22:47:10,244 - INFO - Processed 60300000 reads so far
2011-05-19 22:47:22,093 - INFO - Processed 60400000 reads so far
2011-05-19 22:47:26,087 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:162990173-183010173
2011-05-19 22:47:34,322 - INFO - Processed 60500000 reads so far
2011-05-19 22:47:46,139 - INFO - Processed 60600000 reads so far
2011-05-19 22:47:57,746 - INFO - Processed 60700000 reads so far
2011-05-19 22:48:11,445 - INFO - Processed 60800000 reads so far
2011-05-19 22:48:24,830 - INFO - Processed 60900000 reads so far
2011-05-19 22:48:36,083 - INFO - Processed 61000000 reads so far
2011-05-19 22:48:48,545 - INFO - Processed 61100000 reads so far
2011-05-19 22:48:57,483 - INFO - Processed 61200000 reads so far
2011-05-19 22:49:07,184 - INFO - Processed 61300000 reads so far
2011-05-19 22:49:17,665 - INFO - Processed 61400000 reads so far
2011-05-19 22:49:28,751 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:182990181-203010181
2011-05-19 22:49:30,653 - INFO - Processed 61500000 reads so far
2011-05-19 22:49:42,177 - INFO - Processed 61600000 reads so far
2011-05-19 22:49:56,181 - INFO - Processed 61700000 reads so far
2011-05-19 22:50:07,371 - INFO - Processed 61800000 reads so far
2011-05-19 22:50:18,935 - INFO - Processed 61900000 reads so far
2011-05-19 22:50:31,686 - INFO - Processed 62000000 reads so far
2011-05-19 22:50:42,933 - INFO - Processed 62100000 reads so far
2011-05-19 22:50:51,915 - INFO - Processed 62200000 reads so far
2011-05-19 22:50:54,313 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1_random:0-20010000
2011-05-19 22:51:00,231 - INFO - Processed 62300000 reads so far
2011-05-19 22:51:03,009 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:2990010-23010010
2011-05-19 22:51:11,661 - INFO - Processed 62400000 reads so far
2011-05-19 22:51:22,955 - INFO - Processed 62500000 reads so far
2011-05-19 22:51:34,625 - INFO - Processed 62600000 reads so far
2011-05-19 22:51:44,621 - INFO - Processed 62700000 reads so far
2011-05-19 22:51:54,312 - INFO - Processed 62800000 reads so far
2011-05-19 22:52:05,505 - INFO - Processed 62900000 reads so far
2011-05-19 22:52:15,809 - INFO - Processed 63000000 reads so far
2011-05-19 22:52:25,095 - INFO - Processed 63100000 reads so far
2011-05-19 22:52:33,965 - INFO - Processed 63200000 reads so far
2011-05-19 22:52:42,980 - INFO - Processed 63300000 reads so far
2011-05-19 22:52:47,796 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:22990014-43010014
2011-05-19 22:52:53,367 - INFO - Processed 63400000 reads so far
2011-05-19 22:53:06,510 - INFO - Processed 63500000 reads so far
2011-05-19 22:53:16,195 - INFO - Processed 63600000 reads so far
2011-05-19 22:53:27,037 - INFO - Processed 63700000 reads so far
2011-05-19 22:53:37,198 - INFO - Processed 63800000 reads so far
2011-05-19 22:53:46,927 - INFO - Processed 63900000 reads so far
2011-05-19 22:53:56,118 - INFO - Processed 64000000 reads so far
2011-05-19 22:54:05,410 - INFO - Processed 64100000 reads so far
2011-05-19 22:54:15,204 - INFO - Processed 64200000 reads so far
2011-05-19 22:54:24,607 - INFO - Processed 64300000 reads so far
2011-05-19 22:54:31,907 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:42990033-63010033
2011-05-19 22:54:34,473 - INFO - Processed 64400000 reads so far
2011-05-19 22:54:44,159 - INFO - Processed 64500000 reads so far
2011-05-19 22:54:53,649 - INFO - Processed 64600000 reads so far
2011-05-19 22:55:03,424 - INFO - Processed 64700000 reads so far
2011-05-19 22:55:14,779 - INFO - Processed 64800000 reads so far
2011-05-19 22:55:24,762 - INFO - Processed 64900000 reads so far
2011-05-19 22:55:35,314 - INFO - Processed 65000000 reads so far
2011-05-19 22:55:45,529 - INFO - Processed 65100000 reads so far
2011-05-19 22:55:56,936 - INFO - Processed 65200000 reads so far
2011-05-19 22:56:07,812 - INFO - Processed 65300000 reads so far
2011-05-19 22:56:11,894 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:62990042-83010042
2011-05-19 22:56:17,533 - INFO - Processed 65400000 reads so far
2011-05-19 22:56:26,720 - INFO - Processed 65500000 reads so far
2011-05-19 22:56:35,701 - INFO - Processed 65600000 reads so far
2011-05-19 22:56:45,937 - INFO - Processed 65700000 reads so far
2011-05-19 22:56:55,473 - INFO - Processed 65800000 reads so far
2011-05-19 22:57:07,148 - INFO - Processed 65900000 reads so far
2011-05-19 22:57:15,659 - INFO - Processed 66000000 reads so far
2011-05-19 22:57:25,378 - INFO - Processed 66100000 reads so far
2011-05-19 22:57:35,933 - INFO - Processed 66200000 reads so far
2011-05-19 22:57:45,993 - INFO - Processed 66300000 reads so far
2011-05-19 22:57:54,155 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:82990064-103010064
2011-05-19 22:57:55,929 - INFO - Processed 66400000 reads so far
2011-05-19 22:58:06,961 - INFO - Processed 66500000 reads so far
2011-05-19 22:58:17,139 - INFO - Processed 66600000 reads so far
2011-05-19 22:58:26,006 - INFO - Processed 66700000 reads so far
2011-05-19 22:58:36,104 - INFO - Processed 66800000 reads so far
2011-05-19 22:58:45,566 - INFO - Processed 66900000 reads so far
2011-05-19 22:58:53,849 - INFO - Processed 67000000 reads so far
2011-05-19 22:59:03,168 - INFO - Processed 67100000 reads so far
2011-05-19 22:59:10,733 - INFO - Processed 67200000 reads so far
2011-05-19 22:59:19,113 - INFO - Processed 67300000 reads so far
2011-05-19 22:59:25,419 - INFO - Processed 67400000 reads so far
2011-05-19 22:59:32,353 - INFO - Processed 67500000 reads so far
2011-05-19 22:59:39,463 - INFO - Processed 67600000 reads so far
2011-05-19 22:59:49,364 - INFO - Processed 67700000 reads so far
2011-05-19 22:59:58,580 - INFO - Processed 67800000 reads so far
2011-05-19 23:00:05,522 - INFO - Processed 67900000 reads so far
2011-05-19 23:00:13,023 - INFO - Processed 68000000 reads so far
2011-05-19 23:00:19,982 - INFO - Processed 68100000 reads so far
2011-05-19 23:00:26,709 - INFO - Processed 68200000 reads so far
2011-05-19 23:00:33,986 - INFO - Processed 68300000 reads so far
2011-05-19 23:00:40,247 - INFO - Processed 68400000 reads so far
2011-05-19 23:00:46,915 - INFO - Processed 68500000 reads so far
2011-05-19 23:00:55,188 - INFO - Processed 68600000 reads so far
2011-05-19 23:01:01,912 - INFO - Processed 68700000 reads so far
2011-05-19 23:01:08,950 - INFO - Processed 68800000 reads so far
2011-05-19 23:01:18,204 - INFO - Processed 68900000 reads so far
2011-05-19 23:01:33,274 - INFO - Processed 69000000 reads so far
2011-05-19 23:01:41,808 - INFO - Processed 69100000 reads so far
2011-05-19 23:01:52,629 - INFO - Processed 69200000 reads so far
2011-05-19 23:02:01,001 - INFO - Processed 69300000 reads so far
2011-05-19 23:02:08,839 - INFO - Processed 69400000 reads so far
2011-05-19 23:02:17,111 - INFO - Processed 69500000 reads so far
2011-05-19 23:02:24,377 - INFO - Processed 69600000 reads so far
2011-05-19 23:02:31,680 - INFO - Processed 69700000 reads so far
2011-05-19 23:02:38,754 - INFO - Processed 69800000 reads so far
2011-05-19 23:02:45,071 - INFO - Processed 69900000 reads so far
2011-05-19 23:02:53,158 - INFO - Processed 70000000 reads so far
2011-05-19 23:03:01,574 - INFO - Processed 70100000 reads so far
2011-05-19 23:03:09,579 - INFO - Processed 70200000 reads so far
2011-05-19 23:03:17,283 - INFO - Processed 70300000 reads so far
2011-05-19 23:03:27,349 - INFO - Processed 70400000 reads so far
2011-05-19 23:03:37,163 - INFO - Processed 70500000 reads so far
2011-05-19 23:03:45,684 - INFO - Processed 70600000 reads so far
2011-05-19 23:03:55,182 - INFO - Processed 70700000 reads so far
2011-05-19 23:04:06,064 - INFO - Processed 70800000 reads so far
2011-05-19 23:04:12,524 - INFO - Processed 70900000 reads so far
2011-05-19 23:04:21,386 - INFO - Processed 71000000 reads so far
2011-05-19 23:04:28,864 - INFO - Processed 71100000 reads so far
2011-05-19 23:04:38,432 - INFO - Processed 71200000 reads so far
2011-05-19 23:04:47,671 - INFO - Processed 71300000 reads so far
2011-05-19 23:04:55,129 - INFO - Processed 71400000 reads so far
2011-05-19 23:05:03,073 - INFO - Processed 71500000 reads so far
2011-05-19 23:05:09,641 - INFO - Processed 71600000 reads so far
2011-05-19 23:05:17,024 - INFO - Processed 71700000 reads so far
2011-05-19 23:05:24,004 - INFO - Processed 71800000 reads so far
2011-05-19 23:05:31,181 - INFO - Processed 71900000 reads so far
2011-05-19 23:05:38,967 - INFO - Processed 72000000 reads so far
2011-05-19 23:05:46,371 - INFO - Processed 72100000 reads so far
2011-05-19 23:05:53,913 - INFO - Processed 72200000 reads so far
2011-05-19 23:06:04,021 - INFO - Processed 72300000 reads so far
2011-05-19 23:06:12,352 - INFO - Processed 72400000 reads so far
2011-05-19 23:06:24,095 - INFO - Processed 72500000 reads so far
2011-05-19 23:06:32,906 - INFO - Processed 72600000 reads so far
2011-05-19 23:06:40,393 - INFO - Processed 72700000 reads so far
2011-05-19 23:06:48,094 - INFO - Processed 72800000 reads so far
2011-05-19 23:06:56,067 - INFO - Processed 72900000 reads so far
2011-05-19 23:07:05,337 - INFO - Processed 73000000 reads so far
2011-05-19 23:07:12,310 - INFO - Processed 73100000 reads so far
2011-05-19 23:07:20,017 - INFO - Processed 73200000 reads so far
2011-05-19 23:07:27,459 - INFO - Processed 73300000 reads so far
2011-05-19 23:07:36,180 - INFO - Processed 73400000 reads so far
2011-05-19 23:07:43,568 - INFO - Processed 73500000 reads so far
2011-05-19 23:07:50,592 - INFO - Processed 73600000 reads so far
2011-05-19 23:07:57,122 - INFO - Processed 73700000 reads so far
2011-05-19 23:08:05,210 - INFO - Processed 73800000 reads so far
2011-05-19 23:08:13,174 - INFO - Processed 73900000 reads so far
2011-05-19 23:08:23,285 - INFO - Processed 74000000 reads so far
2011-05-19 23:08:31,316 - INFO - Processed 74100000 reads so far
2011-05-19 23:08:38,773 - INFO - Processed 74200000 reads so far
2011-05-19 23:08:47,489 - INFO - Processed 74300000 reads so far
2011-05-19 23:08:55,263 - INFO - Processed 74400000 reads so far
2011-05-19 23:09:01,855 - INFO - Processed 74500000 reads so far
2011-05-19 23:09:09,012 - INFO - Processed 74600000 reads so far
2011-05-19 23:09:17,074 - INFO - Processed 74700000 reads so far
2011-05-19 23:09:25,286 - INFO - Processed 74800000 reads so far
2011-05-19 23:09:32,911 - INFO - Processed 74900000 reads so far
2011-05-19 23:09:41,616 - INFO - Processed 75000000 reads so far
2011-05-19 23:09:50,010 - INFO - Processed 75100000 reads so far
2011-05-19 23:09:59,978 - INFO - Processed 75200000 reads so far
2011-05-19 23:10:07,943 - INFO - Processed 75300000 reads so far
2011-05-19 23:10:17,874 - INFO - Processed 75400000 reads so far
2011-05-19 23:10:27,344 - INFO - Processed 75500000 reads so far
2011-05-19 23:10:38,038 - INFO - Processed 75600000 reads so far
2011-05-19 23:10:48,521 - INFO - Processed 75700000 reads so far
2011-05-19 23:10:56,155 - INFO - Processed 75800000 reads so far
2011-05-19 23:11:04,750 - INFO - Processed 75900000 reads so far
2011-05-19 23:11:15,302 - INFO - Processed 76000000 reads so far
2011-05-19 23:11:23,455 - INFO - Processed 76100000 reads so far
2011-05-19 23:11:31,289 - INFO - Processed 76200000 reads so far
2011-05-19 23:11:41,967 - INFO - Processed 76300000 reads so far
2011-05-19 23:11:50,241 - INFO - Processed 76400000 reads so far
2011-05-19 23:11:59,301 - INFO - Processed 76500000 reads so far
2011-05-19 23:12:09,343 - INFO - Processed 76600000 reads so far
2011-05-19 23:12:20,464 - INFO - Processed 76700000 reads so far
2011-05-19 23:12:32,107 - INFO - Processed 76800000 reads so far
2011-05-19 23:12:36,021 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:102990066-123010066
2011-05-19 23:12:46,869 - INFO - Processed 76900000 reads so far
2011-05-19 23:12:56,676 - INFO - Processed 77000000 reads so far
2011-05-19 23:13:07,443 - INFO - Processed 77100000 reads so far
2011-05-19 23:13:16,514 - INFO - Processed 77200000 reads so far
2011-05-19 23:13:27,019 - INFO - Processed 77300000 reads so far
2011-05-19 23:13:35,841 - INFO - Processed 77400000 reads so far
2011-05-19 23:13:45,406 - INFO - Processed 77500000 reads so far
2011-05-19 23:13:55,761 - INFO - Processed 77600000 reads so far
2011-05-19 23:14:04,722 - INFO - Processed 77700000 reads so far
2011-05-19 23:14:16,645 - INFO - Processed 77800000 reads so far
2011-05-19 23:14:18,099 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:122990220-143010220
2011-05-19 23:14:25,510 - INFO - Processed 77900000 reads so far
2011-05-19 23:14:35,771 - INFO - Processed 78000000 reads so far
2011-05-19 23:14:47,600 - INFO - Processed 78100000 reads so far
2011-05-19 23:14:58,248 - INFO - Processed 78200000 reads so far
2011-05-19 23:15:08,330 - INFO - Processed 78300000 reads so far
2011-05-19 23:15:18,505 - INFO - Processed 78400000 reads so far
2011-05-19 23:15:27,329 - INFO - Processed 78500000 reads so far
2011-05-19 23:15:38,474 - INFO - Processed 78600000 reads so far
2011-05-19 23:15:50,550 - INFO - Processed 78700000 reads so far
2011-05-19 23:16:00,153 - INFO - Processed 78800000 reads so far
2011-05-19 23:16:04,127 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:142990221-163010221
2011-05-19 23:16:11,826 - INFO - Processed 78900000 reads so far
2011-05-19 23:16:29,769 - INFO - Processed 79000000 reads so far
2011-05-19 23:16:38,646 - INFO - Processed 79100000 reads so far
2011-05-19 23:16:50,393 - INFO - Processed 79200000 reads so far
2011-05-19 23:17:01,453 - INFO - Processed 79300000 reads so far
2011-05-19 23:17:12,600 - INFO - Processed 79400000 reads so far
2011-05-19 23:17:22,910 - INFO - Processed 79500000 reads so far
2011-05-19 23:17:34,767 - INFO - Processed 79600000 reads so far
2011-05-19 23:17:46,083 - INFO - Processed 79700000 reads so far
2011-05-19 23:17:56,566 - INFO - Processed 79800000 reads so far
2011-05-19 23:18:05,623 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:162990267-183010267
2011-05-19 23:18:08,226 - INFO - Processed 79900000 reads so far
2011-05-19 23:18:18,377 - INFO - Processed 80000000 reads so far
2011-05-19 23:18:27,389 - INFO - Processed 80100000 reads so far
2011-05-19 23:18:37,314 - INFO - Processed 80200000 reads so far
2011-05-19 23:19:01,162 - INFO - Processed 80300000 reads so far
2011-05-19 23:19:11,740 - INFO - Processed 80400000 reads so far
2011-05-19 23:19:20,600 - INFO - Processed 80500000 reads so far
2011-05-19 23:19:30,320 - INFO - Processed 80600000 reads so far
2011-05-19 23:19:39,104 - INFO - Processed 80700000 reads so far
2011-05-19 23:19:47,591 - INFO - Processed 80800000 reads so far
2011-05-19 23:19:58,878 - INFO - Processed 80900000 reads so far
2011-05-19 23:20:03,470 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:2989994-23009994
2011-05-19 23:20:08,668 - INFO - Processed 81000000 reads so far
2011-05-19 23:20:19,158 - INFO - Processed 81100000 reads so far
2011-05-19 23:20:28,667 - INFO - Processed 81200000 reads so far
2011-05-19 23:20:37,571 - INFO - Processed 81300000 reads so far
2011-05-19 23:20:46,721 - INFO - Processed 81400000 reads so far
2011-05-19 23:20:56,494 - INFO - Processed 81500000 reads so far
2011-05-19 23:21:08,028 - INFO - Processed 81600000 reads so far
2011-05-19 23:21:19,127 - INFO - Processed 81700000 reads so far
2011-05-19 23:21:28,018 - INFO - Processed 81800000 reads so far
2011-05-19 23:21:36,558 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:22990001-43010001
2011-05-19 23:21:36,774 - INFO - Processed 81900000 reads so far
2011-05-19 23:21:46,189 - INFO - Processed 82000000 reads so far
2011-05-19 23:21:55,687 - INFO - Processed 82100000 reads so far
2011-05-19 23:22:05,196 - INFO - Processed 82200000 reads so far
2011-05-19 23:22:14,785 - INFO - Processed 82300000 reads so far
2011-05-19 23:22:26,501 - INFO - Processed 82400000 reads so far
2011-05-19 23:22:35,201 - INFO - Processed 82500000 reads so far
2011-05-19 23:22:43,808 - INFO - Processed 82600000 reads so far
2011-05-19 23:22:53,240 - INFO - Processed 82700000 reads so far
2011-05-19 23:23:03,084 - INFO - Processed 82800000 reads so far
2011-05-19 23:23:13,772 - INFO - Processed 82900000 reads so far
2011-05-19 23:23:13,873 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:42990006-63010006
2011-05-19 23:23:23,373 - INFO - Processed 83000000 reads so far
2011-05-19 23:23:33,160 - INFO - Processed 83100000 reads so far
2011-05-19 23:23:41,977 - INFO - Processed 83200000 reads so far
2011-05-19 23:23:50,503 - INFO - Processed 83300000 reads so far
2011-05-19 23:24:00,144 - INFO - Processed 83400000 reads so far
2011-05-19 23:24:10,838 - INFO - Processed 83500000 reads so far
2011-05-19 23:24:19,999 - INFO - Processed 83600000 reads so far
2011-05-19 23:24:30,495 - INFO - Processed 83700000 reads so far
2011-05-19 23:24:40,268 - INFO - Processed 83800000 reads so far
2011-05-19 23:24:45,065 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:62990027-83010027
2011-05-19 23:24:50,105 - INFO - Processed 83900000 reads so far
2011-05-19 23:25:01,366 - INFO - Processed 84000000 reads so far
2011-05-19 23:25:10,698 - INFO - Processed 84100000 reads so far
2011-05-19 23:25:30,059 - INFO - Processed 84200000 reads so far
2011-05-19 23:25:43,312 - INFO - Processed 84300000 reads so far
2011-05-19 23:25:54,793 - INFO - Processed 84400000 reads so far
2011-05-19 23:26:06,715 - INFO - Processed 84500000 reads so far
2011-05-19 23:26:18,349 - INFO - Processed 84600000 reads so far
2011-05-19 23:26:29,089 - INFO - Processed 84700000 reads so far
2011-05-19 23:26:40,551 - INFO - Processed 84800000 reads so far
2011-05-19 23:26:40,552 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:82990043-103010043
2011-05-19 23:26:52,389 - INFO - Processed 84900000 reads so far
2011-05-19 23:27:03,938 - INFO - Processed 85000000 reads so far
2011-05-19 23:27:17,289 - INFO - Processed 85100000 reads so far
2011-05-19 23:27:29,070 - INFO - Processed 85200000 reads so far
2011-05-19 23:27:41,264 - INFO - Processed 85300000 reads so far
2011-05-19 23:27:54,177 - INFO - Processed 85400000 reads so far
2011-05-19 23:28:06,076 - INFO - Processed 85500000 reads so far
2011-05-19 23:28:17,570 - INFO - Processed 85600000 reads so far
2011-05-19 23:28:28,803 - INFO - Processed 85700000 reads so far
2011-05-19 23:28:40,389 - INFO - Processed 85800000 reads so far
2011-05-19 23:28:43,055 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:102990045-123010045
2011-05-19 23:28:52,071 - INFO - Processed 85900000 reads so far
2011-05-19 23:29:03,734 - INFO - Processed 86000000 reads so far
2011-05-19 23:29:15,992 - INFO - Processed 86100000 reads so far
2011-05-19 23:29:27,963 - INFO - Processed 86200000 reads so far
2011-05-19 23:29:39,948 - INFO - Processed 86300000 reads so far
2011-05-19 23:29:51,150 - INFO - Processed 86400000 reads so far
2011-05-19 23:30:03,625 - INFO - Processed 86500000 reads so far
2011-05-19 23:30:12,981 - INFO - Processed 86600000 reads so far
2011-05-19 23:30:23,439 - INFO - Processed 86700000 reads so far
2011-05-19 23:30:33,600 - INFO - Processed 86800000 reads so far
2011-05-19 23:30:33,873 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:122990055-143010055
2011-05-19 23:30:43,891 - INFO - Processed 86900000 reads so far
2011-05-19 23:30:52,498 - INFO - Processed 87000000 reads so far
2011-05-19 23:31:01,946 - INFO - Processed 87100000 reads so far
2011-05-19 23:31:13,208 - INFO - Processed 87200000 reads so far
2011-05-19 23:31:22,094 - INFO - Processed 87300000 reads so far
2011-05-19 23:31:35,309 - INFO - Processed 87400000 reads so far
2011-05-19 23:31:44,080 - INFO - Processed 87500000 reads so far
2011-05-19 23:31:57,424 - INFO - Processed 87600000 reads so far
2011-05-19 23:32:07,321 - INFO - Processed 87700000 reads so far
2011-05-19 23:32:16,231 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:142990111-163010111
2011-05-19 23:32:17,053 - INFO - Processed 87800000 reads so far
2011-05-19 23:32:28,577 - INFO - Processed 87900000 reads so far
2011-05-19 23:32:39,717 - INFO - Processed 88000000 reads so far
2011-05-19 23:32:50,123 - INFO - Processed 88100000 reads so far
2011-05-19 23:33:00,858 - INFO - Processed 88200000 reads so far
2011-05-19 23:33:10,677 - INFO - Processed 88300000 reads so far
2011-05-19 23:33:25,859 - INFO - Processed 88400000 reads so far
2011-05-19 23:33:37,529 - INFO - Processed 88500000 reads so far
2011-05-19 23:33:47,268 - INFO - Processed 88600000 reads so far
2011-05-19 23:33:50,715 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3_random:0-20010071
2011-05-19 23:33:50,853 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:2989979-23009979
2011-05-19 23:33:57,578 - INFO - Processed 88700000 reads so far
2011-05-19 23:34:10,715 - INFO - Processed 88800000 reads so far
2011-05-19 23:34:23,448 - INFO - Processed 88900000 reads so far
2011-05-19 23:34:32,572 - INFO - Processed 89000000 reads so far
2011-05-19 23:34:44,955 - INFO - Processed 89100000 reads so far
2011-05-19 23:34:54,828 - INFO - Processed 89200000 reads so far
2011-05-19 23:35:03,941 - INFO - Processed 89300000 reads so far
2011-05-19 23:35:13,463 - INFO - Processed 89400000 reads so far
2011-05-19 23:35:23,304 - INFO - Processed 89500000 reads so far
2011-05-19 23:35:33,133 - INFO - Processed 89600000 reads so far
2011-05-19 23:35:38,006 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:22989988-43009988
2011-05-19 23:35:43,824 - INFO - Processed 89700000 reads so far
2011-05-19 23:35:54,825 - INFO - Processed 89800000 reads so far
2011-05-19 23:36:05,492 - INFO - Processed 89900000 reads so far
2011-05-19 23:36:15,353 - INFO - Processed 90000000 reads so far
2011-05-19 23:36:25,482 - INFO - Processed 90100000 reads so far
2011-05-19 23:36:36,956 - INFO - Processed 90200000 reads so far
2011-05-19 23:36:49,200 - INFO - Processed 90300000 reads so far
2011-05-19 23:37:00,838 - INFO - Processed 90400000 reads so far
2011-05-19 23:37:12,717 - INFO - Processed 90500000 reads so far
2011-05-19 23:37:19,774 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:42990005-63010005
2011-05-19 23:37:24,010 - INFO - Processed 90600000 reads so far
2011-05-19 23:37:35,509 - INFO - Processed 90700000 reads so far
2011-05-19 23:37:48,033 - INFO - Processed 90800000 reads so far
2011-05-19 23:37:59,545 - INFO - Processed 90900000 reads so far
2011-05-19 23:38:15,173 - INFO - Processed 91000000 reads so far
2011-05-19 23:38:23,854 - INFO - Processed 91100000 reads so far
2011-05-19 23:38:32,891 - INFO - Processed 91200000 reads so far
2011-05-19 23:38:43,172 - INFO - Processed 91300000 reads so far
2011-05-19 23:39:08,343 - INFO - Processed 91400000 reads so far
2011-05-19 23:39:36,627 - INFO - Processed 91500000 reads so far
2011-05-19 23:39:48,005 - INFO - Processed 91600000 reads so far
2011-05-19 23:39:49,400 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:62990013-83010013
2011-05-19 23:39:58,107 - INFO - Processed 91700000 reads so far
2011-05-19 23:40:10,259 - INFO - Processed 91800000 reads so far
2011-05-19 23:40:20,723 - INFO - Processed 91900000 reads so far
2011-05-19 23:40:31,340 - INFO - Processed 92000000 reads so far
2011-05-19 23:40:44,093 - INFO - Processed 92100000 reads so far
2011-05-19 23:40:56,689 - INFO - Processed 92200000 reads so far
2011-05-19 23:41:09,868 - INFO - Processed 92300000 reads so far
2011-05-19 23:41:21,377 - INFO - Processed 92400000 reads so far
2011-05-19 23:41:32,306 - INFO - Processed 92500000 reads so far
2011-05-19 23:41:40,512 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:82990028-103010028
2011-05-19 23:41:43,424 - INFO - Processed 92600000 reads so far
2011-05-19 23:41:56,979 - INFO - Processed 92700000 reads so far
2011-05-19 23:42:07,921 - INFO - Processed 92800000 reads so far
2011-05-19 23:42:18,725 - INFO - Processed 92900000 reads so far
2011-05-19 23:42:30,494 - INFO - Processed 93000000 reads so far
2011-05-19 23:42:41,069 - INFO - Processed 93100000 reads so far
2011-05-19 23:42:50,933 - INFO - Processed 93200000 reads so far
2011-05-19 23:43:01,909 - INFO - Processed 93300000 reads so far
2011-05-19 23:43:13,913 - INFO - Processed 93400000 reads so far
2011-05-19 23:43:24,846 - INFO - Processed 93500000 reads so far
2011-05-19 23:43:36,028 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:102990039-123010039
2011-05-19 23:43:38,853 - INFO - Processed 93600000 reads so far
2011-05-19 23:43:48,113 - INFO - Processed 93700000 reads so far
2011-05-19 23:44:00,138 - INFO - Processed 93800000 reads so far
2011-05-19 23:44:09,502 - INFO - Processed 93900000 reads so far
2011-05-19 23:44:23,152 - INFO - Processed 94000000 reads so far
2011-05-19 23:44:35,458 - INFO - Processed 94100000 reads so far
2011-05-19 23:44:46,478 - INFO - Processed 94200000 reads so far
2011-05-19 23:44:58,342 - INFO - Processed 94300000 reads so far
2011-05-19 23:45:08,006 - INFO - Processed 94400000 reads so far
2011-05-19 23:45:17,314 - INFO - Processed 94500000 reads so far
2011-05-19 23:45:19,693 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:122990041-143010041
2011-05-19 23:45:28,225 - INFO - Processed 94600000 reads so far
2011-05-19 23:45:41,601 - INFO - Processed 94700000 reads so far
2011-05-19 23:45:53,651 - INFO - Processed 94800000 reads so far
2011-05-19 23:46:06,847 - INFO - Processed 94900000 reads so far
2011-05-19 23:46:18,521 - INFO - Processed 95000000 reads so far
2011-05-19 23:46:31,684 - INFO - Processed 95100000 reads so far
2011-05-19 23:46:45,967 - INFO - Processed 95200000 reads so far
2011-05-19 23:46:57,479 - INFO - Processed 95300000 reads so far
2011-05-19 23:47:11,019 - INFO - Processed 95400000 reads so far
2011-05-19 23:47:23,321 - INFO - Processed 95500000 reads so far
2011-05-19 23:47:31,930 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:142990078-163010078
2011-05-19 23:47:33,463 - INFO - Processed 95600000 reads so far
2011-05-19 23:47:43,726 - INFO - Processed 95700000 reads so far
2011-05-19 23:47:54,124 - INFO - Processed 95800000 reads so far
2011-05-19 23:48:04,388 - INFO - Processed 95900000 reads so far
2011-05-19 23:48:17,032 - INFO - Processed 96000000 reads so far
2011-05-19 23:48:49,542 - INFO - Processed 96100000 reads so far
2011-05-19 23:49:00,056 - INFO - Processed 96200000 reads so far
2011-05-19 23:49:11,473 - INFO - Processed 96300000 reads so far
2011-05-19 23:49:13,590 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4_random:0-20010103
2011-05-19 23:49:14,476 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:2990048-23010048
2011-05-19 23:49:24,564 - INFO - Processed 96400000 reads so far
2011-05-19 23:49:35,578 - INFO - Processed 96500000 reads so far
2011-05-19 23:49:45,541 - INFO - Processed 96600000 reads so far
2011-05-19 23:49:55,127 - INFO - Processed 96700000 reads so far
2011-05-19 23:50:07,746 - INFO - Processed 96800000 reads so far
2011-05-19 23:50:17,784 - INFO - Processed 96900000 reads so far
2011-05-19 23:50:28,058 - INFO - Processed 97000000 reads so far
2011-05-19 23:50:39,194 - INFO - Processed 97100000 reads so far
2011-05-19 23:50:49,298 - INFO - Processed 97200000 reads so far
2011-05-19 23:51:00,408 - INFO - Processed 97300000 reads so far
2011-05-19 23:51:02,784 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:22990544-43010544
2011-05-19 23:51:12,707 - INFO - Processed 97400000 reads so far
2011-05-19 23:51:25,561 - INFO - Processed 97500000 reads so far
2011-05-19 23:51:36,958 - INFO - Processed 97600000 reads so far
2011-05-19 23:51:49,773 - INFO - Processed 97700000 reads so far
2011-05-19 23:52:02,052 - INFO - Processed 97800000 reads so far
2011-05-19 23:52:16,289 - INFO - Processed 97900000 reads so far
2011-05-19 23:52:27,791 - INFO - Processed 98000000 reads so far
2011-05-19 23:52:38,020 - INFO - Processed 98100000 reads so far
2011-05-19 23:52:50,365 - INFO - Processed 98200000 reads so far
2011-05-19 23:53:00,928 - INFO - Processed 98300000 reads so far
2011-05-19 23:53:05,670 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:42991763-63011763
2011-05-19 23:53:10,934 - INFO - Processed 98400000 reads so far
2011-05-19 23:53:21,229 - INFO - Processed 98500000 reads so far
2011-05-19 23:53:32,317 - INFO - Processed 98600000 reads so far
2011-05-19 23:53:41,248 - INFO - Processed 98700000 reads so far
2011-05-19 23:53:53,797 - INFO - Processed 98800000 reads so far
2011-05-19 23:54:03,517 - INFO - Processed 98900000 reads so far
2011-05-19 23:54:13,030 - INFO - Processed 99000000 reads so far
2011-05-19 23:54:22,596 - INFO - Processed 99100000 reads so far
2011-05-19 23:54:33,174 - INFO - Processed 99200000 reads so far
2011-05-19 23:54:41,584 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:62991824-83011824
2011-05-19 23:54:42,640 - INFO - Processed 99300000 reads so far
2011-05-19 23:54:55,802 - INFO - Processed 99400000 reads so far
2011-05-19 23:55:07,646 - INFO - Processed 99500000 reads so far
2011-05-19 23:55:18,943 - INFO - Processed 99600000 reads so far
2011-05-19 23:55:42,517 - INFO - Processed 99700000 reads so far
2011-05-19 23:56:06,075 - INFO - Processed 99800000 reads so far
2011-05-19 23:56:18,047 - INFO - Processed 99900000 reads so far
2011-05-19 23:56:31,160 - INFO - Processed 100000000 reads so far
2011-05-19 23:56:43,259 - INFO - Processed 100100000 reads so far
2011-05-19 23:56:53,182 - INFO - Processed 100200000 reads so far
2011-05-19 23:56:59,749 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:82991872-103011872
2011-05-19 23:57:04,478 - INFO - Processed 100300000 reads so far
2011-05-19 23:57:14,979 - INFO - Processed 100400000 reads so far
2011-05-19 23:57:28,290 - INFO - Processed 100500000 reads so far
2011-05-19 23:57:39,278 - INFO - Processed 100600000 reads so far
2011-05-19 23:57:50,341 - INFO - Processed 100700000 reads so far
2011-05-19 23:58:01,897 - INFO - Processed 100800000 reads so far
2011-05-19 23:58:15,310 - INFO - Processed 100900000 reads so far
2011-05-19 23:58:27,328 - INFO - Processed 101000000 reads so far
2011-05-19 23:58:39,609 - INFO - Processed 101100000 reads so far
2011-05-19 23:58:51,143 - INFO - Processed 101200000 reads so far
2011-05-19 23:58:53,557 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:102991902-123011902
2011-05-19 23:59:03,352 - INFO - Processed 101300000 reads so far
2011-05-19 23:59:15,086 - INFO - Processed 101400000 reads so far
2011-05-19 23:59:26,897 - INFO - Processed 101500000 reads so far
2011-05-19 23:59:39,357 - INFO - Processed 101600000 reads so far
2011-05-19 23:59:52,955 - INFO - Processed 101700000 reads so far
2011-05-20 00:00:04,812 - INFO - Processed 101800000 reads so far
2011-05-20 00:00:15,774 - INFO - Processed 101900000 reads so far
2011-05-20 00:00:30,103 - INFO - Processed 102000000 reads so far
2011-05-20 00:00:41,241 - INFO - Processed 102100000 reads so far
2011-05-20 00:00:52,426 - INFO - Processed 102200000 reads so far
2011-05-20 00:01:04,365 - INFO - Processed 102300000 reads so far
2011-05-20 00:01:04,894 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:122991903-143011903
2011-05-20 00:01:16,210 - INFO - Processed 102400000 reads so far
2011-05-20 00:01:29,639 - INFO - Processed 102500000 reads so far
2011-05-20 00:01:42,443 - INFO - Processed 102600000 reads so far
2011-05-20 00:01:53,954 - INFO - Processed 102700000 reads so far
2011-05-20 00:02:03,436 - INFO - Processed 102800000 reads so far
2011-05-20 00:02:11,317 - INFO - Processed 102900000 reads so far
2011-05-20 00:02:23,122 - INFO - Processed 103000000 reads so far
2011-05-20 00:02:31,111 - INFO - Processed 103100000 reads so far
2011-05-20 00:02:39,247 - INFO - Processed 103200000 reads so far
2011-05-20 00:02:47,149 - INFO - Processed 103300000 reads so far
2011-05-20 00:02:52,206 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:142991982-163011982
2011-05-20 00:02:55,993 - INFO - Processed 103400000 reads so far
2011-05-20 00:03:04,058 - INFO - Processed 103500000 reads so far
2011-05-20 00:03:13,736 - INFO - Processed 103600000 reads so far
2011-05-20 00:03:22,943 - INFO - Processed 103700000 reads so far
2011-05-20 00:03:32,338 - INFO - Processed 103800000 reads so far
2011-05-20 00:03:44,497 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5_random:0-20010066
2011-05-20 00:03:45,012 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:2989994-23009994
2011-05-20 00:03:56,699 - INFO - Processed 103900000 reads so far
2011-05-20 00:04:22,113 - INFO - Processed 104000000 reads so far
2011-05-20 00:04:31,308 - INFO - Processed 104100000 reads so far
2011-05-20 00:04:42,591 - INFO - Processed 104200000 reads so far
2011-05-20 00:04:51,116 - INFO - Processed 104300000 reads so far
2011-05-20 00:05:00,245 - INFO - Processed 104400000 reads so far
2011-05-20 00:05:13,038 - INFO - Processed 104500000 reads so far
2011-05-20 00:05:22,431 - INFO - Processed 104600000 reads so far
2011-05-20 00:05:36,562 - INFO - Processed 104700000 reads so far
2011-05-20 00:05:46,089 - INFO - Processed 104800000 reads so far
2011-05-20 00:05:48,298 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:22990003-43010003
2011-05-20 00:05:56,103 - INFO - Processed 104900000 reads so far
2011-05-20 00:06:13,510 - INFO - Processed 105000000 reads so far
2011-05-20 00:06:22,670 - INFO - Processed 105100000 reads so far
2011-05-20 00:06:34,365 - INFO - Processed 105200000 reads so far
2011-05-20 00:06:44,050 - INFO - Processed 105300000 reads so far
2011-05-20 00:06:56,553 - INFO - Processed 105400000 reads so far
2011-05-20 00:07:06,236 - INFO - Processed 105500000 reads so far
2011-05-20 00:07:19,601 - INFO - Processed 105600000 reads so far
2011-05-20 00:07:28,700 - INFO - Processed 105700000 reads so far
2011-05-20 00:07:37,395 - INFO - Processed 105800000 reads so far
2011-05-20 00:07:39,252 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:42990017-63010017
2011-05-20 00:07:46,907 - INFO - Processed 105900000 reads so far
2011-05-20 00:08:00,173 - INFO - Processed 106000000 reads so far
2011-05-20 00:08:09,935 - INFO - Processed 106100000 reads so far
2011-05-20 00:08:21,805 - INFO - Processed 106200000 reads so far
2011-05-20 00:08:32,800 - INFO - Processed 106300000 reads so far
2011-05-20 00:08:41,036 - INFO - Processed 106400000 reads so far
2011-05-20 00:08:50,522 - INFO - Processed 106500000 reads so far
2011-05-20 00:09:04,118 - INFO - Processed 106600000 reads so far
2011-05-20 00:09:15,378 - INFO - Processed 106700000 reads so far
2011-05-20 00:09:25,038 - INFO - Processed 106800000 reads so far
2011-05-20 00:09:28,630 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:62990028-83010028
2011-05-20 00:09:34,452 - INFO - Processed 106900000 reads so far
2011-05-20 00:09:44,927 - INFO - Processed 107000000 reads so far
2011-05-20 00:09:54,122 - INFO - Processed 107100000 reads so far
2011-05-20 00:10:05,717 - INFO - Processed 107200000 reads so far
2011-05-20 00:10:15,797 - INFO - Processed 107300000 reads so far
2011-05-20 00:10:35,200 - INFO - Processed 107400000 reads so far
2011-05-20 00:11:04,759 - INFO - Processed 107500000 reads so far
2011-05-20 00:11:20,279 - INFO - Processed 107600000 reads so far
2011-05-20 00:11:31,355 - INFO - Processed 107700000 reads so far
2011-05-20 00:11:41,093 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:82990050-103010050
2011-05-20 00:11:41,968 - INFO - Processed 107800000 reads so far
2011-05-20 00:11:51,604 - INFO - Processed 107900000 reads so far
2011-05-20 00:12:08,246 - INFO - Processed 108000000 reads so far
2011-05-20 00:12:29,545 - INFO - Processed 108100000 reads so far
2011-05-20 00:12:38,854 - INFO - Processed 108200000 reads so far
2011-05-20 00:13:05,000 - INFO - Processed 108300000 reads so far
2011-05-20 00:13:15,565 - INFO - Processed 108400000 reads so far
2011-05-20 00:13:25,782 - INFO - Processed 108500000 reads so far
2011-05-20 00:13:37,682 - INFO - Processed 108600000 reads so far
2011-05-20 00:13:46,537 - INFO - Processed 108700000 reads so far
2011-05-20 00:13:56,243 - INFO - Processed 108800000 reads so far
2011-05-20 00:14:00,663 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:102990079-123010079
2011-05-20 00:14:05,034 - INFO - Processed 108900000 reads so far
2011-05-20 00:14:13,642 - INFO - Processed 109000000 reads so far
2011-05-20 00:14:25,364 - INFO - Processed 109100000 reads so far
2011-05-20 00:14:34,348 - INFO - Processed 109200000 reads so far
2011-05-20 00:14:41,513 - INFO - Processed 109300000 reads so far
2011-05-20 00:14:49,709 - INFO - Processed 109400000 reads so far
2011-05-20 00:15:12,793 - INFO - Processed 109500000 reads so far
2011-05-20 00:15:21,849 - INFO - Processed 109600000 reads so far
2011-05-20 00:15:31,340 - INFO - Processed 109700000 reads so far
2011-05-20 00:15:40,626 - INFO - Processed 109800000 reads so far
2011-05-20 00:15:51,722 - INFO - Processed 109900000 reads so far
2011-05-20 00:16:02,172 - INFO - Processed 110000000 reads so far
2011-05-20 00:16:13,811 - INFO - Processed 110100000 reads so far
2011-05-20 00:16:23,993 - INFO - Processed 110200000 reads so far
2011-05-20 00:16:36,645 - INFO - Processed 110300000 reads so far
2011-05-20 00:16:45,900 - INFO - Processed 110400000 reads so far
2011-05-20 00:16:55,192 - INFO - Processed 110500000 reads so far
2011-05-20 00:16:55,761 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:122990164-143010164
2011-05-20 00:17:04,538 - INFO - Processed 110600000 reads so far
2011-05-20 00:17:13,872 - INFO - Processed 110700000 reads so far
2011-05-20 00:17:23,164 - INFO - Processed 110800000 reads so far
2011-05-20 00:17:34,413 - INFO - Processed 110900000 reads so far
2011-05-20 00:17:45,307 - INFO - Processed 111000000 reads so far
2011-05-20 00:17:54,485 - INFO - Processed 111100000 reads so far
2011-05-20 00:18:03,614 - INFO - Processed 111200000 reads so far
2011-05-20 00:18:16,874 - INFO - Processed 111300000 reads so far
2011-05-20 00:18:27,385 - INFO - Processed 111400000 reads so far
2011-05-20 00:18:36,629 - INFO - Processed 111500000 reads so far
2011-05-20 00:18:40,262 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:142990174-163010174
2011-05-20 00:18:47,206 - INFO - Processed 111600000 reads so far
2011-05-20 00:18:57,287 - INFO - Processed 111700000 reads so far
2011-05-20 00:19:11,678 - INFO - Processed 111800000 reads so far
2011-05-20 00:19:21,915 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:2990007-23010007
2011-05-20 00:19:24,799 - INFO - Processed 111900000 reads so far
2011-05-20 00:19:34,954 - INFO - Processed 112000000 reads so far
2011-05-20 00:19:46,629 - INFO - Processed 112100000 reads so far
2011-05-20 00:19:58,253 - INFO - Processed 112200000 reads so far
2011-05-20 00:20:10,375 - INFO - Processed 112300000 reads so far
2011-05-20 00:20:21,078 - INFO - Processed 112400000 reads so far
2011-05-20 00:20:30,146 - INFO - Processed 112500000 reads so far
2011-05-20 00:20:40,817 - INFO - Processed 112600000 reads so far
2011-05-20 00:20:53,800 - INFO - Processed 112700000 reads so far
2011-05-20 00:21:01,271 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:22990097-43010097
2011-05-20 00:21:06,604 - INFO - Processed 112800000 reads so far
2011-05-20 00:21:18,328 - INFO - Processed 112900000 reads so far
2011-05-20 00:21:30,679 - INFO - Processed 113000000 reads so far
2011-05-20 00:21:42,556 - INFO - Processed 113100000 reads so far
2011-05-20 00:21:54,702 - INFO - Processed 113200000 reads so far
2011-05-20 00:22:06,645 - INFO - Processed 113300000 reads so far
2011-05-20 00:22:22,416 - INFO - Processed 113400000 reads so far
2011-05-20 00:22:33,912 - INFO - Processed 113500000 reads so far
2011-05-20 00:22:40,005 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:46352099-66372099
2011-05-20 00:22:43,698 - INFO - Processed 113600000 reads so far
2011-05-20 00:22:54,612 - INFO - Processed 113700000 reads so far
2011-05-20 00:23:06,315 - INFO - Processed 113800000 reads so far
2011-05-20 00:23:15,566 - INFO - Processed 113900000 reads so far
2011-05-20 00:23:31,247 - INFO - Processed 114000000 reads so far
2011-05-20 00:23:42,320 - INFO - Processed 114100000 reads so far
2011-05-20 00:23:51,854 - INFO - Processed 114200000 reads so far
2011-05-20 00:24:02,074 - INFO - Processed 114300000 reads so far
2011-05-20 00:24:12,569 - INFO - Processed 114400000 reads so far
2011-05-20 00:24:22,535 - INFO - Processed 114500000 reads so far
2011-05-20 00:24:29,125 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:66352102-86372102
2011-05-20 00:24:35,564 - INFO - Processed 114600000 reads so far
2011-05-20 00:24:44,496 - INFO - Processed 114700000 reads so far
2011-05-20 00:24:54,587 - INFO - Processed 114800000 reads so far
2011-05-20 00:25:03,838 - INFO - Processed 114900000 reads so far
2011-05-20 00:25:14,855 - INFO - Processed 115000000 reads so far
2011-05-20 00:25:23,288 - INFO - Processed 115100000 reads so far
2011-05-20 00:25:31,751 - INFO - Processed 115200000 reads so far
2011-05-20 00:25:40,102 - INFO - Processed 115300000 reads so far
2011-05-20 00:25:51,627 - INFO - Processed 115400000 reads so far
2011-05-20 00:26:04,064 - INFO - Processed 115500000 reads so far
2011-05-20 00:26:15,284 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:86352125-106372125
2011-05-20 00:26:17,220 - INFO - Processed 115600000 reads so far
2011-05-20 00:26:29,901 - INFO - Processed 115700000 reads so far
2011-05-20 00:26:41,500 - INFO - Processed 115800000 reads so far
2011-05-20 00:26:54,899 - INFO - Processed 115900000 reads so far
2011-05-20 00:27:06,651 - INFO - Processed 116000000 reads so far
2011-05-20 00:27:18,993 - INFO - Processed 116100000 reads so far
2011-05-20 00:27:31,768 - INFO - Processed 116200000 reads so far
2011-05-20 00:27:43,897 - INFO - Processed 116300000 reads so far
2011-05-20 00:28:13,450 - INFO - Processed 116400000 reads so far
2011-05-20 00:28:31,854 - INFO - Processed 116500000 reads so far
2011-05-20 00:28:43,515 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:106352197-126372197
2011-05-20 00:28:46,499 - INFO - Processed 116600000 reads so far
2011-05-20 00:29:01,536 - INFO - Processed 116700000 reads so far
2011-05-20 00:29:13,374 - INFO - Processed 116800000 reads so far
2011-05-20 00:29:24,815 - INFO - Processed 116900000 reads so far
2011-05-20 00:29:39,505 - INFO - Processed 117000000 reads so far
2011-05-20 00:29:52,011 - INFO - Processed 117100000 reads so far
2011-05-20 00:30:01,332 - INFO - Processed 117200000 reads so far
2011-05-20 00:30:14,358 - INFO - Processed 117300000 reads so far
2011-05-20 00:30:26,593 - INFO - Processed 117400000 reads so far
2011-05-20 00:30:38,125 - INFO - Processed 117500000 reads so far
2011-05-20 00:30:48,060 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:126352209-146372209
2011-05-20 00:30:49,206 - INFO - Processed 117600000 reads so far
2011-05-20 00:31:01,470 - INFO - Processed 117700000 reads so far
2011-05-20 00:31:10,184 - INFO - Processed 117800000 reads so far
2011-05-20 00:31:21,835 - INFO - Processed 117900000 reads so far
2011-05-20 00:31:34,549 - INFO - Processed 118000000 reads so far
2011-05-20 00:31:47,070 - INFO - Processed 118100000 reads so far
2011-05-20 00:31:58,014 - INFO - Processed 118200000 reads so far
2011-05-20 00:32:09,343 - INFO - Processed 118300000 reads so far
2011-05-20 00:32:22,522 - INFO - Processed 118400000 reads so far
2011-05-20 00:32:34,134 - INFO - Processed 118500000 reads so far
2011-05-20 00:32:46,997 - INFO - Processed 118600000 reads so far
2011-05-20 00:32:53,506 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:146352223-166372223
2011-05-20 00:32:56,752 - INFO - Processed 118700000 reads so far
2011-05-20 00:33:06,669 - INFO - Processed 118800000 reads so far
2011-05-20 00:33:17,188 - INFO - Processed 118900000 reads so far
2011-05-20 00:33:27,104 - INFO - Processed 119000000 reads so far
2011-05-20 00:33:28,302 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7_random:0-20010022
2011-05-20 00:33:29,389 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:2990052-23010052
2011-05-20 00:33:37,308 - INFO - Processed 119100000 reads so far
2011-05-20 00:33:47,829 - INFO - Processed 119200000 reads so far
2011-05-20 00:34:00,250 - INFO - Processed 119300000 reads so far
2011-05-20 00:34:10,911 - INFO - Processed 119400000 reads so far
2011-05-20 00:34:23,228 - INFO - Processed 119500000 reads so far
2011-05-20 00:34:35,770 - INFO - Processed 119600000 reads so far
2011-05-20 00:34:47,091 - INFO - Processed 119700000 reads so far
2011-05-20 00:34:56,504 - INFO - Processed 119800000 reads so far
2011-05-20 00:35:08,040 - INFO - Processed 119900000 reads so far
2011-05-20 00:35:16,443 - INFO - Processed 120000000 reads so far
2011-05-20 00:35:19,276 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:22990068-43010068
2011-05-20 00:35:26,138 - INFO - Processed 120100000 reads so far
2011-05-20 00:35:34,768 - INFO - Processed 120200000 reads so far
2011-05-20 00:35:43,652 - INFO - Processed 120300000 reads so far
2011-05-20 00:35:52,141 - INFO - Processed 120400000 reads so far
2011-05-20 00:36:02,729 - INFO - Processed 120500000 reads so far
2011-05-20 00:36:12,156 - INFO - Processed 120600000 reads so far
2011-05-20 00:36:24,251 - INFO - Processed 120700000 reads so far
2011-05-20 00:36:36,661 - INFO - Processed 120800000 reads so far
2011-05-20 00:36:46,716 - INFO - Processed 120900000 reads so far
2011-05-20 00:36:56,741 - INFO - Processed 121000000 reads so far
2011-05-20 00:36:59,750 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:42990077-63010077
2011-05-20 00:37:07,892 - INFO - Processed 121100000 reads so far
2011-05-20 00:37:17,526 - INFO - Processed 121200000 reads so far
2011-05-20 00:37:29,342 - INFO - Processed 121300000 reads so far
2011-05-20 00:37:40,291 - INFO - Processed 121400000 reads so far
2011-05-20 00:37:49,988 - INFO - Processed 121500000 reads so far
2011-05-20 00:38:00,948 - INFO - Processed 121600000 reads so far
2011-05-20 00:38:12,128 - INFO - Processed 121700000 reads so far
2011-05-20 00:38:22,763 - INFO - Processed 121800000 reads so far
2011-05-20 00:38:32,676 - INFO - Processed 121900000 reads so far
2011-05-20 00:38:32,695 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:62990137-83010137
2011-05-20 00:38:42,424 - INFO - Processed 122000000 reads so far
2011-05-20 00:38:55,009 - INFO - Processed 122100000 reads so far
2011-05-20 00:39:05,210 - INFO - Processed 122200000 reads so far
2011-05-20 00:39:15,906 - INFO - Processed 122300000 reads so far
2011-05-20 00:39:26,133 - INFO - Processed 122400000 reads so far
2011-05-20 00:39:37,421 - INFO - Processed 122500000 reads so far
2011-05-20 00:39:51,296 - INFO - Processed 122600000 reads so far
2011-05-20 00:40:01,452 - INFO - Processed 122700000 reads so far
2011-05-20 00:40:09,996 - INFO - Processed 122800000 reads so far
2011-05-20 00:40:19,463 - INFO - Processed 122900000 reads so far
2011-05-20 00:40:19,662 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:82990223-103010223
2011-05-20 00:40:29,365 - INFO - Processed 123000000 reads so far
2011-05-20 00:40:40,485 - INFO - Processed 123100000 reads so far
2011-05-20 00:40:52,171 - INFO - Processed 123200000 reads so far
2011-05-20 00:41:02,928 - INFO - Processed 123300000 reads so far
2011-05-20 00:41:14,478 - INFO - Processed 123400000 reads so far
2011-05-20 00:41:25,015 - INFO - Processed 123500000 reads so far
2011-05-20 00:41:39,020 - INFO - Processed 123600000 reads so far
2011-05-20 00:41:48,421 - INFO - Processed 123700000 reads so far
2011-05-20 00:41:58,614 - INFO - Processed 123800000 reads so far
2011-05-20 00:42:09,493 - INFO - Processed 123900000 reads so far
2011-05-20 00:42:11,536 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:102990268-123010268
2011-05-20 00:42:22,366 - INFO - Processed 124000000 reads so far
2011-05-20 00:42:33,903 - INFO - Processed 124100000 reads so far
2011-05-20 00:42:45,815 - INFO - Processed 124200000 reads so far
2011-05-20 00:43:00,242 - INFO - Processed 124300000 reads so far
2011-05-20 00:43:09,680 - INFO - Processed 124400000 reads so far
2011-05-20 00:43:19,056 - INFO - Processed 124500000 reads so far
2011-05-20 00:43:29,824 - INFO - Processed 124600000 reads so far
2011-05-20 00:43:39,987 - INFO - Processed 124700000 reads so far
2011-05-20 00:43:50,638 - INFO - Processed 124800000 reads so far
2011-05-20 00:44:00,984 - INFO - Processed 124900000 reads so far
2011-05-20 00:44:04,854 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:122990277-143010277
2011-05-20 00:44:09,206 - INFO - Processed 125000000 reads so far
2011-05-20 00:44:19,477 - INFO - Processed 125100000 reads so far
2011-05-20 00:44:30,624 - INFO - Processed 125200000 reads so far
2011-05-20 00:44:41,082 - INFO - Processed 125300000 reads so far
2011-05-20 00:44:50,445 - INFO - Processed 125400000 reads so far
2011-05-20 00:44:55,272 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8_random:0-20010032
2011-05-20 00:44:59,562 - INFO - Processed 125500000 reads so far
2011-05-20 00:45:01,319 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:2989934-23009934
2011-05-20 00:45:11,331 - INFO - Processed 125600000 reads so far
2011-05-20 00:45:19,155 - INFO - Processed 125700000 reads so far
2011-05-20 00:45:27,666 - INFO - Processed 125800000 reads so far
2011-05-20 00:45:35,322 - INFO - Processed 125900000 reads so far
2011-05-20 00:45:42,953 - INFO - Processed 126000000 reads so far
2011-05-20 00:45:49,312 - INFO - Processed 126100000 reads so far
2011-05-20 00:45:56,379 - INFO - Processed 126200000 reads so far
2011-05-20 00:46:02,521 - INFO - Processed 126300000 reads so far
2011-05-20 00:46:09,683 - INFO - Processed 126400000 reads so far
2011-05-20 00:46:18,928 - INFO - Processed 126500000 reads so far
2011-05-20 00:46:26,119 - INFO - Processed 126600000 reads so far
2011-05-20 00:46:33,976 - INFO - Processed 126700000 reads so far
2011-05-20 00:46:40,928 - INFO - Processed 126800000 reads so far
2011-05-20 00:46:48,010 - INFO - Processed 126900000 reads so far
2011-05-20 00:46:55,117 - INFO - Processed 127000000 reads so far
2011-05-20 00:47:01,468 - INFO - Processed 127100000 reads so far
2011-05-20 00:47:09,104 - INFO - Processed 127200000 reads so far
2011-05-20 00:47:15,497 - INFO - Processed 127300000 reads so far
2011-05-20 00:47:21,340 - INFO - Processed 127400000 reads so far
2011-05-20 00:47:27,973 - INFO - Processed 127500000 reads so far
2011-05-20 00:47:35,120 - INFO - Processed 127600000 reads so far
2011-05-20 00:47:43,789 - INFO - Processed 127700000 reads so far
2011-05-20 00:47:52,173 - INFO - Processed 127800000 reads so far
2011-05-20 00:47:59,805 - INFO - Processed 127900000 reads so far
2011-05-20 00:48:08,248 - INFO - Processed 128000000 reads so far
2011-05-20 00:48:16,364 - INFO - Processed 128100000 reads so far
2011-05-20 00:48:25,245 - INFO - Processed 128200000 reads so far
2011-05-20 00:48:34,332 - INFO - Processed 128300000 reads so far
2011-05-20 00:48:43,376 - INFO - Processed 128400000 reads so far
2011-05-20 00:48:51,827 - INFO - Processed 128500000 reads so far
2011-05-20 00:49:00,409 - INFO - Processed 128600000 reads so far
2011-05-20 00:49:10,019 - INFO - Processed 128700000 reads so far
2011-05-20 00:49:22,293 - INFO - Processed 128800000 reads so far
2011-05-20 00:49:30,572 - INFO - Processed 128900000 reads so far
2011-05-20 00:49:37,751 - INFO - Processed 129000000 reads so far
2011-05-20 00:49:46,223 - INFO - Processed 129100000 reads so far
2011-05-20 00:49:54,588 - INFO - Processed 129200000 reads so far
2011-05-20 00:50:01,751 - INFO - Processed 129300000 reads so far
2011-05-20 00:50:14,620 - INFO - Processed 129400000 reads so far
2011-05-20 00:50:23,876 - INFO - Processed 129500000 reads so far
2011-05-20 00:50:34,122 - INFO - Processed 129600000 reads so far
2011-05-20 00:50:42,040 - INFO - Processed 129700000 reads so far
2011-05-20 00:50:49,351 - INFO - Processed 129800000 reads so far
2011-05-20 00:50:55,386 - INFO - Processed 129900000 reads so far
2011-05-20 00:51:02,455 - INFO - Processed 130000000 reads so far
2011-05-20 00:51:08,131 - INFO - Processed 130100000 reads so far
2011-05-20 00:51:17,364 - INFO - Processed 130200000 reads so far
2011-05-20 00:51:27,194 - INFO - Processed 130300000 reads so far
2011-05-20 00:51:38,080 - INFO - Processed 130400000 reads so far
2011-05-20 00:51:49,202 - INFO - Processed 130500000 reads so far
2011-05-20 00:51:58,680 - INFO - Processed 130600000 reads so far
2011-05-20 00:52:08,868 - INFO - Processed 130700000 reads so far
2011-05-20 00:52:20,576 - INFO - Processed 130800000 reads so far
2011-05-20 00:52:29,180 - INFO - Processed 130900000 reads so far
2011-05-20 00:52:36,452 - INFO - Processed 131000000 reads so far
2011-05-20 00:52:46,990 - INFO - Processed 131100000 reads so far
2011-05-20 00:52:55,491 - INFO - Processed 131200000 reads so far
2011-05-20 00:53:04,081 - INFO - Processed 131300000 reads so far
2011-05-20 00:53:11,995 - INFO - Processed 131400000 reads so far
2011-05-20 00:53:22,047 - INFO - Processed 131500000 reads so far
2011-05-20 00:53:29,519 - INFO - Processed 131600000 reads so far
2011-05-20 00:53:40,734 - INFO - Processed 131700000 reads so far
2011-05-20 00:53:48,124 - INFO - Processed 131800000 reads so far
2011-05-20 00:53:56,184 - INFO - Processed 131900000 reads so far
2011-05-20 00:54:03,663 - INFO - Processed 132000000 reads so far
2011-05-20 00:54:14,828 - INFO - Processed 132100000 reads so far
2011-05-20 00:54:22,627 - INFO - Processed 132200000 reads so far
2011-05-20 00:54:30,834 - INFO - Processed 132300000 reads so far
2011-05-20 00:54:42,000 - INFO - Processed 132400000 reads so far
2011-05-20 00:54:51,494 - INFO - Processed 132500000 reads so far
2011-05-20 00:55:01,145 - INFO - Processed 132600000 reads so far
2011-05-20 00:55:11,635 - INFO - Processed 132700000 reads so far
2011-05-20 00:55:22,902 - INFO - Processed 132800000 reads so far
2011-05-20 00:55:33,744 - INFO - Processed 132900000 reads so far
2011-05-20 00:55:44,967 - INFO - Processed 133000000 reads so far
2011-05-20 00:55:55,124 - INFO - Processed 133100000 reads so far
2011-05-20 00:56:08,871 - INFO - Processed 133200000 reads so far
2011-05-20 00:56:20,729 - INFO - Processed 133300000 reads so far
2011-05-20 00:56:21,220 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:22989936-43009936
2011-05-20 00:56:33,612 - INFO - Processed 133400000 reads so far
2011-05-20 00:56:45,083 - INFO - Processed 133500000 reads so far
2011-05-20 00:56:56,318 - INFO - Processed 133600000 reads so far
2011-05-20 00:57:08,464 - INFO - Processed 133700000 reads so far
2011-05-20 00:57:18,724 - INFO - Processed 133800000 reads so far
2011-05-20 00:57:29,805 - INFO - Processed 133900000 reads so far
2011-05-20 00:57:38,735 - INFO - Processed 134000000 reads so far
2011-05-20 00:57:47,377 - INFO - Processed 134100000 reads so far
2011-05-20 00:57:57,432 - INFO - Processed 134200000 reads so far
2011-05-20 00:58:10,999 - INFO - Processed 134300000 reads so far
2011-05-20 00:58:22,171 - INFO - Processed 134400000 reads so far
2011-05-20 00:58:32,853 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:42989944-63009944
2011-05-20 00:58:34,875 - INFO - Processed 134500000 reads so far
2011-05-20 00:58:46,807 - INFO - Processed 134600000 reads so far
2011-05-20 00:58:58,604 - INFO - Processed 134700000 reads so far
2011-05-20 00:59:12,776 - INFO - Processed 134800000 reads so far
2011-05-20 00:59:22,738 - INFO - Processed 134900000 reads so far
2011-05-20 00:59:32,315 - INFO - Processed 135000000 reads so far
2011-05-20 00:59:41,656 - INFO - Processed 135100000 reads so far
2011-05-20 00:59:53,907 - INFO - Processed 135200000 reads so far
2011-05-20 01:00:05,868 - INFO - Processed 135300000 reads so far
2011-05-20 01:00:18,264 - INFO - Processed 135400000 reads so far
2011-05-20 01:00:29,362 - INFO - Processed 135500000 reads so far
2011-05-20 01:00:35,432 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:62989979-83009979
2011-05-20 01:00:40,805 - INFO - Processed 135600000 reads so far
2011-05-20 01:00:53,780 - INFO - Processed 135700000 reads so far
2011-05-20 01:01:02,287 - INFO - Processed 135800000 reads so far
2011-05-20 01:01:12,274 - INFO - Processed 135900000 reads so far
2011-05-20 01:01:27,596 - INFO - Processed 136000000 reads so far
2011-05-20 01:01:39,520 - INFO - Processed 136100000 reads so far
2011-05-20 01:01:49,395 - INFO - Processed 136200000 reads so far
2011-05-20 01:01:58,634 - INFO - Processed 136300000 reads so far
2011-05-20 01:02:10,251 - INFO - Processed 136400000 reads so far
2011-05-20 01:02:19,439 - INFO - Processed 136500000 reads so far
2011-05-20 01:02:26,557 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:82989995-103009995
2011-05-20 01:02:30,069 - INFO - Processed 136600000 reads so far
2011-05-20 01:02:47,658 - INFO - Processed 136700000 reads so far
2011-05-20 01:02:59,262 - INFO - Processed 136800000 reads so far
2011-05-20 01:03:11,025 - INFO - Processed 136900000 reads so far
2011-05-20 01:03:23,651 - INFO - Processed 137000000 reads so far
2011-05-20 01:03:35,239 - INFO - Processed 137100000 reads so far
2011-05-20 01:03:46,798 - INFO - Processed 137200000 reads so far
2011-05-20 01:03:59,901 - INFO - Processed 137300000 reads so far
2011-05-20 01:04:11,657 - INFO - Processed 137400000 reads so far
2011-05-20 01:04:23,201 - INFO - Processed 137500000 reads so far
2011-05-20 01:04:31,177 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:102990015-123010015
2011-05-20 01:04:35,073 - INFO - Processed 137600000 reads so far
2011-05-20 01:04:48,326 - INFO - Processed 137700000 reads so far
2011-05-20 01:04:58,077 - INFO - Processed 137800000 reads so far
2011-05-20 01:05:13,004 - INFO - Processed 137900000 reads so far
2011-05-20 01:05:25,620 - INFO - Processed 138000000 reads so far
2011-05-20 01:05:38,449 - INFO - Processed 138100000 reads so far
2011-05-20 01:05:48,993 - INFO - Processed 138200000 reads so far
2011-05-20 01:06:00,910 - INFO - Processed 138300000 reads so far
2011-05-20 01:06:12,455 - INFO - Processed 138400000 reads so far
2011-05-20 01:06:25,583 - INFO - Processed 138500000 reads so far
2011-05-20 01:06:38,471 - INFO - Processed 138600000 reads so far
2011-05-20 01:06:43,602 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:122990027-143010027
2011-05-20 01:06:49,856 - INFO - Processed 138700000 reads so far
2011-05-20 01:06:51,113 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9_random:0-20010005
2011-05-20 01:06:54,857 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrM:0-20010000
2011-05-20 01:07:00,997 - INFO - Processed 138800000 reads so far
2011-05-20 01:07:01,692 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrUn_random:0-20010221
2011-05-20 01:07:11,881 - INFO - Processed 138900000 reads so far
2011-05-20 01:07:21,759 - INFO - Processed 139000000 reads so far
2011-05-20 01:07:30,735 - INFO - Processed 139100000 reads so far
2011-05-20 01:07:38,244 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:2990205-23010205
2011-05-20 01:07:39,838 - INFO - Processed 139200000 reads so far
2011-05-20 01:07:51,356 - INFO - Processed 139300000 reads so far
2011-05-20 01:08:03,210 - INFO - Processed 139400000 reads so far
2011-05-20 01:08:14,178 - INFO - Processed 139500000 reads so far
2011-05-20 01:08:26,393 - INFO - Processed 139600000 reads so far
2011-05-20 01:08:38,280 - INFO - Processed 139700000 reads so far
2011-05-20 01:08:41,152 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:22990209-43010209
2011-05-20 01:08:48,104 - INFO - Processed 139800000 reads so far
2011-05-20 01:09:00,460 - INFO - Processed 139900000 reads so far
2011-05-20 01:09:10,613 - INFO - Processed 140000000 reads so far
2011-05-20 01:09:20,906 - INFO - Processed 140100000 reads so far
2011-05-20 01:09:33,550 - INFO - Processed 140200000 reads so far
2011-05-20 01:09:36,712 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:42990283-63010283
2011-05-20 01:09:45,353 - INFO - Processed 140300000 reads so far
2011-05-20 01:10:36,220 - INFO - Processed 140400000 reads so far
2011-05-20 01:11:31,394 - INFO - Processed 140500000 reads so far
2011-05-20 01:12:34,657 - INFO - Processed 140600000 reads so far
2011-05-20 01:13:06,520 - INFO - Processed 140700000 reads so far
2011-05-20 01:13:12,434 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:62990301-83010301
2011-05-20 01:13:24,522 - INFO - Processed 140800000 reads so far
2011-05-20 01:13:37,619 - INFO - Processed 140900000 reads so far
2011-05-20 01:13:54,968 - INFO - Processed 141000000 reads so far
2011-05-20 01:14:08,288 - INFO - Processed 141100000 reads so far
2011-05-20 01:14:22,522 - INFO - Processed 141200000 reads so far
2011-05-20 01:14:28,015 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:82990306-103010306
2011-05-20 01:14:35,691 - INFO - Processed 141300000 reads so far
2011-05-20 01:14:48,289 - INFO - Processed 141400000 reads so far
2011-05-20 01:15:00,693 - INFO - Processed 141500000 reads so far
2011-05-20 01:15:12,893 - INFO - Processed 141600000 reads so far
2011-05-20 01:15:24,986 - INFO - Processed 141700000 reads so far
2011-05-20 01:15:27,867 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:102990330-123010330
2011-05-20 01:15:37,241 - INFO - Processed 141800000 reads so far
2011-05-20 01:15:47,033 - INFO - Processed 141900000 reads so far
2011-05-20 01:15:56,438 - INFO - Processed 142000000 reads so far
2011-05-20 01:16:08,321 - INFO - Processed 142100000 reads so far
2011-05-20 01:16:17,510 - INFO - Processed 142200000 reads so far
2011-05-20 01:16:28,620 - INFO - Processed 142300000 reads so far
2011-05-20 01:16:34,036 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:122990391-143010391
2011-05-20 01:16:43,337 - INFO - Processed 142400000 reads so far
2011-05-20 01:16:52,399 - INFO - Processed 142500000 reads so far
2011-05-20 01:17:05,207 - INFO - Processed 142600000 reads so far
2011-05-20 01:17:18,823 - INFO - Processed 142700000 reads so far
2011-05-20 01:17:28,365 - INFO - Processed 142800000 reads so far
2011-05-20 01:17:34,684 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:142990407-163010407
2011-05-20 01:17:38,765 - INFO - Processed 142900000 reads so far
2011-05-20 01:17:53,405 - INFO - Processed 143000000 reads so far
2011-05-20 01:18:07,589 - INFO - Processed 143100000 reads so far
2011-05-20 01:18:17,813 - INFO - Processed 143200000 reads so far
2011-05-20 01:18:30,704 - INFO - Processed 143300000 reads so far
2011-05-20 01:18:36,869 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:162990424-183010424
2011-05-20 01:18:44,151 - INFO - Processed 143400000 reads so far
2011-05-20 01:18:52,520 - INFO - Processed 143500000 reads so far
2011-05-20 01:18:56,909 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX_random:0-20010000
2011-05-20 01:19:00,255 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY:0-20010000
2011-05-20 01:19:02,392 - INFO - Processed 143600000 reads so far
2011-05-20 01:19:08,308 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:0-20010327
2011-05-20 01:19:12,624 - INFO - Processed 143700000 reads so far
2011-05-20 01:19:26,031 - INFO - Processed 143800000 reads so far
2011-05-20 01:19:37,286 - INFO - Processed 143900000 reads so far
2011-05-20 01:19:48,408 - INFO - Processed 144000000 reads so far
2011-05-20 01:20:05,706 - INFO - Processed 144100000 reads so far
2011-05-20 01:20:13,933 - INFO - Processed 144200000 reads so far
2011-05-20 01:20:25,390 - INFO - Processed 144300000 reads so far
2011-05-20 01:20:32,865 - INFO - Processed 144400000 reads so far
2011-05-20 01:20:36,221 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:19990333-40010333
2011-05-20 01:20:43,618 - INFO - Processed 144500000 reads so far
2011-05-20 01:20:54,194 - INFO - Processed 144600000 reads so far
2011-05-20 01:21:05,610 - INFO - Processed 144700000 reads so far
2011-05-20 01:21:17,764 - INFO - Processed 144800000 reads so far
2011-05-20 01:21:22,889 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:39990355-60010355
2011-05-20 01:21:29,470 - INFO - Processed 144900000 reads so far
2011-05-20 01:21:41,665 - INFO - Processed 145000000 reads so far
2011-05-20 01:21:52,159 - INFO - Processed 145100000 reads so far
2011-05-20 01:22:02,876 - INFO - Processed 145200000 reads so far
2011-05-20 01:22:13,962 - INFO - Processed 145300000 reads so far
2011-05-20 01:22:24,114 - INFO - Processed 145400000 reads so far
2011-05-20 01:22:30,680 - INFO - Processed 145500000 reads so far
2011-05-20 01:22:34,996 - INFO - Processed 145600000 reads so far
2011-05-20 01:22:39,263 - INFO - Processed 145700000 reads so far
2011-05-20 01:22:43,523 - INFO - Processed 145800000 reads so far
2011-05-20 01:22:49,226 - INFO - Processed 145900000 reads so far
2011-05-20 01:22:53,137 - INFO - Processed 146000000 reads so far
2011-05-20 01:22:56,390 - INFO - Processed 146100000 reads so far
2011-05-20 01:23:00,406 - INFO - Processed 146200000 reads so far
2011-05-20 01:23:05,365 - INFO - Processed 146300000 reads so far
2011-05-20 01:23:08,946 - INFO - Processed 146400000 reads so far
2011-05-20 01:23:13,785 - INFO - Processed 146500000 reads so far
2011-05-20 01:23:18,073 - INFO - Processed 146600000 reads so far
2011-05-20 01:23:25,039 - INFO - Processed 146700000 reads so far
2011-05-20 01:23:29,024 - INFO - Processed 146800000 reads so far
2011-05-20 01:23:33,714 - INFO - Processed 146900000 reads so far
2011-05-20 01:23:37,983 - INFO - Processed 147000000 reads so far
2011-05-20 01:23:42,256 - INFO - Processed 147100000 reads so far
2011-05-20 01:23:46,432 - INFO - Processed 147200000 reads so far
2011-05-20 01:23:52,419 - INFO - Processed 147300000 reads so far
2011-05-20 01:23:57,914 - INFO - Processed 147400000 reads so far
2011-05-20 01:24:02,524 - INFO - Processed 147500000 reads so far
2011-05-20 01:24:04,590 - INFO - Finished loading data. Outputting QC metrics
2011-05-20 01:24:30,568 - INFO - Finished outputting QC metrics
2011-05-20 01:24:30,673 - INFO - Finished generating QC metrics