2011-05-19 15:51:43,216 - INFO - Generating QC metrics for BAM File ['WTCHG_13229.bam']
2011-05-19 15:51:43,216 - INFO - Output will go to WTCHG_13229.qc.txt.tmp
2011-05-19 15:51:43,216 - INFO - Reading GC Map from file /data/Genomes/gcMap/Mouse37.gcMap.gz
2011-05-19 15:54:53,323 - INFO - Finished reading GC Map
2011-05-19 15:54:53,324 - INFO - Reading CDS from exon definition file /data/Genomes/annotation/Mouse37.refGene.txt.gz
2011-05-19 15:54:56,012 - INFO - Read 382138 exons (33804740 nucleotides) for 32 chromosomes
2011-05-19 15:54:56,013 - INFO - Computing coverage cut-off
2011-05-19 15:54:56,013 - INFO - Retrieving BAM file coverage info from samtools pileup
2011-05-19 15:55:01,026 - INFO - Processed 1000000 pile-up sites
2011-05-19 15:55:05,752 - INFO - Processed 2000000 pile-up sites
2011-05-19 15:55:10,358 - INFO - Processed 3000000 pile-up sites
2011-05-19 15:55:14,907 - INFO - Processed 4000000 pile-up sites
2011-05-19 15:55:19,156 - INFO - Processed 5000000 pile-up sites
2011-05-19 15:55:24,164 - INFO - Processed 6000000 pile-up sites
2011-05-19 15:55:29,177 - INFO - Processed 7000000 pile-up sites
2011-05-19 15:55:33,795 - INFO - Processed 8000000 pile-up sites
2011-05-19 15:55:38,698 - INFO - Processed 9000000 pile-up sites
2011-05-19 15:55:42,406 - INFO - Processed 10000000 pile-up sites
2011-05-19 15:55:47,029 - INFO - Processed 11000000 pile-up sites
2011-05-19 15:55:51,328 - INFO - Processed 12000000 pile-up sites
2011-05-19 15:55:57,516 - INFO - Processed 13000000 pile-up sites
2011-05-19 15:56:02,162 - INFO - Processed 14000000 pile-up sites
2011-05-19 15:56:08,274 - INFO - Processed 15000000 pile-up sites
2011-05-19 15:56:15,461 - INFO - Processed 16000000 pile-up sites
2011-05-19 15:56:22,313 - INFO - Processed 17000000 pile-up sites
2011-05-19 15:56:26,937 - INFO - Processed 18000000 pile-up sites
2011-05-19 15:56:33,109 - INFO - Processed 19000000 pile-up sites
2011-05-19 15:56:37,966 - INFO - Processed 20000000 pile-up sites
2011-05-19 15:56:42,799 - INFO - Processed 21000000 pile-up sites
2011-05-19 15:56:50,247 - INFO - Processed 22000000 pile-up sites
2011-05-19 15:56:54,942 - INFO - Processed 23000000 pile-up sites
2011-05-19 15:56:59,615 - INFO - Processed 24000000 pile-up sites
2011-05-19 15:57:04,301 - INFO - Processed 25000000 pile-up sites
2011-05-19 15:57:08,920 - INFO - Processed 26000000 pile-up sites
2011-05-19 15:57:13,385 - INFO - Processed 27000000 pile-up sites
2011-05-19 15:57:17,504 - INFO - Processed 28000000 pile-up sites
2011-05-19 15:57:21,092 - INFO - Processed 29000000 pile-up sites
2011-05-19 15:57:25,498 - INFO - Processed 30000000 pile-up sites
2011-05-19 15:57:29,803 - INFO - Processed 31000000 pile-up sites
2011-05-19 15:57:34,351 - INFO - Processed 32000000 pile-up sites
2011-05-19 15:57:38,033 - INFO - Processed 33000000 pile-up sites
2011-05-19 15:57:41,753 - INFO - Processed 34000000 pile-up sites
2011-05-19 15:57:45,769 - INFO - Processed 35000000 pile-up sites
2011-05-19 15:57:49,842 - INFO - Processed 36000000 pile-up sites
2011-05-19 15:57:54,720 - INFO - Processed 37000000 pile-up sites
2011-05-19 15:57:55,684 - INFO - Finished processing pile-up on 37211600 sites (200000000 nucleotides)
2011-05-19 15:57:55,685 - INFO - Coverage cut-off value is 21
2011-05-19 15:57:55,685 - INFO - Loading data into QC data manager
2011-05-19 15:57:55,905 - INFO - Reading data from BAM file WTCHG_13229.bam. All reads in file will be read
2011-05-19 15:57:55,946 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:2990003-23010003
2011-05-19 15:58:06,745 - INFO - Processed 100000 reads so far
2011-05-19 15:58:18,420 - INFO - Processed 200000 reads so far
2011-05-19 15:58:29,873 - INFO - Processed 300000 reads so far
2011-05-19 15:58:41,284 - INFO - Processed 400000 reads so far
2011-05-19 15:58:51,758 - INFO - Processed 500000 reads so far
2011-05-19 15:59:02,331 - INFO - Processed 600000 reads so far
2011-05-19 15:59:14,303 - INFO - Processed 700000 reads so far
2011-05-19 15:59:25,883 - INFO - Processed 800000 reads so far
2011-05-19 15:59:37,828 - INFO - Processed 900000 reads so far
2011-05-19 15:59:49,437 - INFO - Processed 1000000 reads so far
2011-05-19 15:59:56,997 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:22990013-43010013
2011-05-19 16:00:02,180 - INFO - Processed 1100000 reads so far
2011-05-19 16:00:14,399 - INFO - Processed 1200000 reads so far
2011-05-19 16:00:28,657 - INFO - Processed 1300000 reads so far
2011-05-19 16:00:40,180 - INFO - Processed 1400000 reads so far
2011-05-19 16:00:52,653 - INFO - Processed 1500000 reads so far
2011-05-19 16:01:06,639 - INFO - Processed 1600000 reads so far
2011-05-19 16:01:17,735 - INFO - Processed 1700000 reads so far
2011-05-19 16:01:31,360 - INFO - Processed 1800000 reads so far
2011-05-19 16:01:43,693 - INFO - Processed 1900000 reads so far
2011-05-19 16:01:55,702 - INFO - Processed 2000000 reads so far
2011-05-19 16:02:07,374 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:42990078-63010078
2011-05-19 16:02:07,863 - INFO - Processed 2100000 reads so far
2011-05-19 16:02:19,710 - INFO - Processed 2200000 reads so far
2011-05-19 16:02:31,762 - INFO - Processed 2300000 reads so far
2011-05-19 16:02:43,726 - INFO - Processed 2400000 reads so far
2011-05-19 16:02:55,128 - INFO - Processed 2500000 reads so far
2011-05-19 16:03:07,797 - INFO - Processed 2600000 reads so far
2011-05-19 16:03:19,150 - INFO - Processed 2700000 reads so far
2011-05-19 16:03:33,011 - INFO - Processed 2800000 reads so far
2011-05-19 16:03:43,391 - INFO - Processed 2900000 reads so far
2011-05-19 16:03:56,383 - INFO - Processed 3000000 reads so far
2011-05-19 16:04:09,965 - INFO - Processed 3100000 reads so far
2011-05-19 16:04:11,058 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:62990101-83010101
2011-05-19 16:04:21,820 - INFO - Processed 3200000 reads so far
2011-05-19 16:04:33,966 - INFO - Processed 3300000 reads so far
2011-05-19 16:04:45,361 - INFO - Processed 3400000 reads so far
2011-05-19 16:04:57,762 - INFO - Processed 3500000 reads so far
2011-05-19 16:05:09,477 - INFO - Processed 3600000 reads so far
2011-05-19 16:05:22,515 - INFO - Processed 3700000 reads so far
2011-05-19 16:05:34,209 - INFO - Processed 3800000 reads so far
2011-05-19 16:05:49,747 - INFO - Processed 3900000 reads so far
2011-05-19 16:06:01,682 - INFO - Processed 4000000 reads so far
2011-05-19 16:06:13,236 - INFO - Processed 4100000 reads so far
2011-05-19 16:06:15,818 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:82990114-103010114
2011-05-19 16:06:24,453 - INFO - Processed 4200000 reads so far
2011-05-19 16:06:36,998 - INFO - Processed 4300000 reads so far
2011-05-19 16:06:48,642 - INFO - Processed 4400000 reads so far
2011-05-19 16:06:58,466 - INFO - Processed 4500000 reads so far
2011-05-19 16:07:07,628 - INFO - Processed 4600000 reads so far
2011-05-19 16:07:17,513 - INFO - Processed 4700000 reads so far
2011-05-19 16:07:28,867 - INFO - Processed 4800000 reads so far
2011-05-19 16:07:40,024 - INFO - Processed 4900000 reads so far
2011-05-19 16:07:51,254 - INFO - Processed 5000000 reads so far
2011-05-19 16:08:04,539 - INFO - Processed 5100000 reads so far
2011-05-19 16:08:13,535 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:102990153-123010153
2011-05-19 16:08:16,776 - INFO - Processed 5200000 reads so far
2011-05-19 16:08:31,688 - INFO - Processed 5300000 reads so far
2011-05-19 16:09:05,074 - INFO - Processed 5400000 reads so far
2011-05-19 16:09:16,848 - INFO - Processed 5500000 reads so far
2011-05-19 16:09:29,040 - INFO - Processed 5600000 reads so far
2011-05-19 16:09:40,633 - INFO - Processed 5700000 reads so far
2011-05-19 16:09:52,613 - INFO - Processed 5800000 reads so far
2011-05-19 16:10:04,433 - INFO - Processed 5900000 reads so far
2011-05-19 16:10:16,372 - INFO - Processed 6000000 reads so far
2011-05-19 16:10:27,830 - INFO - Processed 6100000 reads so far
2011-05-19 16:10:39,158 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:122990192-143010192
2011-05-19 16:10:40,178 - INFO - Processed 6200000 reads so far
2011-05-19 16:10:52,872 - INFO - Processed 6300000 reads so far
2011-05-19 16:11:05,077 - INFO - Processed 6400000 reads so far
2011-05-19 16:11:17,808 - INFO - Processed 6500000 reads so far
2011-05-19 16:11:24,396 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:2990004-23010004
2011-05-19 16:11:29,915 - INFO - Processed 6600000 reads so far
2011-05-19 16:11:39,357 - INFO - Processed 6700000 reads so far
2011-05-19 16:11:51,109 - INFO - Processed 6800000 reads so far
2011-05-19 16:12:03,241 - INFO - Processed 6900000 reads so far
2011-05-19 16:12:15,662 - INFO - Processed 7000000 reads so far
2011-05-19 16:12:28,226 - INFO - Processed 7100000 reads so far
2011-05-19 16:12:40,498 - INFO - Processed 7200000 reads so far
2011-05-19 16:12:52,969 - INFO - Processed 7300000 reads so far
2011-05-19 16:13:10,186 - INFO - Processed 7400000 reads so far
2011-05-19 16:13:21,903 - INFO - Processed 7500000 reads so far
2011-05-19 16:13:33,891 - INFO - Processed 7600000 reads so far
2011-05-19 16:13:45,658 - INFO - Processed 7700000 reads so far
2011-05-19 16:13:52,497 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:22990031-43010031
2011-05-19 16:13:56,974 - INFO - Processed 7800000 reads so far
2011-05-19 16:14:08,675 - INFO - Processed 7900000 reads so far
2011-05-19 16:14:20,590 - INFO - Processed 8000000 reads so far
2011-05-19 16:14:31,538 - INFO - Processed 8100000 reads so far
2011-05-19 16:14:42,528 - INFO - Processed 8200000 reads so far
2011-05-19 16:14:54,531 - INFO - Processed 8300000 reads so far
2011-05-19 16:15:06,538 - INFO - Processed 8400000 reads so far
2011-05-19 16:15:18,726 - INFO - Processed 8500000 reads so far
2011-05-19 16:15:30,723 - INFO - Processed 8600000 reads so far
2011-05-19 16:15:44,478 - INFO - Processed 8700000 reads so far
2011-05-19 16:15:55,588 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:42990071-63010071
2011-05-19 16:15:57,101 - INFO - Processed 8800000 reads so far
2011-05-19 16:16:09,172 - INFO - Processed 8900000 reads so far
2011-05-19 16:16:20,041 - INFO - Processed 9000000 reads so far
2011-05-19 16:16:31,907 - INFO - Processed 9100000 reads so far
2011-05-19 16:17:12,333 - INFO - Processed 9200000 reads so far
2011-05-19 16:17:23,555 - INFO - Processed 9300000 reads so far
2011-05-19 16:17:35,440 - INFO - Processed 9400000 reads so far
2011-05-19 16:17:50,207 - INFO - Processed 9500000 reads so far
2011-05-19 16:18:02,139 - INFO - Processed 9600000 reads so far
2011-05-19 16:18:14,589 - INFO - Processed 9700000 reads so far
2011-05-19 16:18:26,350 - INFO - Processed 9800000 reads so far
2011-05-19 16:18:31,287 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:62990073-83010073
2011-05-19 16:18:37,997 - INFO - Processed 9900000 reads so far
2011-05-19 16:18:53,720 - INFO - Processed 10000000 reads so far
2011-05-19 16:19:05,199 - INFO - Processed 10100000 reads so far
2011-05-19 16:19:16,080 - INFO - Processed 10200000 reads so far
2011-05-19 16:19:27,745 - INFO - Processed 10300000 reads so far
2011-05-19 16:19:40,856 - INFO - Processed 10400000 reads so far
2011-05-19 16:19:52,997 - INFO - Processed 10500000 reads so far
2011-05-19 16:20:05,617 - INFO - Processed 10600000 reads so far
2011-05-19 16:20:17,601 - INFO - Processed 10700000 reads so far
2011-05-19 16:20:30,699 - INFO - Processed 10800000 reads so far
2011-05-19 16:20:40,474 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:82990081-103010081
2011-05-19 16:20:43,631 - INFO - Processed 10900000 reads so far
2011-05-19 16:20:54,246 - INFO - Processed 11000000 reads so far
2011-05-19 16:21:04,995 - INFO - Processed 11100000 reads so far
2011-05-19 16:21:17,852 - INFO - Processed 11200000 reads so far
2011-05-19 16:21:29,902 - INFO - Processed 11300000 reads so far
2011-05-19 16:21:43,204 - INFO - Processed 11400000 reads so far
2011-05-19 16:21:55,415 - INFO - Processed 11500000 reads so far
2011-05-19 16:22:07,277 - INFO - Processed 11600000 reads so far
2011-05-19 16:22:19,764 - INFO - Processed 11700000 reads so far
2011-05-19 16:22:31,934 - INFO - Processed 11800000 reads so far
2011-05-19 16:22:43,889 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:102990096-123010096
2011-05-19 16:22:45,616 - INFO - Processed 11900000 reads so far
2011-05-19 16:22:57,868 - INFO - Processed 12000000 reads so far
2011-05-19 16:23:09,348 - INFO - Processed 12100000 reads so far
2011-05-19 16:23:20,475 - INFO - Processed 12200000 reads so far
2011-05-19 16:23:32,109 - INFO - Processed 12300000 reads so far
2011-05-19 16:23:45,200 - INFO - Processed 12400000 reads so far
2011-05-19 16:23:57,150 - INFO - Processed 12500000 reads so far
2011-05-19 16:24:10,210 - INFO - Processed 12600000 reads so far
2011-05-19 16:24:23,921 - INFO - Processed 12700000 reads so far
2011-05-19 16:24:35,999 - INFO - Processed 12800000 reads so far
2011-05-19 16:24:40,968 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:2990085-23010085
2011-05-19 16:24:46,889 - INFO - Processed 12900000 reads so far
2011-05-19 16:24:55,851 - INFO - Processed 13000000 reads so far
2011-05-19 16:25:08,640 - INFO - Processed 13100000 reads so far
2011-05-19 16:25:22,442 - INFO - Processed 13200000 reads so far
2011-05-19 16:25:34,603 - INFO - Processed 13300000 reads so far
2011-05-19 16:25:46,580 - INFO - Processed 13400000 reads so far
2011-05-19 16:26:00,088 - INFO - Processed 13500000 reads so far
2011-05-19 16:26:11,840 - INFO - Processed 13600000 reads so far
2011-05-19 16:26:24,140 - INFO - Processed 13700000 reads so far
2011-05-19 16:26:35,677 - INFO - Processed 13800000 reads so far
2011-05-19 16:26:47,678 - INFO - Processed 13900000 reads so far
2011-05-19 16:26:58,867 - INFO - Processed 14000000 reads so far
2011-05-19 16:27:07,646 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:22990185-43010185
2011-05-19 16:27:11,202 - INFO - Processed 14100000 reads so far
2011-05-19 16:27:24,285 - INFO - Processed 14200000 reads so far
2011-05-19 16:27:37,187 - INFO - Processed 14300000 reads so far
2011-05-19 16:27:50,493 - INFO - Processed 14400000 reads so far
2011-05-19 16:28:03,746 - INFO - Processed 14500000 reads so far
2011-05-19 16:28:17,738 - INFO - Processed 14600000 reads so far
2011-05-19 16:28:32,147 - INFO - Processed 14700000 reads so far
2011-05-19 16:28:47,034 - INFO - Processed 14800000 reads so far
2011-05-19 16:29:02,256 - INFO - Processed 14900000 reads so far
2011-05-19 16:29:15,410 - INFO - Processed 15000000 reads so far
2011-05-19 16:29:23,802 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:42990190-63010190
2011-05-19 16:29:31,179 - INFO - Processed 15100000 reads so far
2011-05-19 16:29:46,777 - INFO - Processed 15200000 reads so far
2011-05-19 16:29:58,384 - INFO - Processed 15300000 reads so far
2011-05-19 16:30:11,875 - INFO - Processed 15400000 reads so far
2011-05-19 16:30:25,405 - INFO - Processed 15500000 reads so far
2011-05-19 16:30:38,550 - INFO - Processed 15600000 reads so far
2011-05-19 16:30:51,347 - INFO - Processed 15700000 reads so far
2011-05-19 16:31:05,808 - INFO - Processed 15800000 reads so far
2011-05-19 16:31:17,388 - INFO - Processed 15900000 reads so far
2011-05-19 16:31:38,802 - INFO - Processed 16000000 reads so far
2011-05-19 16:31:44,893 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:62990195-83010195
2011-05-19 16:31:52,953 - INFO - Processed 16100000 reads so far
2011-05-19 16:32:07,685 - INFO - Processed 16200000 reads so far
2011-05-19 16:32:23,925 - INFO - Processed 16300000 reads so far
2011-05-19 16:32:39,328 - INFO - Processed 16400000 reads so far
2011-05-19 16:32:52,891 - INFO - Processed 16500000 reads so far
2011-05-19 16:33:04,325 - INFO - Processed 16600000 reads so far
2011-05-19 16:33:16,385 - INFO - Processed 16700000 reads so far
2011-05-19 16:33:29,776 - INFO - Processed 16800000 reads so far
2011-05-19 16:33:41,957 - INFO - Processed 16900000 reads so far
2011-05-19 16:33:54,214 - INFO - Processed 17000000 reads so far
2011-05-19 16:34:10,766 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:82990201-103010201
2011-05-19 16:34:13,851 - INFO - Processed 17100000 reads so far
2011-05-19 16:34:27,190 - INFO - Processed 17200000 reads so far
2011-05-19 16:34:39,141 - INFO - Processed 17300000 reads so far
2011-05-19 16:34:52,768 - INFO - Processed 17400000 reads so far
2011-05-19 16:35:04,979 - INFO - Processed 17500000 reads so far
2011-05-19 16:35:17,072 - INFO - Processed 17600000 reads so far
2011-05-19 16:35:30,521 - INFO - Processed 17700000 reads so far
2011-05-19 16:35:42,552 - INFO - Processed 17800000 reads so far
2011-05-19 16:35:54,745 - INFO - Processed 17900000 reads so far
2011-05-19 16:36:05,659 - INFO - Processed 18000000 reads so far
2011-05-19 16:36:17,045 - INFO - Processed 18100000 reads so far
2011-05-19 16:36:17,254 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:102990240-123010240
2011-05-19 16:36:29,133 - INFO - Processed 18200000 reads so far
2011-05-19 16:36:40,101 - INFO - Processed 18300000 reads so far
2011-05-19 16:36:51,009 - INFO - Processed 18400000 reads so far
2011-05-19 16:37:01,915 - INFO - Processed 18500000 reads so far
2011-05-19 16:37:12,996 - INFO - Processed 18600000 reads so far
2011-05-19 16:37:25,342 - INFO - Processed 18700000 reads so far
2011-05-19 16:37:34,780 - INFO - Processed 18800000 reads so far
2011-05-19 16:37:44,057 - INFO - Processed 18900000 reads so far
2011-05-19 16:37:56,127 - INFO - Processed 19000000 reads so far
2011-05-19 16:38:02,649 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:2990055-23010055
2011-05-19 16:38:07,729 - INFO - Processed 19100000 reads so far
2011-05-19 16:38:21,219 - INFO - Processed 19200000 reads so far
2011-05-19 16:38:32,577 - INFO - Processed 19300000 reads so far
2011-05-19 16:39:56,243 - INFO - Processed 19400000 reads so far
2011-05-19 16:40:26,452 - INFO - Processed 19500000 reads so far
2011-05-19 16:40:38,055 - INFO - Processed 19600000 reads so far
2011-05-19 16:40:48,952 - INFO - Processed 19700000 reads so far
2011-05-19 16:40:59,844 - INFO - Processed 19800000 reads so far
2011-05-19 16:41:10,422 - INFO - Processed 19900000 reads so far
2011-05-19 16:41:24,410 - INFO - Processed 20000000 reads so far
2011-05-19 16:41:32,561 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:22990085-43010085
2011-05-19 16:41:35,383 - INFO - Processed 20100000 reads so far
2011-05-19 16:41:47,086 - INFO - Processed 20200000 reads so far
2011-05-19 16:42:00,236 - INFO - Processed 20300000 reads so far
2011-05-19 16:42:11,977 - INFO - Processed 20400000 reads so far
2011-05-19 16:42:23,921 - INFO - Processed 20500000 reads so far
2011-05-19 16:42:36,124 - INFO - Processed 20600000 reads so far
2011-05-19 16:42:48,117 - INFO - Processed 20700000 reads so far
2011-05-19 16:43:01,869 - INFO - Processed 20800000 reads so far
2011-05-19 16:43:15,287 - INFO - Processed 20900000 reads so far
2011-05-19 16:43:30,442 - INFO - Processed 21000000 reads so far
2011-05-19 16:43:45,061 - INFO - Processed 21100000 reads so far
2011-05-19 16:43:50,154 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:42990111-63010111
2011-05-19 16:43:57,779 - INFO - Processed 21200000 reads so far
2011-05-19 16:44:13,151 - INFO - Processed 21300000 reads so far
2011-05-19 16:44:22,131 - INFO - Processed 21400000 reads so far
2011-05-19 16:44:34,771 - INFO - Processed 21500000 reads so far
2011-05-19 16:44:46,740 - INFO - Processed 21600000 reads so far
2011-05-19 16:45:02,800 - INFO - Processed 21700000 reads so far
2011-05-19 16:45:16,280 - INFO - Processed 21800000 reads so far
2011-05-19 16:45:29,884 - INFO - Processed 21900000 reads so far
2011-05-19 16:45:42,680 - INFO - Processed 22000000 reads so far
2011-05-19 16:45:53,590 - INFO - Processed 22100000 reads so far
2011-05-19 16:46:00,613 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:62990115-83010115
2011-05-19 16:46:01,584 - INFO - Processed 22200000 reads so far
2011-05-19 16:46:16,605 - INFO - Processed 22300000 reads so far
2011-05-19 16:46:33,532 - INFO - Processed 22400000 reads so far
2011-05-19 16:46:48,050 - INFO - Processed 22500000 reads so far
2011-05-19 16:47:00,181 - INFO - Processed 22600000 reads so far
2011-05-19 16:47:11,836 - INFO - Processed 22700000 reads so far
2011-05-19 16:47:23,144 - INFO - Processed 22800000 reads so far
2011-05-19 16:47:35,818 - INFO - Processed 22900000 reads so far
2011-05-19 16:47:47,152 - INFO - Processed 23000000 reads so far
2011-05-19 16:48:04,587 - INFO - Processed 23100000 reads so far
2011-05-19 16:48:17,868 - INFO - Processed 23200000 reads so far
2011-05-19 16:48:21,443 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:82990138-103010138
2011-05-19 16:48:32,521 - INFO - Processed 23300000 reads so far
2011-05-19 16:48:43,631 - INFO - Processed 23400000 reads so far
2011-05-19 16:48:54,899 - INFO - Processed 23500000 reads so far
2011-05-19 16:49:07,228 - INFO - Processed 23600000 reads so far
2011-05-19 16:49:21,917 - INFO - Processed 23700000 reads so far
2011-05-19 16:49:34,234 - INFO - Processed 23800000 reads so far
2011-05-19 16:49:45,500 - INFO - Processed 23900000 reads so far
2011-05-19 16:49:56,501 - INFO - Processed 24000000 reads so far
2011-05-19 16:50:08,034 - INFO - Processed 24100000 reads so far
2011-05-19 16:50:20,318 - INFO - Processed 24200000 reads so far
2011-05-19 16:50:23,568 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:102990142-123010142
2011-05-19 16:50:33,159 - INFO - Processed 24300000 reads so far
2011-05-19 16:50:44,350 - INFO - Processed 24400000 reads so far
2011-05-19 16:50:56,380 - INFO - Processed 24500000 reads so far
2011-05-19 16:51:06,633 - INFO - Processed 24600000 reads so far
2011-05-19 16:51:17,651 - INFO - Processed 24700000 reads so far
2011-05-19 16:51:28,673 - INFO - Processed 24800000 reads so far
2011-05-19 16:51:39,942 - INFO - Processed 24900000 reads so far
2011-05-19 16:51:50,746 - INFO - Processed 25000000 reads so far
2011-05-19 16:52:03,901 - INFO - Processed 25100000 reads so far
2011-05-19 16:52:05,944 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13_random:0-20010000
2011-05-19 16:52:07,193 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:2990007-23010007
2011-05-19 16:52:15,636 - INFO - Processed 25200000 reads so far
2011-05-19 16:52:28,156 - INFO - Processed 25300000 reads so far
2011-05-19 16:52:43,549 - INFO - Processed 25400000 reads so far
2011-05-19 16:52:59,484 - INFO - Processed 25500000 reads so far
2011-05-19 16:53:11,133 - INFO - Processed 25600000 reads so far
2011-05-19 16:53:23,013 - INFO - Processed 25700000 reads so far
2011-05-19 16:53:39,948 - INFO - Processed 25800000 reads so far
2011-05-19 16:53:51,884 - INFO - Processed 25900000 reads so far
2011-05-19 16:54:09,432 - INFO - Processed 26000000 reads so far
2011-05-19 16:54:21,094 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:22990024-43010024
2011-05-19 16:54:22,204 - INFO - Processed 26100000 reads so far
2011-05-19 16:54:33,892 - INFO - Processed 26200000 reads so far
2011-05-19 16:54:48,347 - INFO - Processed 26300000 reads so far
2011-05-19 16:55:03,123 - INFO - Processed 26400000 reads so far
2011-05-19 16:55:15,156 - INFO - Processed 26500000 reads so far
2011-05-19 16:55:27,031 - INFO - Processed 26600000 reads so far
2011-05-19 16:55:39,176 - INFO - Processed 26700000 reads so far
2011-05-19 16:55:51,852 - INFO - Processed 26800000 reads so far
2011-05-19 16:56:02,774 - INFO - Processed 26900000 reads so far
2011-05-19 16:56:17,311 - INFO - Processed 27000000 reads so far
2011-05-19 16:56:31,033 - INFO - Processed 27100000 reads so far
2011-05-19 16:56:33,737 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:42990155-63010155
2011-05-19 16:56:45,722 - INFO - Processed 27200000 reads so far
2011-05-19 16:56:55,998 - INFO - Processed 27300000 reads so far
2011-05-19 16:57:08,499 - INFO - Processed 27400000 reads so far
2011-05-19 16:57:20,586 - INFO - Processed 27500000 reads so far
2011-05-19 16:57:32,809 - INFO - Processed 27600000 reads so far
2011-05-19 16:57:46,631 - INFO - Processed 27700000 reads so far
2011-05-19 16:57:59,407 - INFO - Processed 27800000 reads so far
2011-05-19 16:58:12,320 - INFO - Processed 27900000 reads so far
2011-05-19 16:58:25,928 - INFO - Processed 28000000 reads so far
2011-05-19 16:58:37,806 - INFO - Processed 28100000 reads so far
2011-05-19 16:58:49,970 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:62990160-83010160
2011-05-19 16:58:50,222 - INFO - Processed 28200000 reads so far
2011-05-19 16:59:04,331 - INFO - Processed 28300000 reads so far
2011-05-19 16:59:16,203 - INFO - Processed 28400000 reads so far
2011-05-19 16:59:30,147 - INFO - Processed 28500000 reads so far
2011-05-19 16:59:42,262 - INFO - Processed 28600000 reads so far
2011-05-19 16:59:54,445 - INFO - Processed 28700000 reads so far
2011-05-19 17:00:08,383 - INFO - Processed 28800000 reads so far
2011-05-19 17:00:20,470 - INFO - Processed 28900000 reads so far
2011-05-19 17:00:32,362 - INFO - Processed 29000000 reads so far
2011-05-19 17:00:44,981 - INFO - Processed 29100000 reads so far
2011-05-19 17:00:57,891 - INFO - Processed 29200000 reads so far
2011-05-19 17:01:04,529 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:82990164-103010164
2011-05-19 17:01:11,779 - INFO - Processed 29300000 reads so far
2011-05-19 17:01:30,262 - INFO - Processed 29400000 reads so far
2011-05-19 17:01:42,569 - INFO - Processed 29500000 reads so far
2011-05-19 17:01:56,942 - INFO - Processed 29600000 reads so far
2011-05-19 17:02:11,880 - INFO - Processed 29700000 reads so far
2011-05-19 17:02:23,864 - INFO - Processed 29800000 reads so far
2011-05-19 17:02:36,835 - INFO - Processed 29900000 reads so far
2011-05-19 17:02:48,435 - INFO - Processed 30000000 reads so far
2011-05-19 17:03:00,042 - INFO - Processed 30100000 reads so far
2011-05-19 17:03:11,796 - INFO - Processed 30200000 reads so far
2011-05-19 17:03:12,581 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:102990171-123010171
2011-05-19 17:03:25,777 - INFO - Processed 30300000 reads so far
2011-05-19 17:03:35,710 - INFO - Processed 30400000 reads so far
2011-05-19 17:03:50,739 - INFO - Processed 30500000 reads so far
2011-05-19 17:04:04,834 - INFO - Processed 30600000 reads so far
2011-05-19 17:04:16,607 - INFO - Processed 30700000 reads so far
2011-05-19 17:04:29,056 - INFO - Processed 30800000 reads so far
2011-05-19 17:04:41,489 - INFO - Processed 30900000 reads so far
2011-05-19 17:04:57,499 - INFO - Processed 31000000 reads so far
2011-05-19 17:05:10,848 - INFO - Processed 31100000 reads so far
2011-05-19 17:05:22,483 - INFO - Processed 31200000 reads so far
2011-05-19 17:05:23,147 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:122990173-143010173
2011-05-19 17:05:34,869 - INFO - Processed 31300000 reads so far
2011-05-19 17:05:37,890 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:2990013-23010013
2011-05-19 17:05:49,625 - INFO - Processed 31400000 reads so far
2011-05-19 17:06:04,569 - INFO - Processed 31500000 reads so far
2011-05-19 17:06:20,150 - INFO - Processed 31600000 reads so far
2011-05-19 17:06:31,789 - INFO - Processed 31700000 reads so far
2011-05-19 17:06:43,763 - INFO - Processed 31800000 reads so far
2011-05-19 17:06:56,835 - INFO - Processed 31900000 reads so far
2011-05-19 17:07:12,844 - INFO - Processed 32000000 reads so far
2011-05-19 17:07:25,601 - INFO - Processed 32100000 reads so far
2011-05-19 17:07:39,930 - INFO - Processed 32200000 reads so far
2011-05-19 17:07:55,535 - INFO - Processed 32300000 reads so far
2011-05-19 17:07:57,750 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:22990022-43010022
2011-05-19 17:08:07,481 - INFO - Processed 32400000 reads so far
2011-05-19 17:08:22,565 - INFO - Processed 32500000 reads so far
2011-05-19 17:08:35,173 - INFO - Processed 32600000 reads so far
2011-05-19 17:08:47,024 - INFO - Processed 32700000 reads so far
2011-05-19 17:08:58,793 - INFO - Processed 32800000 reads so far
2011-05-19 17:09:12,197 - INFO - Processed 32900000 reads so far
2011-05-19 17:09:24,232 - INFO - Processed 33000000 reads so far
2011-05-19 17:09:36,739 - INFO - Processed 33100000 reads so far
2011-05-19 17:09:50,170 - INFO - Processed 33200000 reads so far
2011-05-19 17:10:03,725 - INFO - Processed 33300000 reads so far
2011-05-19 17:10:10,723 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:42990024-63010024
2011-05-19 17:10:16,508 - INFO - Processed 33400000 reads so far
2011-05-19 17:10:28,189 - INFO - Processed 33500000 reads so far
2011-05-19 17:10:39,505 - INFO - Processed 33600000 reads so far
2011-05-19 17:10:52,051 - INFO - Processed 33700000 reads so far
2011-05-19 17:11:05,350 - INFO - Processed 33800000 reads so far
2011-05-19 17:11:17,254 - INFO - Processed 33900000 reads so far
2011-05-19 17:11:31,655 - INFO - Processed 34000000 reads so far
2011-05-19 17:11:43,215 - INFO - Processed 34100000 reads so far
2011-05-19 17:11:53,472 - INFO - Processed 34200000 reads so far
2011-05-19 17:12:05,531 - INFO - Processed 34300000 reads so far
2011-05-19 17:12:14,508 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:62990082-83010082
2011-05-19 17:12:17,366 - INFO - Processed 34400000 reads so far
2011-05-19 17:12:30,498 - INFO - Processed 34500000 reads so far
2011-05-19 17:12:42,395 - INFO - Processed 34600000 reads so far
2011-05-19 17:12:52,911 - INFO - Processed 34700000 reads so far
2011-05-19 17:13:05,147 - INFO - Processed 34800000 reads so far
2011-05-19 17:13:17,333 - INFO - Processed 34900000 reads so far
2011-05-19 17:13:30,316 - INFO - Processed 35000000 reads so far
2011-05-19 17:13:45,099 - INFO - Processed 35100000 reads so far
2011-05-19 17:14:01,415 - INFO - Processed 35200000 reads so far
2011-05-19 17:14:14,803 - INFO - Processed 35300000 reads so far
2011-05-19 17:14:29,632 - INFO - Processed 35400000 reads so far
2011-05-19 17:14:34,691 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:82990117-103010117
2011-05-19 17:14:42,791 - INFO - Processed 35500000 reads so far
2011-05-19 17:14:54,898 - INFO - Processed 35600000 reads so far
2011-05-19 17:15:09,266 - INFO - Processed 35700000 reads so far
2011-05-19 17:15:22,707 - INFO - Processed 35800000 reads so far
2011-05-19 17:15:35,393 - INFO - Processed 35900000 reads so far
2011-05-19 17:15:47,128 - INFO - Processed 36000000 reads so far
2011-05-19 17:15:58,241 - INFO - Processed 36100000 reads so far
2011-05-19 17:16:09,367 - INFO - Processed 36200000 reads so far
2011-05-19 17:16:21,291 - INFO - Processed 36300000 reads so far
2011-05-19 17:16:40,557 - INFO - Processed 36400000 reads so far
2011-05-19 17:16:49,123 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:102990189-123010189
2011-05-19 17:16:52,063 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:2990049-23010049
2011-05-19 17:16:52,802 - INFO - Processed 36500000 reads so far
2011-05-19 17:17:05,501 - INFO - Processed 36600000 reads so far
2011-05-19 17:17:17,234 - INFO - Processed 36700000 reads so far
2011-05-19 17:17:28,884 - INFO - Processed 36800000 reads so far
2011-05-19 17:17:42,160 - INFO - Processed 36900000 reads so far
2011-05-19 17:17:55,239 - INFO - Processed 37000000 reads so far
2011-05-19 17:18:09,822 - INFO - Processed 37100000 reads so far
2011-05-19 17:18:24,456 - INFO - Processed 37200000 reads so far
2011-05-19 17:18:39,431 - INFO - Processed 37300000 reads so far
2011-05-19 17:18:53,580 - INFO - Processed 37400000 reads so far
2011-05-19 17:19:05,695 - INFO - Processed 37500000 reads so far
2011-05-19 17:19:20,031 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:22990056-43010056
2011-05-19 17:19:20,452 - INFO - Processed 37600000 reads so far
2011-05-19 17:19:32,379 - INFO - Processed 37700000 reads so far
2011-05-19 17:19:44,029 - INFO - Processed 37800000 reads so far
2011-05-19 17:19:56,452 - INFO - Processed 37900000 reads so far
2011-05-19 17:20:06,022 - INFO - Processed 38000000 reads so far
2011-05-19 17:20:17,829 - INFO - Processed 38100000 reads so far
2011-05-19 17:20:33,445 - INFO - Processed 38200000 reads so far
2011-05-19 17:20:46,913 - INFO - Processed 38300000 reads so far
2011-05-19 17:20:58,014 - INFO - Processed 38400000 reads so far
2011-05-19 17:21:11,275 - INFO - Processed 38500000 reads so far
2011-05-19 17:21:21,775 - INFO - Processed 38600000 reads so far
2011-05-19 17:21:26,993 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:42990057-63010057
2011-05-19 17:21:33,484 - INFO - Processed 38700000 reads so far
2011-05-19 17:21:45,769 - INFO - Processed 38800000 reads so far
2011-05-19 17:21:57,439 - INFO - Processed 38900000 reads so far
2011-05-19 17:22:09,900 - INFO - Processed 39000000 reads so far
2011-05-19 17:22:23,137 - INFO - Processed 39100000 reads so far
2011-05-19 17:22:34,345 - INFO - Processed 39200000 reads so far
2011-05-19 17:22:46,674 - INFO - Processed 39300000 reads so far
2011-05-19 17:22:57,910 - INFO - Processed 39400000 reads so far
2011-05-19 17:23:14,359 - INFO - Processed 39500000 reads so far
2011-05-19 17:23:28,499 - INFO - Processed 39600000 reads so far
2011-05-19 17:23:35,163 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:62990063-83010063
2011-05-19 17:23:40,207 - INFO - Processed 39700000 reads so far
2011-05-19 17:23:53,065 - INFO - Processed 39800000 reads so far
2011-05-19 17:24:07,803 - INFO - Processed 39900000 reads so far
2011-05-19 17:24:20,453 - INFO - Processed 40000000 reads so far
2011-05-19 17:24:36,143 - INFO - Processed 40100000 reads so far
2011-05-19 17:24:47,914 - INFO - Processed 40200000 reads so far
2011-05-19 17:24:59,232 - INFO - Processed 40300000 reads so far
2011-05-19 17:25:14,483 - INFO - Processed 40400000 reads so far
2011-05-19 17:25:28,037 - INFO - Processed 40500000 reads so far
2011-05-19 17:25:45,463 - INFO - Processed 40600000 reads so far
2011-05-19 17:25:49,425 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:82990070-103010070
2011-05-19 17:25:59,616 - INFO - Processed 40700000 reads so far
2011-05-19 17:26:12,021 - INFO - Processed 40800000 reads so far
2011-05-19 17:26:24,384 - INFO - Processed 40900000 reads so far
2011-05-19 17:26:35,545 - INFO - Processed 41000000 reads so far
2011-05-19 17:26:48,099 - INFO - Processed 41100000 reads so far
2011-05-19 17:27:01,785 - INFO - Processed 41200000 reads so far
2011-05-19 17:27:12,093 - INFO - Processed 41300000 reads so far
2011-05-19 17:27:23,139 - INFO - Processed 41400000 reads so far
2011-05-19 17:27:26,086 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16_random:0-20010099
2011-05-19 17:27:26,121 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:2989982-23009982
2011-05-19 17:27:34,394 - INFO - Processed 41500000 reads so far
2011-05-19 17:27:46,097 - INFO - Processed 41600000 reads so far
2011-05-19 17:27:57,551 - INFO - Processed 41700000 reads so far
2011-05-19 17:28:10,488 - INFO - Processed 41800000 reads so far
2011-05-19 17:28:21,522 - INFO - Processed 41900000 reads so far
2011-05-19 17:28:34,326 - INFO - Processed 42000000 reads so far
2011-05-19 17:28:46,513 - INFO - Processed 42100000 reads so far
2011-05-19 17:28:58,310 - INFO - Processed 42200000 reads so far
2011-05-19 17:29:11,752 - INFO - Processed 42300000 reads so far
2011-05-19 17:29:25,939 - INFO - Processed 42400000 reads so far
2011-05-19 17:29:37,692 - INFO - Processed 42500000 reads so far
2011-05-19 17:29:41,506 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:22990000-43010000
2011-05-19 17:29:55,057 - INFO - Processed 42600000 reads so far
2011-05-19 17:30:07,916 - INFO - Processed 42700000 reads so far
2011-05-19 17:30:22,278 - INFO - Processed 42800000 reads so far
2011-05-19 17:30:36,147 - INFO - Processed 42900000 reads so far
2011-05-19 17:30:48,173 - INFO - Processed 43000000 reads so far
2011-05-19 17:31:01,203 - INFO - Processed 43100000 reads so far
2011-05-19 17:31:15,978 - INFO - Processed 43200000 reads so far
2011-05-19 17:31:33,821 - INFO - Processed 43300000 reads so far
2011-05-19 17:31:44,814 - INFO - Processed 43400000 reads so far
2011-05-19 17:31:56,115 - INFO - Processed 43500000 reads so far
2011-05-19 17:32:04,677 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:42990014-63010014
2011-05-19 17:32:08,729 - INFO - Processed 43600000 reads so far
2011-05-19 17:32:20,712 - INFO - Processed 43700000 reads so far
2011-05-19 17:32:33,969 - INFO - Processed 43800000 reads so far
2011-05-19 17:32:51,233 - INFO - Processed 43900000 reads so far
2011-05-19 17:33:03,087 - INFO - Processed 44000000 reads so far
2011-05-19 17:33:16,151 - INFO - Processed 44100000 reads so far
2011-05-19 17:33:28,343 - INFO - Processed 44200000 reads so far
2011-05-19 17:33:41,137 - INFO - Processed 44300000 reads so far
2011-05-19 17:33:54,510 - INFO - Processed 44400000 reads so far
2011-05-19 17:34:05,553 - INFO - Processed 44500000 reads so far
2011-05-19 17:34:17,092 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:62990017-83010017
2011-05-19 17:34:21,458 - INFO - Processed 44600000 reads so far
2011-05-19 17:34:36,408 - INFO - Processed 44700000 reads so far
2011-05-19 17:34:51,262 - INFO - Processed 44800000 reads so far
2011-05-19 17:35:04,476 - INFO - Processed 44900000 reads so far
2011-05-19 17:35:16,757 - INFO - Processed 45000000 reads so far
2011-05-19 17:35:28,335 - INFO - Processed 45100000 reads so far
2011-05-19 17:35:42,051 - INFO - Processed 45200000 reads so far
2011-05-19 17:35:55,533 - INFO - Processed 45300000 reads so far
2011-05-19 17:36:10,313 - INFO - Processed 45400000 reads so far
2011-05-19 17:36:22,250 - INFO - Processed 45500000 reads so far
2011-05-19 17:36:32,109 - INFO - Processed 45600000 reads so far
2011-05-19 17:36:33,496 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:82990161-103010161
2011-05-19 17:36:43,581 - INFO - Processed 45700000 reads so far
2011-05-19 17:36:55,559 - INFO - Processed 45800000 reads so far
2011-05-19 17:37:08,264 - INFO - Processed 45900000 reads so far
2011-05-19 17:37:20,030 - INFO - Processed 46000000 reads so far
2011-05-19 17:37:32,174 - INFO - Processed 46100000 reads so far
2011-05-19 17:37:45,007 - INFO - Processed 46200000 reads so far
2011-05-19 17:37:49,316 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17_random:0-20010032
2011-05-19 17:37:51,434 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:2990016-23010016
2011-05-19 17:37:55,972 - INFO - Processed 46300000 reads so far
2011-05-19 17:38:09,271 - INFO - Processed 46400000 reads so far
2011-05-19 17:38:23,432 - INFO - Processed 46500000 reads so far
2011-05-19 17:38:39,209 - INFO - Processed 46600000 reads so far
2011-05-19 17:38:51,789 - INFO - Processed 46700000 reads so far
2011-05-19 17:39:02,491 - INFO - Processed 46800000 reads so far
2011-05-19 17:39:18,817 - INFO - Processed 46900000 reads so far
2011-05-19 17:39:28,407 - INFO - Processed 47000000 reads so far
2011-05-19 17:39:39,173 - INFO - Processed 47100000 reads so far
2011-05-19 17:39:49,905 - INFO - Processed 47200000 reads so far
2011-05-19 17:39:59,314 - INFO - Processed 47300000 reads so far
2011-05-19 17:40:04,037 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:22990032-43010032
2011-05-19 17:40:09,842 - INFO - Processed 47400000 reads so far
2011-05-19 17:40:21,805 - INFO - Processed 47500000 reads so far
2011-05-19 17:40:32,770 - INFO - Processed 47600000 reads so far
2011-05-19 17:40:42,203 - INFO - Processed 47700000 reads so far
2011-05-19 17:40:56,687 - INFO - Processed 47800000 reads so far
2011-05-19 17:41:07,866 - INFO - Processed 47900000 reads so far
2011-05-19 17:41:18,475 - INFO - Processed 48000000 reads so far
2011-05-19 17:41:33,782 - INFO - Processed 48100000 reads so far
2011-05-19 17:41:45,226 - INFO - Processed 48200000 reads so far
2011-05-19 17:41:59,852 - INFO - Processed 48300000 reads so far
2011-05-19 17:42:11,810 - INFO - Processed 48400000 reads so far
2011-05-19 17:42:12,027 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:42990071-63010071
2011-05-19 17:42:24,550 - INFO - Processed 48500000 reads so far
2011-05-19 17:42:36,468 - INFO - Processed 48600000 reads so far
2011-05-19 17:42:51,713 - INFO - Processed 48700000 reads so far
2011-05-19 17:43:04,226 - INFO - Processed 48800000 reads so far
2011-05-19 17:43:16,523 - INFO - Processed 48900000 reads so far
2011-05-19 17:43:32,459 - INFO - Processed 49000000 reads so far
2011-05-19 17:43:45,170 - INFO - Processed 49100000 reads so far
2011-05-19 17:43:58,659 - INFO - Processed 49200000 reads so far
2011-05-19 17:44:10,365 - INFO - Processed 49300000 reads so far
2011-05-19 17:44:22,997 - INFO - Processed 49400000 reads so far
2011-05-19 17:44:28,637 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:62990081-83010081
2011-05-19 17:44:34,864 - INFO - Processed 49500000 reads so far
2011-05-19 17:44:45,213 - INFO - Processed 49600000 reads so far
2011-05-19 17:44:56,815 - INFO - Processed 49700000 reads so far
2011-05-19 17:45:08,472 - INFO - Processed 49800000 reads so far
2011-05-19 17:45:20,469 - INFO - Processed 49900000 reads so far
2011-05-19 17:45:32,286 - INFO - Processed 50000000 reads so far
2011-05-19 17:45:46,709 - INFO - Processed 50100000 reads so far
2011-05-19 17:45:58,639 - INFO - Processed 50200000 reads so far
2011-05-19 17:46:11,098 - INFO - Processed 50300000 reads so far
2011-05-19 17:46:24,239 - INFO - Processed 50400000 reads so far
2011-05-19 17:46:36,131 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:82990084-103010084
2011-05-19 17:46:37,932 - INFO - Processed 50500000 reads so far
2011-05-19 17:46:49,050 - INFO - Processed 50600000 reads so far
2011-05-19 17:47:01,360 - INFO - Processed 50700000 reads so far
2011-05-19 17:47:14,076 - INFO - Processed 50800000 reads so far
2011-05-19 17:47:23,400 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:2990030-23010030
2011-05-19 17:47:25,807 - INFO - Processed 50900000 reads so far
2011-05-19 17:47:41,083 - INFO - Processed 51000000 reads so far
2011-05-19 17:47:55,003 - INFO - Processed 51100000 reads so far
2011-05-19 17:48:06,769 - INFO - Processed 51200000 reads so far
2011-05-19 17:48:19,380 - INFO - Processed 51300000 reads so far
2011-05-19 17:48:30,840 - INFO - Processed 51400000 reads so far
2011-05-19 17:48:42,449 - INFO - Processed 51500000 reads so far
2011-05-19 17:48:54,865 - INFO - Processed 51600000 reads so far
2011-05-19 17:49:06,683 - INFO - Processed 51700000 reads so far
2011-05-19 17:49:19,137 - INFO - Processed 51800000 reads so far
2011-05-19 17:49:30,013 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:22990146-43010146
2011-05-19 17:49:32,112 - INFO - Processed 51900000 reads so far
2011-05-19 17:49:43,961 - INFO - Processed 52000000 reads so far
2011-05-19 17:49:56,691 - INFO - Processed 52100000 reads so far
2011-05-19 17:50:12,763 - INFO - Processed 52200000 reads so far
2011-05-19 17:50:24,347 - INFO - Processed 52300000 reads so far
2011-05-19 17:50:37,680 - INFO - Processed 52400000 reads so far
2011-05-19 17:50:50,653 - INFO - Processed 52500000 reads so far
2011-05-19 17:51:01,831 - INFO - Processed 52600000 reads so far
2011-05-19 17:51:16,703 - INFO - Processed 52700000 reads so far
2011-05-19 17:51:29,129 - INFO - Processed 52800000 reads so far
2011-05-19 17:51:40,970 - INFO - Processed 52900000 reads so far
2011-05-19 17:51:43,132 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:42990148-63010148
2011-05-19 17:51:54,531 - INFO - Processed 53000000 reads so far
2011-05-19 17:52:06,292 - INFO - Processed 53100000 reads so far
2011-05-19 17:52:17,845 - INFO - Processed 53200000 reads so far
2011-05-19 17:52:31,527 - INFO - Processed 53300000 reads so far
2011-05-19 17:52:43,830 - INFO - Processed 53400000 reads so far
2011-05-19 17:52:57,125 - INFO - Processed 53500000 reads so far
2011-05-19 17:53:09,080 - INFO - Processed 53600000 reads so far
2011-05-19 17:53:20,138 - INFO - Processed 53700000 reads so far
2011-05-19 17:53:31,245 - INFO - Processed 53800000 reads so far
2011-05-19 17:53:41,330 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:2989993-23009993
2011-05-19 17:53:43,089 - INFO - Processed 53900000 reads so far
2011-05-19 17:53:50,523 - INFO - Processed 54000000 reads so far
2011-05-19 17:53:59,854 - INFO - Processed 54100000 reads so far
2011-05-19 17:54:07,474 - INFO - Processed 54200000 reads so far
2011-05-19 17:54:18,246 - INFO - Processed 54300000 reads so far
2011-05-19 17:54:26,612 - INFO - Processed 54400000 reads so far
2011-05-19 17:54:37,594 - INFO - Processed 54500000 reads so far
2011-05-19 17:54:45,424 - INFO - Processed 54600000 reads so far
2011-05-19 17:54:55,934 - INFO - Processed 54700000 reads so far
2011-05-19 17:55:03,624 - INFO - Processed 54800000 reads so far
2011-05-19 17:55:11,482 - INFO - Processed 54900000 reads so far
2011-05-19 17:55:12,103 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:22990007-43010007
2011-05-19 17:55:21,573 - INFO - Processed 55000000 reads so far
2011-05-19 17:55:29,286 - INFO - Processed 55100000 reads so far
2011-05-19 17:55:36,862 - INFO - Processed 55200000 reads so far
2011-05-19 17:55:44,483 - INFO - Processed 55300000 reads so far
2011-05-19 17:55:56,337 - INFO - Processed 55400000 reads so far
2011-05-19 17:56:07,845 - INFO - Processed 55500000 reads so far
2011-05-19 17:56:23,627 - INFO - Processed 55600000 reads so far
2011-05-19 17:56:36,708 - INFO - Processed 55700000 reads so far
2011-05-19 17:56:45,760 - INFO - Processed 55800000 reads so far
2011-05-19 17:56:58,738 - INFO - Processed 55900000 reads so far
2011-05-19 17:57:05,141 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:42990023-63010023
2011-05-19 17:57:11,026 - INFO - Processed 56000000 reads so far
2011-05-19 17:57:22,641 - INFO - Processed 56100000 reads so far
2011-05-19 17:57:35,552 - INFO - Processed 56200000 reads so far
2011-05-19 17:57:46,252 - INFO - Processed 56300000 reads so far
2011-05-19 17:57:56,749 - INFO - Processed 56400000 reads so far
2011-05-19 17:58:09,419 - INFO - Processed 56500000 reads so far
2011-05-19 17:58:21,267 - INFO - Processed 56600000 reads so far
2011-05-19 17:58:32,701 - INFO - Processed 56700000 reads so far
2011-05-19 17:58:45,770 - INFO - Processed 56800000 reads so far
2011-05-19 17:58:56,549 - INFO - Processed 56900000 reads so far
2011-05-19 17:59:05,681 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:62990032-83010032
2011-05-19 17:59:07,951 - INFO - Processed 57000000 reads so far
2011-05-19 17:59:20,780 - INFO - Processed 57100000 reads so far
2011-05-19 17:59:34,291 - INFO - Processed 57200000 reads so far
2011-05-19 17:59:46,689 - INFO - Processed 57300000 reads so far
2011-05-19 17:59:59,726 - INFO - Processed 57400000 reads so far
2011-05-19 18:00:11,265 - INFO - Processed 57500000 reads so far
2011-05-19 18:00:21,180 - INFO - Processed 57600000 reads so far
2011-05-19 18:00:32,137 - INFO - Processed 57700000 reads so far
2011-05-19 18:00:42,773 - INFO - Processed 57800000 reads so far
2011-05-19 18:00:53,231 - INFO - Processed 57900000 reads so far
2011-05-19 18:01:06,411 - INFO - Processed 58000000 reads so far
2011-05-19 18:01:08,086 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:82990063-103010063
2011-05-19 18:01:16,796 - INFO - Processed 58100000 reads so far
2011-05-19 18:01:27,895 - INFO - Processed 58200000 reads so far
2011-05-19 18:01:38,831 - INFO - Processed 58300000 reads so far
2011-05-19 18:01:50,511 - INFO - Processed 58400000 reads so far
2011-05-19 18:02:03,171 - INFO - Processed 58500000 reads so far
2011-05-19 18:02:17,785 - INFO - Processed 58600000 reads so far
2011-05-19 18:02:29,429 - INFO - Processed 58700000 reads so far
2011-05-19 18:02:40,988 - INFO - Processed 58800000 reads so far
2011-05-19 18:02:52,458 - INFO - Processed 58900000 reads so far
2011-05-19 18:03:04,010 - INFO - Processed 59000000 reads so far
2011-05-19 18:03:13,169 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:102990072-123010072
2011-05-19 18:03:15,661 - INFO - Processed 59100000 reads so far
2011-05-19 18:03:27,847 - INFO - Processed 59200000 reads so far
2011-05-19 18:03:39,152 - INFO - Processed 59300000 reads so far
2011-05-19 18:03:50,444 - INFO - Processed 59400000 reads so far
2011-05-19 18:04:02,383 - INFO - Processed 59500000 reads so far
2011-05-19 18:04:13,705 - INFO - Processed 59600000 reads so far
2011-05-19 18:04:32,253 - INFO - Processed 59700000 reads so far
2011-05-19 18:04:43,715 - INFO - Processed 59800000 reads so far
2011-05-19 18:04:59,312 - INFO - Processed 59900000 reads so far
2011-05-19 18:05:11,547 - INFO - Processed 60000000 reads so far
2011-05-19 18:05:20,989 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:122990091-143010091
2011-05-19 18:05:22,584 - INFO - Processed 60100000 reads so far
2011-05-19 18:05:36,786 - INFO - Processed 60200000 reads so far
2011-05-19 18:05:51,098 - INFO - Processed 60300000 reads so far
2011-05-19 18:06:03,867 - INFO - Processed 60400000 reads so far
2011-05-19 18:06:15,540 - INFO - Processed 60500000 reads so far
2011-05-19 18:06:28,015 - INFO - Processed 60600000 reads so far
2011-05-19 18:06:42,603 - INFO - Processed 60700000 reads so far
2011-05-19 18:06:53,649 - INFO - Processed 60800000 reads so far
2011-05-19 18:07:05,164 - INFO - Processed 60900000 reads so far
2011-05-19 18:07:17,258 - INFO - Processed 61000000 reads so far
2011-05-19 18:07:28,997 - INFO - Processed 61100000 reads so far
2011-05-19 18:07:32,531 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:142990162-163010162
2011-05-19 18:07:40,464 - INFO - Processed 61200000 reads so far
2011-05-19 18:07:53,613 - INFO - Processed 61300000 reads so far
2011-05-19 18:08:05,651 - INFO - Processed 61400000 reads so far
2011-05-19 18:08:17,688 - INFO - Processed 61500000 reads so far
2011-05-19 18:08:32,569 - INFO - Processed 61600000 reads so far
2011-05-19 18:08:46,440 - INFO - Processed 61700000 reads so far
2011-05-19 18:09:00,139 - INFO - Processed 61800000 reads so far
2011-05-19 18:09:12,952 - INFO - Processed 61900000 reads so far
2011-05-19 18:09:26,006 - INFO - Processed 62000000 reads so far
2011-05-19 18:09:39,429 - INFO - Processed 62100000 reads so far
2011-05-19 18:09:43,627 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:162990257-183010257
2011-05-19 18:09:50,341 - INFO - Processed 62200000 reads so far
2011-05-19 18:10:00,287 - INFO - Processed 62300000 reads so far
2011-05-19 18:10:11,146 - INFO - Processed 62400000 reads so far
2011-05-19 18:10:22,675 - INFO - Processed 62500000 reads so far
2011-05-19 18:10:32,970 - INFO - Processed 62600000 reads so far
2011-05-19 18:10:43,029 - INFO - Processed 62700000 reads so far
2011-05-19 18:10:57,109 - INFO - Processed 62800000 reads so far
2011-05-19 18:11:07,286 - INFO - Processed 62900000 reads so far
2011-05-19 18:11:15,976 - INFO - Processed 63000000 reads so far
2011-05-19 18:11:26,262 - INFO - Processed 63100000 reads so far
2011-05-19 18:11:40,287 - INFO - Processed 63200000 reads so far
2011-05-19 18:11:42,495 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:182990291-203010291
2011-05-19 18:11:52,021 - INFO - Processed 63300000 reads so far
2011-05-19 18:12:04,071 - INFO - Processed 63400000 reads so far
2011-05-19 18:12:15,740 - INFO - Processed 63500000 reads so far
2011-05-19 18:12:27,195 - INFO - Processed 63600000 reads so far
2011-05-19 18:12:43,994 - INFO - Processed 63700000 reads so far
2011-05-19 18:12:54,797 - INFO - Processed 63800000 reads so far
2011-05-19 18:13:05,692 - INFO - Processed 63900000 reads so far
2011-05-19 18:13:15,344 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1_random:0-20010003
2011-05-19 18:13:19,069 - INFO - Processed 64000000 reads so far
2011-05-19 18:13:29,289 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:2990044-23010044
2011-05-19 18:13:29,941 - INFO - Processed 64100000 reads so far
2011-05-19 18:13:41,280 - INFO - Processed 64200000 reads so far
2011-05-19 18:13:54,321 - INFO - Processed 64300000 reads so far
2011-05-19 18:14:07,554 - INFO - Processed 64400000 reads so far
2011-05-19 18:14:21,129 - INFO - Processed 64500000 reads so far
2011-05-19 18:14:37,062 - INFO - Processed 64600000 reads so far
2011-05-19 18:14:50,226 - INFO - Processed 64700000 reads so far
2011-05-19 18:15:01,578 - INFO - Processed 64800000 reads so far
2011-05-19 18:15:15,172 - INFO - Processed 64900000 reads so far
2011-05-19 18:15:29,401 - INFO - Processed 65000000 reads so far
2011-05-19 18:15:40,764 - INFO - Processed 65100000 reads so far
2011-05-19 18:15:47,250 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:22990088-43010088
2011-05-19 18:15:52,731 - INFO - Processed 65200000 reads so far
2011-05-19 18:16:06,240 - INFO - Processed 65300000 reads so far
2011-05-19 18:16:17,645 - INFO - Processed 65400000 reads so far
2011-05-19 18:16:31,003 - INFO - Processed 65500000 reads so far
2011-05-19 18:16:41,475 - INFO - Processed 65600000 reads so far
2011-05-19 18:16:50,816 - INFO - Processed 65700000 reads so far
2011-05-19 18:17:00,257 - INFO - Processed 65800000 reads so far
2011-05-19 18:17:12,109 - INFO - Processed 65900000 reads so far
2011-05-19 18:17:23,378 - INFO - Processed 66000000 reads so far
2011-05-19 18:17:35,332 - INFO - Processed 66100000 reads so far
2011-05-19 18:17:42,176 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:42990110-63010110
2011-05-19 18:17:47,619 - INFO - Processed 66200000 reads so far
2011-05-19 18:17:56,138 - INFO - Processed 66300000 reads so far
2011-05-19 18:18:04,797 - INFO - Processed 66400000 reads so far
2011-05-19 18:24:17,145 - INFO - Processed 66500000 reads so far
2011-05-19 18:24:28,384 - INFO - Processed 66600000 reads so far
2011-05-19 18:24:38,243 - INFO - Processed 66700000 reads so far
2011-05-19 18:24:47,793 - INFO - Processed 66800000 reads so far
2011-05-19 18:24:57,017 - INFO - Processed 66900000 reads so far
2011-05-19 18:25:09,048 - INFO - Processed 67000000 reads so far
2011-05-19 18:25:18,084 - INFO - Processed 67100000 reads so far
2011-05-19 18:25:25,311 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:62990116-83010116
2011-05-19 18:25:26,997 - INFO - Processed 67200000 reads so far
2011-05-19 18:25:35,265 - INFO - Processed 67300000 reads so far
2011-05-19 18:25:44,384 - INFO - Processed 67400000 reads so far
2011-05-19 18:25:54,228 - INFO - Processed 67500000 reads so far
2011-05-19 18:26:02,195 - INFO - Processed 67600000 reads so far
2011-05-19 18:26:10,184 - INFO - Processed 67700000 reads so far
2011-05-19 18:26:18,779 - INFO - Processed 67800000 reads so far
2011-05-19 18:26:28,170 - INFO - Processed 67900000 reads so far
2011-05-19 18:26:36,799 - INFO - Processed 68000000 reads so far
2011-05-19 18:26:45,016 - INFO - Processed 68100000 reads so far
2011-05-19 18:26:55,455 - INFO - Processed 68200000 reads so far
2011-05-19 18:26:55,941 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:82990181-103010181
2011-05-19 18:27:07,387 - INFO - Processed 68300000 reads so far
2011-05-19 18:27:19,999 - INFO - Processed 68400000 reads so far
2011-05-19 18:27:30,852 - INFO - Processed 68500000 reads so far
2011-05-19 18:27:43,025 - INFO - Processed 68600000 reads so far
2011-05-19 18:27:54,508 - INFO - Processed 68700000 reads so far
2011-05-19 18:28:05,838 - INFO - Processed 68800000 reads so far
2011-05-19 18:28:16,682 - INFO - Processed 68900000 reads so far
2011-05-19 18:28:28,392 - INFO - Processed 69000000 reads so far
2011-05-19 18:28:38,083 - INFO - Processed 69100000 reads so far
2011-05-19 18:28:48,074 - INFO - Processed 69200000 reads so far
2011-05-19 18:28:56,418 - INFO - Processed 69300000 reads so far
2011-05-19 18:29:08,239 - INFO - Processed 69400000 reads so far
2011-05-19 18:29:16,568 - INFO - Processed 69500000 reads so far
2011-05-19 18:29:25,417 - INFO - Processed 69600000 reads so far
2011-05-19 18:29:35,657 - INFO - Processed 69700000 reads so far
2011-05-19 18:29:42,388 - INFO - Processed 69800000 reads so far
2011-05-19 18:29:49,447 - INFO - Processed 69900000 reads so far
2011-05-19 18:29:57,420 - INFO - Processed 70000000 reads so far
2011-05-19 18:30:04,865 - INFO - Processed 70100000 reads so far
2011-05-19 18:30:12,514 - INFO - Processed 70200000 reads so far
2011-05-19 18:30:22,596 - INFO - Processed 70300000 reads so far
2011-05-19 18:30:33,754 - INFO - Processed 70400000 reads so far
2011-05-19 18:30:41,275 - INFO - Processed 70500000 reads so far
2011-05-19 18:30:49,830 - INFO - Processed 70600000 reads so far
2011-05-19 18:30:57,867 - INFO - Processed 70700000 reads so far
2011-05-19 18:31:05,651 - INFO - Processed 70800000 reads so far
2011-05-19 18:31:15,161 - INFO - Processed 70900000 reads so far
2011-05-19 18:31:24,971 - INFO - Processed 71000000 reads so far
2011-05-19 18:31:35,816 - INFO - Processed 71100000 reads so far
2011-05-19 18:31:45,139 - INFO - Processed 71200000 reads so far
2011-05-19 18:31:57,138 - INFO - Processed 71300000 reads so far
2011-05-19 18:32:08,581 - INFO - Processed 71400000 reads so far
2011-05-19 18:32:17,813 - INFO - Processed 71500000 reads so far
2011-05-19 18:32:27,456 - INFO - Processed 71600000 reads so far
2011-05-19 18:32:36,611 - INFO - Processed 71700000 reads so far
2011-05-19 18:32:45,695 - INFO - Processed 71800000 reads so far
2011-05-19 18:32:54,730 - INFO - Processed 71900000 reads so far
2011-05-19 18:33:04,816 - INFO - Processed 72000000 reads so far
2011-05-19 18:33:14,954 - INFO - Processed 72100000 reads so far
2011-05-19 18:33:23,989 - INFO - Processed 72200000 reads so far
2011-05-19 18:33:31,317 - INFO - Processed 72300000 reads so far
2011-05-19 18:33:43,567 - INFO - Processed 72400000 reads so far
2011-05-19 18:33:52,054 - INFO - Processed 72500000 reads so far
2011-05-19 18:34:03,403 - INFO - Processed 72600000 reads so far
2011-05-19 18:34:13,948 - INFO - Processed 72700000 reads so far
2011-05-19 18:34:23,654 - INFO - Processed 72800000 reads so far
2011-05-19 18:34:33,920 - INFO - Processed 72900000 reads so far
2011-05-19 18:34:46,116 - INFO - Processed 73000000 reads so far
2011-05-19 18:34:54,919 - INFO - Processed 73100000 reads so far
2011-05-19 18:35:03,509 - INFO - Processed 73200000 reads so far
2011-05-19 18:35:11,995 - INFO - Processed 73300000 reads so far
2011-05-19 18:35:21,846 - INFO - Processed 73400000 reads so far
2011-05-19 18:35:31,269 - INFO - Processed 73500000 reads so far
2011-05-19 18:35:40,651 - INFO - Processed 73600000 reads so far
2011-05-19 18:35:48,832 - INFO - Processed 73700000 reads so far
2011-05-19 18:36:00,580 - INFO - Processed 73800000 reads so far
2011-05-19 18:36:10,170 - INFO - Processed 73900000 reads so far
2011-05-19 18:36:19,670 - INFO - Processed 74000000 reads so far
2011-05-19 18:36:36,005 - INFO - Processed 74100000 reads so far
2011-05-19 18:36:45,313 - INFO - Processed 74200000 reads so far
2011-05-19 18:36:53,785 - INFO - Processed 74300000 reads so far
2011-05-19 18:37:01,156 - INFO - Processed 74400000 reads so far
2011-05-19 18:37:11,146 - INFO - Processed 74500000 reads so far
2011-05-19 18:37:20,832 - INFO - Processed 74600000 reads so far
2011-05-19 18:37:28,930 - INFO - Processed 74700000 reads so far
2011-05-19 18:37:39,386 - INFO - Processed 74800000 reads so far
2011-05-19 18:37:47,215 - INFO - Processed 74900000 reads so far
2011-05-19 18:37:54,805 - INFO - Processed 75000000 reads so far
2011-05-19 18:38:04,184 - INFO - Processed 75100000 reads so far
2011-05-19 18:38:15,180 - INFO - Processed 75200000 reads so far
2011-05-19 18:38:21,670 - INFO - Processed 75300000 reads so far
2011-05-19 18:38:29,243 - INFO - Processed 75400000 reads so far
2011-05-19 18:38:38,203 - INFO - Processed 75500000 reads so far
2011-05-19 18:38:50,301 - INFO - Processed 75600000 reads so far
2011-05-19 18:38:59,359 - INFO - Processed 75700000 reads so far
2011-05-19 18:39:09,189 - INFO - Processed 75800000 reads so far
2011-05-19 18:39:17,287 - INFO - Processed 75900000 reads so far
2011-05-19 18:39:26,737 - INFO - Processed 76000000 reads so far
2011-05-19 18:39:34,505 - INFO - Processed 76100000 reads so far
2011-05-19 18:39:42,929 - INFO - Processed 76200000 reads so far
2011-05-19 18:39:51,492 - INFO - Processed 76300000 reads so far
2011-05-19 18:40:01,872 - INFO - Processed 76400000 reads so far
2011-05-19 18:40:11,076 - INFO - Processed 76500000 reads so far
2011-05-19 18:40:19,604 - INFO - Processed 76600000 reads so far
2011-05-19 18:40:28,476 - INFO - Processed 76700000 reads so far
2011-05-19 18:40:37,761 - INFO - Processed 76800000 reads so far
2011-05-19 18:40:47,178 - INFO - Processed 76900000 reads so far
2011-05-19 18:40:57,717 - INFO - Processed 77000000 reads so far
2011-05-19 18:41:06,387 - INFO - Processed 77100000 reads so far
2011-05-19 18:41:15,260 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:102990186-123010186
2011-05-19 18:41:20,629 - INFO - Processed 77200000 reads so far
2011-05-19 18:41:30,015 - INFO - Processed 77300000 reads so far
2011-05-19 18:41:39,103 - INFO - Processed 77400000 reads so far
2011-05-19 18:41:49,458 - INFO - Processed 77500000 reads so far
2011-05-19 18:41:58,207 - INFO - Processed 77600000 reads so far
2011-05-19 18:42:08,922 - INFO - Processed 77700000 reads so far
2011-05-19 18:42:19,513 - INFO - Processed 77800000 reads so far
2011-05-19 18:42:27,568 - INFO - Processed 77900000 reads so far
2011-05-19 18:42:36,678 - INFO - Processed 78000000 reads so far
2011-05-19 18:42:46,404 - INFO - Processed 78100000 reads so far
2011-05-19 18:42:54,989 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:122990189-143010189
2011-05-19 18:42:57,258 - INFO - Processed 78200000 reads so far
2011-05-19 18:43:06,163 - INFO - Processed 78300000 reads so far
2011-05-19 18:43:15,383 - INFO - Processed 78400000 reads so far
2011-05-19 18:43:28,183 - INFO - Processed 78500000 reads so far
2011-05-19 18:43:41,027 - INFO - Processed 78600000 reads so far
2011-05-19 18:43:54,802 - INFO - Processed 78700000 reads so far
2011-05-19 18:44:09,334 - INFO - Processed 78800000 reads so far
2011-05-19 18:44:22,343 - INFO - Processed 78900000 reads so far
2011-05-19 18:44:34,409 - INFO - Processed 79000000 reads so far
2011-05-19 18:44:50,111 - INFO - Processed 79100000 reads so far
2011-05-19 18:45:02,467 - INFO - Processed 79200000 reads so far
2011-05-19 18:45:06,676 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:142990224-163010224
2011-05-19 18:45:14,926 - INFO - Processed 79300000 reads so far
2011-05-19 18:45:27,144 - INFO - Processed 79400000 reads so far
2011-05-19 18:45:36,869 - INFO - Processed 79500000 reads so far
2011-05-19 18:45:48,963 - INFO - Processed 79600000 reads so far
2011-05-19 18:46:01,238 - INFO - Processed 79700000 reads so far
2011-05-19 18:46:12,739 - INFO - Processed 79800000 reads so far
2011-05-19 18:46:27,509 - INFO - Processed 79900000 reads so far
2011-05-19 18:46:40,378 - INFO - Processed 80000000 reads so far
2011-05-19 18:46:50,612 - INFO - Processed 80100000 reads so far
2011-05-19 18:47:01,031 - INFO - Processed 80200000 reads so far
2011-05-19 18:47:09,713 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:162990232-183010232
2011-05-19 18:47:10,638 - INFO - Processed 80300000 reads so far
2011-05-19 18:47:22,871 - INFO - Processed 80400000 reads so far
2011-05-19 18:47:34,061 - INFO - Processed 80500000 reads so far
2011-05-19 18:47:47,360 - INFO - Processed 80600000 reads so far
2011-05-19 18:47:59,097 - INFO - Processed 80700000 reads so far
2011-05-19 18:48:12,014 - INFO - Processed 80800000 reads so far
2011-05-19 18:48:25,153 - INFO - Processed 80900000 reads so far
2011-05-19 18:48:37,544 - INFO - Processed 81000000 reads so far
2011-05-19 18:48:49,724 - INFO - Processed 81100000 reads so far
2011-05-19 18:49:02,205 - INFO - Processed 81200000 reads so far
2011-05-19 18:49:12,811 - INFO - Processed 81300000 reads so far
2011-05-19 18:49:14,232 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:2989998-23009998
2011-05-19 18:49:25,785 - INFO - Processed 81400000 reads so far
2011-05-19 18:49:36,040 - INFO - Processed 81500000 reads so far
2011-05-19 18:49:50,930 - INFO - Processed 81600000 reads so far
2011-05-19 18:50:06,382 - INFO - Processed 81700000 reads so far
2011-05-19 18:50:18,556 - INFO - Processed 81800000 reads so far
2011-05-19 18:50:31,741 - INFO - Processed 81900000 reads so far
2011-05-19 18:50:41,813 - INFO - Processed 82000000 reads so far
2011-05-19 18:50:52,604 - INFO - Processed 82100000 reads so far
2011-05-19 18:51:04,404 - INFO - Processed 82200000 reads so far
2011-05-19 18:51:16,014 - INFO - Processed 82300000 reads so far
2011-05-19 18:51:21,115 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:22990000-43010000
2011-05-19 18:51:27,621 - INFO - Processed 82400000 reads so far
2011-05-19 18:51:39,723 - INFO - Processed 82500000 reads so far
2011-05-19 18:51:51,609 - INFO - Processed 82600000 reads so far
2011-05-19 18:52:02,400 - INFO - Processed 82700000 reads so far
2011-05-19 18:52:15,619 - INFO - Processed 82800000 reads so far
2011-05-19 18:52:28,801 - INFO - Processed 82900000 reads so far
2011-05-19 18:52:40,401 - INFO - Processed 83000000 reads so far
2011-05-19 18:52:53,649 - INFO - Processed 83100000 reads so far
2011-05-19 18:53:04,905 - INFO - Processed 83200000 reads so far
2011-05-19 18:53:16,016 - INFO - Processed 83300000 reads so far
2011-05-19 18:53:26,090 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:42990043-63010043
2011-05-19 18:53:27,323 - INFO - Processed 83400000 reads so far
2011-05-19 18:53:40,724 - INFO - Processed 83500000 reads so far
2011-05-19 18:53:50,847 - INFO - Processed 83600000 reads so far
2011-05-19 18:54:01,760 - INFO - Processed 83700000 reads so far
2011-05-19 18:54:11,638 - INFO - Processed 83800000 reads so far
2011-05-19 18:54:58,272 - INFO - Processed 83900000 reads so far
2011-05-19 18:55:08,361 - INFO - Processed 84000000 reads so far
2011-05-19 18:55:18,483 - INFO - Processed 84100000 reads so far
2011-05-19 18:55:30,723 - INFO - Processed 84200000 reads so far
2011-05-19 18:55:39,855 - INFO - Processed 84300000 reads so far
2011-05-19 18:55:50,394 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:62990046-83010046
2011-05-19 18:55:51,104 - INFO - Processed 84400000 reads so far
2011-05-19 18:56:03,146 - INFO - Processed 84500000 reads so far
2011-05-19 18:56:13,793 - INFO - Processed 84600000 reads so far
2011-05-19 18:56:26,085 - INFO - Processed 84700000 reads so far
2011-05-19 18:56:38,569 - INFO - Processed 84800000 reads so far
2011-05-19 18:56:52,493 - INFO - Processed 84900000 reads so far
2011-05-19 18:57:04,783 - INFO - Processed 85000000 reads so far
2011-05-19 18:57:18,029 - INFO - Processed 85100000 reads so far
2011-05-19 18:57:28,291 - INFO - Processed 85200000 reads so far
2011-05-19 18:57:39,217 - INFO - Processed 85300000 reads so far
2011-05-19 18:57:51,556 - INFO - Processed 85400000 reads so far
2011-05-19 18:57:51,766 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:82990073-103010073
2011-05-19 18:58:00,428 - INFO - Processed 85500000 reads so far
2011-05-19 18:58:08,812 - INFO - Processed 85600000 reads so far
2011-05-19 18:58:18,510 - INFO - Processed 85700000 reads so far
2011-05-19 18:58:29,039 - INFO - Processed 85800000 reads so far
2011-05-19 18:58:37,498 - INFO - Processed 85900000 reads so far
2011-05-19 18:58:46,801 - INFO - Processed 86000000 reads so far
2011-05-19 18:58:56,648 - INFO - Processed 86100000 reads so far
2011-05-19 18:59:07,940 - INFO - Processed 86200000 reads so far
2011-05-19 18:59:17,329 - INFO - Processed 86300000 reads so far
2011-05-19 18:59:27,592 - INFO - Processed 86400000 reads so far
2011-05-19 18:59:31,248 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:102990122-123010122
2011-05-19 18:59:36,459 - INFO - Processed 86500000 reads so far
2011-05-19 18:59:48,042 - INFO - Processed 86600000 reads so far
2011-05-19 18:59:56,265 - INFO - Processed 86700000 reads so far
2011-05-19 19:00:05,728 - INFO - Processed 86800000 reads so far
2011-05-19 19:00:15,181 - INFO - Processed 86900000 reads so far
2011-05-19 19:00:24,244 - INFO - Processed 87000000 reads so far
2011-05-19 19:00:33,187 - INFO - Processed 87100000 reads so far
2011-05-19 19:00:42,289 - INFO - Processed 87200000 reads so far
2011-05-19 19:00:51,734 - INFO - Processed 87300000 reads so far
2011-05-19 19:01:00,627 - INFO - Processed 87400000 reads so far
2011-05-19 19:01:09,671 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:122990123-143010123
2011-05-19 19:01:13,979 - INFO - Processed 87500000 reads so far
2011-05-19 19:01:24,503 - INFO - Processed 87600000 reads so far
2011-05-19 19:01:38,914 - INFO - Processed 87700000 reads so far
2011-05-19 19:01:48,607 - INFO - Processed 87800000 reads so far
2011-05-19 19:01:58,966 - INFO - Processed 87900000 reads so far
2011-05-19 19:02:08,295 - INFO - Processed 88000000 reads so far
2011-05-19 19:02:21,381 - INFO - Processed 88100000 reads so far
2011-05-19 19:02:31,961 - INFO - Processed 88200000 reads so far
2011-05-19 19:02:41,350 - INFO - Processed 88300000 reads so far
2011-05-19 19:02:52,414 - INFO - Processed 88400000 reads so far
2011-05-19 19:03:02,866 - INFO - Processed 88500000 reads so far
2011-05-19 19:03:03,053 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:142990143-163010143
2011-05-19 19:03:12,494 - INFO - Processed 88600000 reads so far
2011-05-19 19:03:24,034 - INFO - Processed 88700000 reads so far
2011-05-19 19:03:36,047 - INFO - Processed 88800000 reads so far
2011-05-19 19:03:48,273 - INFO - Processed 88900000 reads so far
2011-05-19 19:03:56,884 - INFO - Processed 89000000 reads so far
2011-05-19 19:04:06,939 - INFO - Processed 89100000 reads so far
2011-05-19 19:04:16,577 - INFO - Processed 89200000 reads so far
2011-05-19 19:04:25,784 - INFO - Processed 89300000 reads so far
2011-05-19 19:04:34,179 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3_random:0-20010015
2011-05-19 19:04:34,316 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:2989969-23009969
2011-05-19 19:04:36,460 - INFO - Processed 89400000 reads so far
2011-05-19 19:04:48,589 - INFO - Processed 89500000 reads so far
2011-05-19 19:04:59,825 - INFO - Processed 89600000 reads so far
2011-05-19 19:05:08,651 - INFO - Processed 89700000 reads so far
2011-05-19 19:05:20,275 - INFO - Processed 89800000 reads so far
2011-05-19 19:05:32,139 - INFO - Processed 89900000 reads so far
2011-05-19 19:05:41,893 - INFO - Processed 90000000 reads so far
2011-05-19 19:05:52,211 - INFO - Processed 90100000 reads so far
2011-05-19 19:06:01,968 - INFO - Processed 90200000 reads so far
2011-05-19 19:06:11,047 - INFO - Processed 90300000 reads so far
2011-05-19 19:06:20,768 - INFO - Processed 90400000 reads so far
2011-05-19 19:06:28,665 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:22989979-43009979
2011-05-19 19:06:35,783 - INFO - Processed 90500000 reads so far
2011-05-19 19:06:46,571 - INFO - Processed 90600000 reads so far
2011-05-19 19:06:57,719 - INFO - Processed 90700000 reads so far
2011-05-19 19:07:09,418 - INFO - Processed 90800000 reads so far
2011-05-19 19:07:17,402 - INFO - Processed 90900000 reads so far
2011-05-19 19:07:25,064 - INFO - Processed 91000000 reads so far
2011-05-19 19:07:35,203 - INFO - Processed 91100000 reads so far
2011-05-19 19:07:43,206 - INFO - Processed 91200000 reads so far
2011-05-19 19:07:54,094 - INFO - Processed 91300000 reads so far
2011-05-19 19:08:06,114 - INFO - Processed 91400000 reads so far
2011-05-19 19:08:07,798 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:42989986-63009986
2011-05-19 19:08:19,713 - INFO - Processed 91500000 reads so far
2011-05-19 19:08:32,442 - INFO - Processed 91600000 reads so far
2011-05-19 19:08:42,108 - INFO - Processed 91700000 reads so far
2011-05-19 19:08:52,123 - INFO - Processed 91800000 reads so far
2011-05-19 19:09:00,462 - INFO - Processed 91900000 reads so far
2011-05-19 19:09:09,155 - INFO - Processed 92000000 reads so far
2011-05-19 19:09:16,926 - INFO - Processed 92100000 reads so far
2011-05-19 19:09:25,812 - INFO - Processed 92200000 reads so far
2011-05-19 19:09:36,695 - INFO - Processed 92300000 reads so far
2011-05-19 19:09:47,664 - INFO - Processed 92400000 reads so far
2011-05-19 19:09:55,630 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:62990013-83010013
2011-05-19 19:10:01,310 - INFO - Processed 92500000 reads so far
2011-05-19 19:10:12,554 - INFO - Processed 92600000 reads so far
2011-05-19 19:10:55,009 - INFO - Processed 92700000 reads so far
2011-05-19 19:11:30,011 - INFO - Processed 92800000 reads so far
2011-05-19 19:11:45,646 - INFO - Processed 92900000 reads so far
2011-05-19 19:12:02,111 - INFO - Processed 93000000 reads so far
2011-05-19 19:12:14,320 - INFO - Processed 93100000 reads so far
2011-05-19 19:12:28,000 - INFO - Processed 93200000 reads so far
2011-05-19 19:12:37,829 - INFO - Processed 93300000 reads so far
2011-05-19 19:12:50,797 - INFO - Processed 93400000 reads so far
2011-05-19 19:13:00,667 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:82990030-103010030
2011-05-19 19:13:02,898 - INFO - Processed 93500000 reads so far
2011-05-19 19:13:10,966 - INFO - Processed 93600000 reads so far
2011-05-19 19:13:20,834 - INFO - Processed 93700000 reads so far
2011-05-19 19:13:30,668 - INFO - Processed 93800000 reads so far
2011-05-19 19:13:43,553 - INFO - Processed 93900000 reads so far
2011-05-19 19:13:56,643 - INFO - Processed 94000000 reads so far
2011-05-19 19:14:05,161 - INFO - Processed 94100000 reads so far
2011-05-19 19:14:16,450 - INFO - Processed 94200000 reads so far
2011-05-19 19:14:28,014 - INFO - Processed 94300000 reads so far
2011-05-19 19:14:38,776 - INFO - Processed 94400000 reads so far
2011-05-19 19:14:48,550 - INFO - Processed 94500000 reads so far
2011-05-19 19:14:53,418 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:102990056-123010056
2011-05-19 19:14:58,981 - INFO - Processed 94600000 reads so far
2011-05-19 19:15:09,281 - INFO - Processed 94700000 reads so far
2011-05-19 19:15:19,267 - INFO - Processed 94800000 reads so far
2011-05-19 19:15:30,787 - INFO - Processed 94900000 reads so far
2011-05-19 19:15:44,821 - INFO - Processed 95000000 reads so far
2011-05-19 19:15:54,644 - INFO - Processed 95100000 reads so far
2011-05-19 19:16:04,766 - INFO - Processed 95200000 reads so far
2011-05-19 19:16:17,822 - INFO - Processed 95300000 reads so far
2011-05-19 19:16:32,302 - INFO - Processed 95400000 reads so far
2011-05-19 19:16:40,711 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:122990125-143010125
2011-05-19 19:16:43,597 - INFO - Processed 95500000 reads so far
2011-05-19 19:16:53,827 - INFO - Processed 95600000 reads so far
2011-05-19 19:17:02,927 - INFO - Processed 95700000 reads so far
2011-05-19 19:17:14,963 - INFO - Processed 95800000 reads so far
2011-05-19 19:17:25,954 - INFO - Processed 95900000 reads so far
2011-05-19 19:17:34,618 - INFO - Processed 96000000 reads so far
2011-05-19 19:17:43,865 - INFO - Processed 96100000 reads so far
2011-05-19 19:17:53,331 - INFO - Processed 96200000 reads so far
2011-05-19 19:18:03,353 - INFO - Processed 96300000 reads so far
2011-05-19 19:18:13,420 - INFO - Processed 96400000 reads so far
2011-05-19 19:18:18,050 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:142990131-163010131
2011-05-19 19:18:21,704 - INFO - Processed 96500000 reads so far
2011-05-19 19:18:32,684 - INFO - Processed 96600000 reads so far
2011-05-19 19:18:42,016 - INFO - Processed 96700000 reads so far
2011-05-19 19:18:50,280 - INFO - Processed 96800000 reads so far
2011-05-19 19:18:58,759 - INFO - Processed 96900000 reads so far
2011-05-19 19:19:10,766 - INFO - Processed 97000000 reads so far
2011-05-19 19:19:19,098 - INFO - Processed 97100000 reads so far
2011-05-19 19:19:26,437 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4_random:0-20010053
2011-05-19 19:19:26,940 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:2990037-23010037
2011-05-19 19:19:28,820 - INFO - Processed 97200000 reads so far
2011-05-19 19:19:42,476 - INFO - Processed 97300000 reads so far
2011-05-19 19:19:54,810 - INFO - Processed 97400000 reads so far
2011-05-19 19:20:03,632 - INFO - Processed 97500000 reads so far
2011-05-19 19:20:12,782 - INFO - Processed 97600000 reads so far
2011-05-19 19:20:22,109 - INFO - Processed 97700000 reads so far
2011-05-19 19:20:30,309 - INFO - Processed 97800000 reads so far
2011-05-19 19:20:39,162 - INFO - Processed 97900000 reads so far
2011-05-19 19:20:47,713 - INFO - Processed 98000000 reads so far
2011-05-19 19:20:58,433 - INFO - Processed 98100000 reads so far
2011-05-19 19:21:06,902 - INFO - Processed 98200000 reads so far
2011-05-19 19:21:08,879 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:22990512-43010512
2011-05-19 19:21:17,248 - INFO - Processed 98300000 reads so far
2011-05-19 19:21:28,684 - INFO - Processed 98400000 reads so far
2011-05-19 19:21:41,757 - INFO - Processed 98500000 reads so far
2011-05-19 19:21:52,653 - INFO - Processed 98600000 reads so far
2011-05-19 19:22:05,743 - INFO - Processed 98700000 reads so far
2011-05-19 19:22:17,034 - INFO - Processed 98800000 reads so far
2011-05-19 19:22:28,223 - INFO - Processed 98900000 reads so far
2011-05-19 19:22:39,790 - INFO - Processed 99000000 reads so far
2011-05-19 19:22:48,942 - INFO - Processed 99100000 reads so far
2011-05-19 19:22:59,909 - INFO - Processed 99200000 reads so far
2011-05-19 19:23:03,036 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:42990530-63010530
2011-05-19 19:23:07,033 - INFO - Processed 99300000 reads so far
2011-05-19 19:23:19,729 - INFO - Processed 99400000 reads so far
2011-05-19 19:23:30,227 - INFO - Processed 99500000 reads so far
2011-05-19 19:23:38,186 - INFO - Processed 99600000 reads so far
2011-05-19 19:23:49,150 - INFO - Processed 99700000 reads so far
2011-05-19 19:23:57,912 - INFO - Processed 99800000 reads so far
2011-05-19 19:24:07,935 - INFO - Processed 99900000 reads so far
2011-05-19 19:24:17,540 - INFO - Processed 100000000 reads so far
2011-05-19 19:24:28,646 - INFO - Processed 100100000 reads so far
2011-05-19 19:24:38,173 - INFO - Processed 100200000 reads so far
2011-05-19 19:24:43,936 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:62990534-83010534
2011-05-19 19:24:50,585 - INFO - Processed 100300000 reads so far
2011-05-19 19:25:01,652 - INFO - Processed 100400000 reads so far
2011-05-19 19:25:12,141 - INFO - Processed 100500000 reads so far
2011-05-19 19:25:22,561 - INFO - Processed 100600000 reads so far
2011-05-19 19:25:32,141 - INFO - Processed 100700000 reads so far
2011-05-19 19:25:44,612 - INFO - Processed 100800000 reads so far
2011-05-19 19:25:57,758 - INFO - Processed 100900000 reads so far
2011-05-19 19:26:08,263 - INFO - Processed 101000000 reads so far
2011-05-19 19:26:20,454 - INFO - Processed 101100000 reads so far
2011-05-19 19:26:30,771 - INFO - Processed 101200000 reads so far
2011-05-19 19:26:36,440 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:82990539-103010539
2011-05-19 19:26:41,594 - INFO - Processed 101300000 reads so far
2011-05-19 19:26:53,582 - INFO - Processed 101400000 reads so far
2011-05-19 19:27:04,365 - INFO - Processed 101500000 reads so far
2011-05-19 19:27:14,542 - INFO - Processed 101600000 reads so far
2011-05-19 19:27:23,606 - INFO - Processed 101700000 reads so far
2011-05-19 19:27:34,061 - INFO - Processed 101800000 reads so far
2011-05-19 19:27:45,846 - INFO - Processed 101900000 reads so far
2011-05-19 19:27:55,016 - INFO - Processed 102000000 reads so far
2011-05-19 19:28:10,909 - INFO - Processed 102100000 reads so far
2011-05-19 19:28:22,720 - INFO - Processed 102200000 reads so far
2011-05-19 19:28:27,383 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:102990549-123010549
2011-05-19 19:28:36,447 - INFO - Processed 102300000 reads so far
2011-05-19 19:28:46,211 - INFO - Processed 102400000 reads so far
2011-05-19 19:28:53,256 - INFO - Processed 102500000 reads so far
2011-05-19 19:29:01,771 - INFO - Processed 102600000 reads so far
2011-05-19 19:29:09,093 - INFO - Processed 102700000 reads so far
2011-05-19 19:29:21,099 - INFO - Processed 102800000 reads so far
2011-05-19 19:29:30,220 - INFO - Processed 102900000 reads so far
2011-05-19 19:29:37,272 - INFO - Processed 103000000 reads so far
2011-05-19 19:29:46,703 - INFO - Processed 103100000 reads so far
2011-05-19 19:29:56,559 - INFO - Processed 103200000 reads so far
2011-05-19 19:30:01,291 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:122990558-143010558
2011-05-19 19:30:06,042 - INFO - Processed 103300000 reads so far
2011-05-19 19:30:14,698 - INFO - Processed 103400000 reads so far
2011-05-19 19:30:24,940 - INFO - Processed 103500000 reads so far
2011-05-19 19:30:32,683 - INFO - Processed 103600000 reads so far
2011-05-19 19:30:41,637 - INFO - Processed 103700000 reads so far
2011-05-19 19:30:49,727 - INFO - Processed 103800000 reads so far
2011-05-19 19:31:01,314 - INFO - Processed 103900000 reads so far
2011-05-19 19:31:11,993 - INFO - Processed 104000000 reads so far
2011-05-19 19:31:19,867 - INFO - Processed 104100000 reads so far
2011-05-19 19:31:34,505 - INFO - Processed 104200000 reads so far
2011-05-19 19:31:39,584 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:142990562-163010562
2011-05-19 19:31:41,547 - INFO - Processed 104300000 reads so far
2011-05-19 19:31:51,565 - INFO - Processed 104400000 reads so far
2011-05-19 19:32:00,701 - INFO - Processed 104500000 reads so far
2011-05-19 19:32:12,812 - INFO - Processed 104600000 reads so far
2011-05-19 19:32:23,273 - INFO - Processed 104700000 reads so far
2011-05-19 19:32:29,494 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5_random:0-20010008
2011-05-19 19:32:29,778 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:2989983-23009983
2011-05-19 19:32:33,636 - INFO - Processed 104800000 reads so far
2011-05-19 19:32:46,874 - INFO - Processed 104900000 reads so far
2011-05-19 19:32:57,438 - INFO - Processed 105000000 reads so far
2011-05-19 19:33:06,474 - INFO - Processed 105100000 reads so far
2011-05-19 19:33:13,801 - INFO - Processed 105200000 reads so far
2011-05-19 19:33:23,127 - INFO - Processed 105300000 reads so far
2011-05-19 19:33:32,410 - INFO - Processed 105400000 reads so far
2011-05-19 19:33:40,995 - INFO - Processed 105500000 reads so far
2011-05-19 19:33:49,116 - INFO - Processed 105600000 reads so far
2011-05-19 19:33:58,852 - INFO - Processed 105700000 reads so far
2011-05-19 19:34:04,585 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:22989988-43009988
2011-05-19 19:34:06,226 - INFO - Processed 105800000 reads so far
2011-05-19 19:34:13,889 - INFO - Processed 105900000 reads so far
2011-05-19 19:34:25,810 - INFO - Processed 106000000 reads so far
2011-05-19 19:34:35,304 - INFO - Processed 106100000 reads so far
2011-05-19 19:34:46,948 - INFO - Processed 106200000 reads so far
2011-05-19 19:34:58,470 - INFO - Processed 106300000 reads so far
2011-05-19 19:35:10,105 - INFO - Processed 106400000 reads so far
2011-05-19 19:35:21,461 - INFO - Processed 106500000 reads so far
2011-05-19 19:35:33,716 - INFO - Processed 106600000 reads so far
2011-05-19 19:35:45,327 - INFO - Processed 106700000 reads so far
2011-05-19 19:35:56,720 - INFO - Processed 106800000 reads so far
2011-05-19 19:36:00,381 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:42990011-63010011
2011-05-19 19:36:08,617 - INFO - Processed 106900000 reads so far
2011-05-19 19:36:20,725 - INFO - Processed 107000000 reads so far
2011-05-19 19:36:32,888 - INFO - Processed 107100000 reads so far
2011-05-19 19:36:45,618 - INFO - Processed 107200000 reads so far
2011-05-19 19:36:57,649 - INFO - Processed 107300000 reads so far
2011-05-19 19:37:10,513 - INFO - Processed 107400000 reads so far
2011-05-19 19:37:22,503 - INFO - Processed 107500000 reads so far
2011-05-19 19:37:33,482 - INFO - Processed 107600000 reads so far
2011-05-19 19:37:45,385 - INFO - Processed 107700000 reads so far
2011-05-19 19:37:57,195 - INFO - Processed 107800000 reads so far
2011-05-19 19:38:05,639 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:62990023-83010023
2011-05-19 19:38:08,312 - INFO - Processed 107900000 reads so far
2011-05-19 19:38:20,852 - INFO - Processed 108000000 reads so far
2011-05-19 19:38:33,629 - INFO - Processed 108100000 reads so far
2011-05-19 19:38:44,759 - INFO - Processed 108200000 reads so far
2011-05-19 19:38:55,748 - INFO - Processed 108300000 reads so far
2011-05-19 19:39:07,349 - INFO - Processed 108400000 reads so far
2011-05-19 19:39:18,522 - INFO - Processed 108500000 reads so far
2011-05-19 19:39:31,478 - INFO - Processed 108600000 reads so far
2011-05-19 19:39:43,134 - INFO - Processed 108700000 reads so far
2011-05-19 19:39:54,278 - INFO - Processed 108800000 reads so far
2011-05-19 19:40:31,465 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:82990051-103010051
2011-05-19 19:40:34,506 - INFO - Processed 108900000 reads so far
2011-05-19 19:40:46,714 - INFO - Processed 109000000 reads so far
2011-05-19 19:40:58,820 - INFO - Processed 109100000 reads so far
2011-05-19 19:41:10,923 - INFO - Processed 109200000 reads so far
2011-05-19 19:41:22,674 - INFO - Processed 109300000 reads so far
2011-05-19 19:41:37,300 - INFO - Processed 109400000 reads so far
2011-05-19 19:41:48,896 - INFO - Processed 109500000 reads so far
2011-05-19 19:42:00,515 - INFO - Processed 109600000 reads so far
2011-05-19 19:42:13,903 - INFO - Processed 109700000 reads so far
2011-05-19 19:42:27,191 - INFO - Processed 109800000 reads so far
2011-05-19 19:42:37,073 - INFO - Processed 109900000 reads so far
2011-05-19 19:42:39,996 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:102990078-123010078
2011-05-19 19:42:51,435 - INFO - Processed 110000000 reads so far
2011-05-19 19:43:00,367 - INFO - Processed 110100000 reads so far
2011-05-19 19:43:08,060 - INFO - Processed 110200000 reads so far
2011-05-19 19:43:17,919 - INFO - Processed 110300000 reads so far
2011-05-19 19:43:27,965 - INFO - Processed 110400000 reads so far
2011-05-19 19:43:36,579 - INFO - Processed 110500000 reads so far
2011-05-19 19:43:45,267 - INFO - Processed 110600000 reads so far
2011-05-19 19:43:59,764 - INFO - Processed 110700000 reads so far
2011-05-19 19:44:09,922 - INFO - Processed 110800000 reads so far
2011-05-19 19:44:20,009 - INFO - Processed 110900000 reads so far
2011-05-19 19:44:27,810 - INFO - Processed 111000000 reads so far
2011-05-19 19:44:36,654 - INFO - Processed 111100000 reads so far
2011-05-19 19:44:48,968 - INFO - Processed 111200000 reads so far
2011-05-19 19:45:00,681 - INFO - Processed 111300000 reads so far
2011-05-19 19:45:16,794 - INFO - Processed 111400000 reads so far
2011-05-19 19:45:25,242 - INFO - Processed 111500000 reads so far
2011-05-19 19:45:32,758 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:122990084-143010084
2011-05-19 19:45:34,310 - INFO - Processed 111600000 reads so far
2011-05-19 19:45:45,875 - INFO - Processed 111700000 reads so far
2011-05-19 19:45:56,679 - INFO - Processed 111800000 reads so far
2011-05-19 19:46:07,508 - INFO - Processed 111900000 reads so far
2011-05-19 19:46:24,296 - INFO - Processed 112000000 reads so far
2011-05-19 19:46:37,687 - INFO - Processed 112100000 reads so far
2011-05-19 19:46:50,321 - INFO - Processed 112200000 reads so far
2011-05-19 19:47:02,014 - INFO - Processed 112300000 reads so far
2011-05-19 19:47:13,370 - INFO - Processed 112400000 reads so far
2011-05-19 19:47:26,734 - INFO - Processed 112500000 reads so far
2011-05-19 19:47:38,146 - INFO - Processed 112600000 reads so far
2011-05-19 19:47:39,821 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:142990087-163010087
2011-05-19 19:47:48,412 - INFO - Processed 112700000 reads so far
2011-05-19 19:48:01,134 - INFO - Processed 112800000 reads so far
2011-05-19 19:48:13,570 - INFO - Processed 112900000 reads so far
2011-05-19 19:48:21,347 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:2990027-23010027
2011-05-19 19:48:24,943 - INFO - Processed 113000000 reads so far
2011-05-19 19:48:37,875 - INFO - Processed 113100000 reads so far
2011-05-19 19:48:48,905 - INFO - Processed 113200000 reads so far
2011-05-19 19:49:00,382 - INFO - Processed 113300000 reads so far
2011-05-19 19:49:11,913 - INFO - Processed 113400000 reads so far
2011-05-19 19:49:23,639 - INFO - Processed 113500000 reads so far
2011-05-19 19:49:37,195 - INFO - Processed 113600000 reads so far
2011-05-19 19:49:50,481 - INFO - Processed 113700000 reads so far
2011-05-19 19:50:00,818 - INFO - Processed 113800000 reads so far
2011-05-19 19:50:06,499 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:22990142-43010142
2011-05-19 19:50:10,007 - INFO - Processed 113900000 reads so far
2011-05-19 19:50:19,094 - INFO - Processed 114000000 reads so far
2011-05-19 19:50:30,425 - INFO - Processed 114100000 reads so far
2011-05-19 19:50:41,836 - INFO - Processed 114200000 reads so far
2011-05-19 19:50:51,512 - INFO - Processed 114300000 reads so far
2011-05-19 19:51:03,489 - INFO - Processed 114400000 reads so far
2011-05-19 19:51:14,917 - INFO - Processed 114500000 reads so far
2011-05-19 19:51:26,257 - INFO - Processed 114600000 reads so far
2011-05-19 19:51:33,897 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:46351877-66371877
2011-05-19 19:51:37,186 - INFO - Processed 114700000 reads so far
2011-05-19 19:51:49,659 - INFO - Processed 114800000 reads so far
2011-05-19 19:51:58,806 - INFO - Processed 114900000 reads so far
2011-05-19 19:52:11,008 - INFO - Processed 115000000 reads so far
2011-05-19 19:52:21,301 - INFO - Processed 115100000 reads so far
2011-05-19 19:52:30,782 - INFO - Processed 115200000 reads so far
2011-05-19 19:52:41,700 - INFO - Processed 115300000 reads so far
2011-05-19 19:52:51,102 - INFO - Processed 115400000 reads so far
2011-05-19 19:53:00,828 - INFO - Processed 115500000 reads so far
2011-05-19 19:53:13,645 - INFO - Processed 115600000 reads so far
2011-05-19 19:53:22,072 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:66351913-86371913
2011-05-19 19:53:24,399 - INFO - Processed 115700000 reads so far
2011-05-19 19:53:34,648 - INFO - Processed 115800000 reads so far
2011-05-19 19:53:46,477 - INFO - Processed 115900000 reads so far
2011-05-19 19:53:55,482 - INFO - Processed 116000000 reads so far
2011-05-19 19:54:04,715 - INFO - Processed 116100000 reads so far
2011-05-19 19:54:14,340 - INFO - Processed 116200000 reads so far
2011-05-19 19:54:27,377 - INFO - Processed 116300000 reads so far
2011-05-19 19:54:38,659 - INFO - Processed 116400000 reads so far
2011-05-19 19:54:48,976 - INFO - Processed 116500000 reads so far
2011-05-19 19:55:01,226 - INFO - Processed 116600000 reads so far
2011-05-19 19:55:09,329 - INFO - Processed 116700000 reads so far
2011-05-19 19:55:14,730 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:86351934-106371934
2011-05-19 19:55:20,428 - INFO - Processed 116800000 reads so far
2011-05-19 19:55:30,787 - INFO - Processed 116900000 reads so far
2011-05-19 19:55:42,150 - INFO - Processed 117000000 reads so far
2011-05-19 19:55:54,416 - INFO - Processed 117100000 reads so far
2011-05-19 19:56:07,337 - INFO - Processed 117200000 reads so far
2011-05-19 19:56:17,750 - INFO - Processed 117300000 reads so far
2011-05-19 19:56:27,131 - INFO - Processed 117400000 reads so far
2011-05-19 19:56:35,379 - INFO - Processed 117500000 reads so far
2011-05-19 19:56:45,260 - INFO - Processed 117600000 reads so far
2011-05-19 19:56:53,529 - INFO - Processed 117700000 reads so far
2011-05-19 19:57:02,396 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:106351938-126371938
2011-05-19 19:57:05,240 - INFO - Processed 117800000 reads so far
2011-05-19 19:57:18,567 - INFO - Processed 117900000 reads so far
2011-05-19 19:57:30,241 - INFO - Processed 118000000 reads so far
2011-05-19 19:57:40,052 - INFO - Processed 118100000 reads so far
2011-05-19 19:57:50,583 - INFO - Processed 118200000 reads so far
2011-05-19 19:58:03,057 - INFO - Processed 118300000 reads so far
2011-05-19 19:58:11,561 - INFO - Processed 118400000 reads so far
2011-05-19 19:58:23,036 - INFO - Processed 118500000 reads so far
2011-05-19 19:58:36,138 - INFO - Processed 118600000 reads so far
2011-05-19 19:58:44,362 - INFO - Processed 118700000 reads so far
2011-05-19 19:58:56,874 - INFO - Processed 118800000 reads so far
2011-05-19 19:58:58,768 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:126351977-146371977
2011-05-19 19:59:08,732 - INFO - Processed 118900000 reads so far
2011-05-19 19:59:20,789 - INFO - Processed 119000000 reads so far
2011-05-19 19:59:33,412 - INFO - Processed 119100000 reads so far
2011-05-19 19:59:47,970 - INFO - Processed 119200000 reads so far
2011-05-19 20:00:00,079 - INFO - Processed 119300000 reads so far
2011-05-19 20:00:09,406 - INFO - Processed 119400000 reads so far
2011-05-19 20:00:22,084 - INFO - Processed 119500000 reads so far
2011-05-19 20:00:33,391 - INFO - Processed 119600000 reads so far
2011-05-19 20:00:44,690 - INFO - Processed 119700000 reads so far
2011-05-19 20:00:56,205 - INFO - Processed 119800000 reads so far
2011-05-19 20:01:04,270 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:146352003-166372003
2011-05-19 20:01:06,533 - INFO - Processed 119900000 reads so far
2011-05-19 20:01:15,851 - INFO - Processed 120000000 reads so far
2011-05-19 20:01:27,516 - INFO - Processed 120100000 reads so far
2011-05-19 20:01:40,076 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7_random:0-20010123
2011-05-19 20:01:40,612 - INFO - Processed 120200000 reads so far
2011-05-19 20:01:42,726 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:2990077-23010077
2011-05-19 20:01:55,704 - INFO - Processed 120300000 reads so far
2011-05-19 20:02:07,560 - INFO - Processed 120400000 reads so far
2011-05-19 20:02:16,741 - INFO - Processed 120500000 reads so far
2011-05-19 20:02:25,394 - INFO - Processed 120600000 reads so far
2011-05-19 20:02:37,392 - INFO - Processed 120700000 reads so far
2011-05-19 20:02:45,973 - INFO - Processed 120800000 reads so far
2011-05-19 20:02:55,911 - INFO - Processed 120900000 reads so far
2011-05-19 20:03:03,977 - INFO - Processed 121000000 reads so far
2011-05-19 20:03:14,207 - INFO - Processed 121100000 reads so far
2011-05-19 20:03:27,388 - INFO - Processed 121200000 reads so far
2011-05-19 20:03:31,386 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:22990091-43010091
2011-05-19 20:03:35,810 - INFO - Processed 121300000 reads so far
2011-05-19 20:03:50,019 - INFO - Processed 121400000 reads so far
2011-05-19 20:04:03,049 - INFO - Processed 121500000 reads so far
2011-05-19 20:04:14,583 - INFO - Processed 121600000 reads so far
2011-05-19 20:04:28,818 - INFO - Processed 121700000 reads so far
2011-05-19 20:04:41,124 - INFO - Processed 121800000 reads so far
2011-05-19 20:04:50,785 - INFO - Processed 121900000 reads so far
2011-05-19 20:05:00,288 - INFO - Processed 122000000 reads so far
2011-05-19 20:05:08,930 - INFO - Processed 122100000 reads so far
2011-05-19 20:05:19,693 - INFO - Processed 122200000 reads so far
2011-05-19 20:05:25,243 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:42990094-63010094
2011-05-19 20:05:27,773 - INFO - Processed 122300000 reads so far
2011-05-19 20:05:37,431 - INFO - Processed 122400000 reads so far
2011-05-19 20:05:44,822 - INFO - Processed 122500000 reads so far
2011-05-19 20:05:54,897 - INFO - Processed 122600000 reads so far
2011-05-19 20:06:02,948 - INFO - Processed 122700000 reads so far
2011-05-19 20:06:12,864 - INFO - Processed 122800000 reads so far
2011-05-19 20:06:23,335 - INFO - Processed 122900000 reads so far
2011-05-19 20:06:32,330 - INFO - Processed 123000000 reads so far
2011-05-19 20:06:39,785 - INFO - Processed 123100000 reads so far
2011-05-19 20:06:48,379 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:62990100-83010100
2011-05-19 20:06:49,254 - INFO - Processed 123200000 reads so far
2011-05-19 20:06:57,896 - INFO - Processed 123300000 reads so far
2011-05-19 20:07:09,426 - INFO - Processed 123400000 reads so far
2011-05-19 20:07:21,751 - INFO - Processed 123500000 reads so far
2011-05-19 20:07:31,605 - INFO - Processed 123600000 reads so far
2011-05-19 20:07:42,763 - INFO - Processed 123700000 reads so far
2011-05-19 20:07:52,687 - INFO - Processed 123800000 reads so far
2011-05-19 20:08:01,609 - INFO - Processed 123900000 reads so far
2011-05-19 20:08:13,059 - INFO - Processed 124000000 reads so far
2011-05-19 20:08:23,448 - INFO - Processed 124100000 reads so far
2011-05-19 20:08:31,988 - INFO - Processed 124200000 reads so far
2011-05-19 20:08:34,230 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:82990154-103010154
2011-05-19 20:08:41,031 - INFO - Processed 124300000 reads so far
2011-05-19 20:08:50,129 - INFO - Processed 124400000 reads so far
2011-05-19 20:09:02,178 - INFO - Processed 124500000 reads so far
2011-05-19 20:09:13,539 - INFO - Processed 124600000 reads so far
2011-05-19 20:09:25,655 - INFO - Processed 124700000 reads so far
2011-05-19 20:09:38,533 - INFO - Processed 124800000 reads so far
2011-05-19 20:09:50,177 - INFO - Processed 124900000 reads so far
2011-05-19 20:10:01,804 - INFO - Processed 125000000 reads so far
2011-05-19 20:10:16,160 - INFO - Processed 125100000 reads so far
2011-05-19 20:10:27,699 - INFO - Processed 125200000 reads so far
2011-05-19 20:10:34,394 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:102990163-123010163
2011-05-19 20:10:42,103 - INFO - Processed 125300000 reads so far
2011-05-19 20:10:54,816 - INFO - Processed 125400000 reads so far
2011-05-19 20:11:06,691 - INFO - Processed 125500000 reads so far
2011-05-19 20:11:17,677 - INFO - Processed 125600000 reads so far
2011-05-19 20:11:29,316 - INFO - Processed 125700000 reads so far
2011-05-19 20:11:41,443 - INFO - Processed 125800000 reads so far
2011-05-19 20:11:54,155 - INFO - Processed 125900000 reads so far
2011-05-19 20:12:03,623 - INFO - Processed 126000000 reads so far
2011-05-19 20:12:14,107 - INFO - Processed 126100000 reads so far
2011-05-19 20:12:23,706 - INFO - Processed 126200000 reads so far
2011-05-19 20:12:33,197 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:122990178-143010178
2011-05-19 20:12:35,403 - INFO - Processed 126300000 reads so far
2011-05-19 20:12:45,799 - INFO - Processed 126400000 reads so far
2011-05-19 20:12:55,567 - INFO - Processed 126500000 reads so far
2011-05-19 20:13:09,597 - INFO - Processed 126600000 reads so far
2011-05-19 20:13:18,795 - INFO - Processed 126700000 reads so far
2011-05-19 20:13:22,234 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8_random:0-20010022
2011-05-19 20:13:27,505 - INFO - Processed 126800000 reads so far
2011-05-19 20:13:29,688 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:2989957-23009957
2011-05-19 20:13:37,812 - INFO - Processed 126900000 reads so far
2011-05-19 20:13:45,658 - INFO - Processed 127000000 reads so far
2011-05-19 20:13:52,695 - INFO - Processed 127100000 reads so far
2011-05-19 20:14:00,393 - INFO - Processed 127200000 reads so far
2011-05-19 20:14:08,152 - INFO - Processed 127300000 reads so far
2011-05-19 20:14:16,341 - INFO - Processed 127400000 reads so far
2011-05-19 20:14:23,783 - INFO - Processed 127500000 reads so far
2011-05-19 20:14:31,214 - INFO - Processed 127600000 reads so far
2011-05-19 20:14:40,955 - INFO - Processed 127700000 reads so far
2011-05-19 20:14:50,323 - INFO - Processed 127800000 reads so far
2011-05-19 20:14:59,714 - INFO - Processed 127900000 reads so far
2011-05-19 20:15:07,118 - INFO - Processed 128000000 reads so far
2011-05-19 20:15:16,870 - INFO - Processed 128100000 reads so far
2011-05-19 20:15:23,661 - INFO - Processed 128200000 reads so far
2011-05-19 20:15:30,447 - INFO - Processed 128300000 reads so far
2011-05-19 20:15:37,724 - INFO - Processed 128400000 reads so far
2011-05-19 20:15:44,599 - INFO - Processed 128500000 reads so far
2011-05-19 20:15:58,730 - INFO - Processed 128600000 reads so far
2011-05-19 20:16:06,001 - INFO - Processed 128700000 reads so far
2011-05-19 20:16:14,798 - INFO - Processed 128800000 reads so far
2011-05-19 20:16:22,760 - INFO - Processed 128900000 reads so far
2011-05-19 20:16:35,638 - INFO - Processed 129000000 reads so far
2011-05-19 20:16:44,322 - INFO - Processed 129100000 reads so far
2011-05-19 20:16:51,661 - INFO - Processed 129200000 reads so far
2011-05-19 20:16:59,393 - INFO - Processed 129300000 reads so far
2011-05-19 20:17:09,265 - INFO - Processed 129400000 reads so far
2011-05-19 20:17:18,746 - INFO - Processed 129500000 reads so far
2011-05-19 20:17:27,519 - INFO - Processed 129600000 reads so far
2011-05-19 20:17:34,715 - INFO - Processed 129700000 reads so far
2011-05-19 20:17:41,283 - INFO - Processed 129800000 reads so far
2011-05-19 20:17:48,528 - INFO - Processed 129900000 reads so far
2011-05-19 20:17:58,974 - INFO - Processed 130000000 reads so far
2011-05-19 20:18:11,912 - INFO - Processed 130100000 reads so far
2011-05-19 20:18:21,414 - INFO - Processed 130200000 reads so far
2011-05-19 20:18:32,348 - INFO - Processed 130300000 reads so far
2011-05-19 20:18:41,865 - INFO - Processed 130400000 reads so far
2011-05-19 20:18:51,433 - INFO - Processed 130500000 reads so far
2011-05-19 20:19:00,493 - INFO - Processed 130600000 reads so far
2011-05-19 20:19:09,364 - INFO - Processed 130700000 reads so far
2011-05-19 20:19:18,556 - INFO - Processed 130800000 reads so far
2011-05-19 20:19:29,180 - INFO - Processed 130900000 reads so far
2011-05-19 20:19:38,189 - INFO - Processed 131000000 reads so far
2011-05-19 20:19:47,351 - INFO - Processed 131100000 reads so far
2011-05-19 20:19:57,108 - INFO - Processed 131200000 reads so far
2011-05-19 20:20:06,540 - INFO - Processed 131300000 reads so far
2011-05-19 20:20:13,487 - INFO - Processed 131400000 reads so far
2011-05-19 20:20:20,747 - INFO - Processed 131500000 reads so far
2011-05-19 20:20:27,309 - INFO - Processed 131600000 reads so far
2011-05-19 20:20:36,114 - INFO - Processed 131700000 reads so far
2011-05-19 20:20:43,170 - INFO - Processed 131800000 reads so far
2011-05-19 20:20:52,653 - INFO - Processed 131900000 reads so far
2011-05-19 20:21:02,528 - INFO - Processed 132000000 reads so far
2011-05-19 20:21:21,431 - INFO - Processed 132100000 reads so far
2011-05-19 20:21:31,225 - INFO - Processed 132200000 reads so far
2011-05-19 20:21:40,232 - INFO - Processed 132300000 reads so far
2011-05-19 20:21:53,631 - INFO - Processed 132400000 reads so far
2011-05-19 20:22:04,326 - INFO - Processed 132500000 reads so far
2011-05-19 20:22:14,107 - INFO - Processed 132600000 reads so far
2011-05-19 20:22:26,382 - INFO - Processed 132700000 reads so far
2011-05-19 20:22:38,119 - INFO - Processed 132800000 reads so far
2011-05-19 20:22:49,590 - INFO - Processed 132900000 reads so far
2011-05-19 20:23:04,793 - INFO - Processed 133000000 reads so far
2011-05-19 20:23:15,798 - INFO - Processed 133100000 reads so far
2011-05-19 20:23:27,442 - INFO - Processed 133200000 reads so far
2011-05-19 20:23:39,290 - INFO - Processed 133300000 reads so far
2011-05-19 20:23:50,429 - INFO - Processed 133400000 reads so far
2011-05-19 20:24:06,477 - INFO - Processed 133500000 reads so far
2011-05-19 20:24:13,470 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:22989971-43009971
2011-05-19 20:24:16,145 - INFO - Processed 133600000 reads so far
2011-05-19 20:24:27,027 - INFO - Processed 133700000 reads so far
2011-05-19 20:24:40,639 - INFO - Processed 133800000 reads so far
2011-05-19 20:24:49,790 - INFO - Processed 133900000 reads so far
2011-05-19 20:25:02,055 - INFO - Processed 134000000 reads so far
2011-05-19 20:25:15,301 - INFO - Processed 134100000 reads so far
2011-05-19 20:25:27,634 - INFO - Processed 134200000 reads so far
2011-05-19 20:25:35,850 - INFO - Processed 134300000 reads so far
2011-05-19 20:25:44,818 - INFO - Processed 134400000 reads so far
2011-05-19 20:25:54,243 - INFO - Processed 134500000 reads so far
2011-05-19 20:26:04,765 - INFO - Processed 134600000 reads so far
2011-05-19 20:26:18,099 - INFO - Processed 134700000 reads so far
2011-05-19 20:26:24,697 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:42989987-63009987
2011-05-19 20:26:29,288 - INFO - Processed 134800000 reads so far
2011-05-19 20:26:42,226 - INFO - Processed 134900000 reads so far
2011-05-19 20:26:53,272 - INFO - Processed 135000000 reads so far
2011-05-19 20:27:04,260 - INFO - Processed 135100000 reads so far
2011-05-19 20:27:17,902 - INFO - Processed 135200000 reads so far
2011-05-19 20:27:29,186 - INFO - Processed 135300000 reads so far
2011-05-19 20:27:40,769 - INFO - Processed 135400000 reads so far
2011-05-19 20:27:51,699 - INFO - Processed 135500000 reads so far
2011-05-19 20:28:09,088 - INFO - Processed 135600000 reads so far
2011-05-19 20:28:19,071 - INFO - Processed 135700000 reads so far
2011-05-19 20:28:30,355 - INFO - Processed 135800000 reads so far
2011-05-19 20:28:31,435 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:62989991-83009991
2011-05-19 20:28:42,062 - INFO - Processed 135900000 reads so far
2011-05-19 20:28:54,445 - INFO - Processed 136000000 reads so far
2011-05-19 20:29:03,981 - INFO - Processed 136100000 reads so far
2011-05-19 20:29:13,955 - INFO - Processed 136200000 reads so far
2011-05-19 20:29:23,642 - INFO - Processed 136300000 reads so far
2011-05-19 20:29:33,299 - INFO - Processed 136400000 reads so far
2011-05-19 20:29:42,924 - INFO - Processed 136500000 reads so far
2011-05-19 20:29:54,051 - INFO - Processed 136600000 reads so far
2011-05-19 20:30:05,193 - INFO - Processed 136700000 reads so far
2011-05-19 20:30:15,643 - INFO - Processed 136800000 reads so far
2011-05-19 20:30:21,248 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:82989995-103009995
2011-05-19 20:30:24,826 - INFO - Processed 136900000 reads so far
2011-05-19 20:30:34,895 - INFO - Processed 137000000 reads so far
2011-05-19 20:30:45,263 - INFO - Processed 137100000 reads so far
2011-05-19 20:30:53,370 - INFO - Processed 137200000 reads so far
2011-05-19 20:31:02,592 - INFO - Processed 137300000 reads so far
2011-05-19 20:31:12,907 - INFO - Processed 137400000 reads so far
2011-05-19 20:31:25,002 - INFO - Processed 137500000 reads so far
2011-05-19 20:31:35,938 - INFO - Processed 137600000 reads so far
2011-05-19 20:31:48,637 - INFO - Processed 137700000 reads so far
2011-05-19 20:32:02,366 - INFO - Processed 137800000 reads so far
2011-05-19 20:32:13,263 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:102990035-123010035
2011-05-19 20:32:14,308 - INFO - Processed 137900000 reads so far
2011-05-19 20:32:26,556 - INFO - Processed 138000000 reads so far
2011-05-19 20:32:38,784 - INFO - Processed 138100000 reads so far
2011-05-19 20:32:50,842 - INFO - Processed 138200000 reads so far
2011-05-19 20:32:59,903 - INFO - Processed 138300000 reads so far
2011-05-19 20:33:13,416 - INFO - Processed 138400000 reads so far
2011-05-19 20:33:25,729 - INFO - Processed 138500000 reads so far
2011-05-19 20:33:36,584 - INFO - Processed 138600000 reads so far
2011-05-19 20:33:47,014 - INFO - Processed 138700000 reads so far
2011-05-19 20:33:57,743 - INFO - Processed 138800000 reads so far
2011-05-19 20:34:09,067 - INFO - Processed 138900000 reads so far
2011-05-19 20:34:14,081 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:122990042-143010042
2011-05-19 20:34:20,149 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9_random:0-20010040
2011-05-19 20:34:20,482 - INFO - Processed 139000000 reads so far
2011-05-19 20:34:23,286 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrM:0-20010000
2011-05-19 20:34:28,875 - INFO - Processed 139100000 reads so far
2011-05-19 20:34:29,759 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrUn_random:0-20010019
2011-05-19 20:34:37,875 - INFO - Processed 139200000 reads so far
2011-05-19 20:34:46,407 - INFO - Processed 139300000 reads so far
2011-05-19 20:34:57,503 - INFO - Processed 139400000 reads so far
2011-05-19 20:35:03,755 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:2990000-23010000
2011-05-19 20:35:07,559 - INFO - Processed 139500000 reads so far
2011-05-19 20:35:15,471 - INFO - Processed 139600000 reads so far
2011-05-19 20:35:28,491 - INFO - Processed 139700000 reads so far
2011-05-19 20:35:38,191 - INFO - Processed 139800000 reads so far
2011-05-19 20:35:50,468 - INFO - Processed 139900000 reads so far
2011-05-19 20:36:02,609 - INFO - Processed 140000000 reads so far
2011-05-19 20:36:07,675 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:22990054-43010054
2011-05-19 20:36:13,510 - INFO - Processed 140100000 reads so far
2011-05-19 20:36:25,172 - INFO - Processed 140200000 reads so far
2011-05-19 20:36:36,207 - INFO - Processed 140300000 reads so far
2011-05-19 20:36:46,566 - INFO - Processed 140400000 reads so far
2011-05-19 20:36:58,031 - INFO - Processed 140500000 reads so far
2011-05-19 20:37:08,602 - INFO - Processed 140600000 reads so far
2011-05-19 20:37:08,938 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:42990227-63010227
2011-05-19 20:37:19,219 - INFO - Processed 140700000 reads so far
2011-05-19 20:37:29,935 - INFO - Processed 140800000 reads so far
2011-05-19 20:37:41,156 - INFO - Processed 140900000 reads so far
2011-05-19 20:37:52,538 - INFO - Processed 141000000 reads so far
2011-05-19 20:38:04,881 - INFO - Processed 141100000 reads so far
2011-05-19 20:38:09,594 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:62990248-83010248
2011-05-19 20:38:17,303 - INFO - Processed 141200000 reads so far
2011-05-19 20:38:28,667 - INFO - Processed 141300000 reads so far
2011-05-19 20:38:41,957 - INFO - Processed 141400000 reads so far
2011-05-19 20:38:52,848 - INFO - Processed 141500000 reads so far
2011-05-19 20:39:03,294 - INFO - Processed 141600000 reads so far
2011-05-19 20:39:12,686 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:82990257-103010257
2011-05-19 20:39:15,772 - INFO - Processed 141700000 reads so far
2011-05-19 20:39:27,424 - INFO - Processed 141800000 reads so far
2011-05-19 20:39:37,429 - INFO - Processed 141900000 reads so far
2011-05-19 20:39:51,102 - INFO - Processed 142000000 reads so far
2011-05-19 20:40:00,935 - INFO - Processed 142100000 reads so far
2011-05-19 20:40:10,448 - INFO - Processed 142200000 reads so far
2011-05-19 20:40:11,178 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:102990285-123010285
2011-05-19 20:40:22,493 - INFO - Processed 142300000 reads so far
2011-05-19 20:40:33,783 - INFO - Processed 142400000 reads so far
2011-05-19 20:40:43,395 - INFO - Processed 142500000 reads so far
2011-05-19 20:40:55,951 - INFO - Processed 142600000 reads so far
2011-05-19 20:41:06,741 - INFO - Processed 142700000 reads so far
2011-05-19 20:41:14,956 - INFO - Processed 142800000 reads so far
2011-05-19 20:41:17,954 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:122990302-143010302
2011-05-19 20:41:25,378 - INFO - Processed 142900000 reads so far
2011-05-19 20:41:35,370 - INFO - Processed 143000000 reads so far
2011-05-19 20:41:45,692 - INFO - Processed 143100000 reads so far
2011-05-19 20:41:57,812 - INFO - Processed 143200000 reads so far
2011-05-19 20:42:09,002 - INFO - Processed 143300000 reads so far
2011-05-19 20:42:20,551 - INFO - Processed 143400000 reads so far
2011-05-19 20:42:21,251 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:142990371-163010371
2011-05-19 20:42:31,434 - INFO - Processed 143500000 reads so far
2011-05-19 20:42:43,742 - INFO - Processed 143600000 reads so far
2011-05-19 20:42:54,446 - INFO - Processed 143700000 reads so far
2011-05-19 20:43:06,048 - INFO - Processed 143800000 reads so far
2011-05-19 20:43:20,065 - INFO - Processed 143900000 reads so far
2011-05-19 20:43:25,638 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:162990398-183010398
2011-05-19 20:43:30,574 - INFO - Processed 144000000 reads so far
2011-05-19 20:43:41,980 - INFO - Processed 144100000 reads so far
2011-05-19 20:43:43,245 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX_random:0-20010019
2011-05-19 20:43:46,467 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY:0-20010000
2011-05-19 20:43:56,836 - INFO - Processed 144200000 reads so far
2011-05-19 20:43:59,582 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:0-20010283
2011-05-19 20:44:07,511 - INFO - Processed 144300000 reads so far
2011-05-19 20:44:18,152 - INFO - Processed 144400000 reads so far
2011-05-19 20:44:29,660 - INFO - Processed 144500000 reads so far
2011-05-19 20:44:40,540 - INFO - Processed 144600000 reads so far
2011-05-19 20:44:52,868 - INFO - Processed 144700000 reads so far
2011-05-19 20:45:02,734 - INFO - Processed 144800000 reads so far
2011-05-19 20:45:12,793 - INFO - Processed 144900000 reads so far
2011-05-19 20:45:23,189 - INFO - Processed 145000000 reads so far
2011-05-19 20:45:27,322 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:19990564-40010564
2011-05-19 20:45:34,463 - INFO - Processed 145100000 reads so far
2011-05-19 20:45:46,973 - INFO - Processed 145200000 reads so far
2011-05-19 20:45:58,335 - INFO - Processed 145300000 reads so far
2011-05-19 20:46:09,419 - INFO - Processed 145400000 reads so far
2011-05-19 20:46:17,487 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:39990575-60010575
2011-05-19 20:46:20,714 - INFO - Processed 145500000 reads so far
2011-05-19 20:46:32,550 - INFO - Processed 145600000 reads so far
2011-05-19 20:46:44,386 - INFO - Processed 145700000 reads so far
2011-05-19 20:46:57,669 - INFO - Processed 145800000 reads so far
2011-05-19 20:47:08,800 - INFO - Processed 145900000 reads so far
2011-05-19 20:47:19,760 - INFO - Processed 146000000 reads so far
2011-05-19 20:47:32,098 - INFO - Processed 146100000 reads so far
2011-05-19 20:47:36,677 - INFO - Processed 146200000 reads so far
2011-05-19 20:47:41,135 - INFO - Processed 146300000 reads so far
2011-05-19 20:47:46,405 - INFO - Processed 146400000 reads so far
2011-05-19 20:47:50,601 - INFO - Processed 146500000 reads so far
2011-05-19 20:47:55,223 - INFO - Processed 146600000 reads so far
2011-05-19 20:47:59,564 - INFO - Processed 146700000 reads so far
2011-05-19 20:48:03,166 - INFO - Processed 146800000 reads so far
2011-05-19 20:48:06,421 - INFO - Processed 146900000 reads so far
2011-05-19 20:48:09,608 - INFO - Processed 147000000 reads so far
2011-05-19 20:48:13,787 - INFO - Processed 147100000 reads so far
2011-05-19 20:48:19,049 - INFO - Processed 147200000 reads so far
2011-05-19 20:48:23,041 - INFO - Processed 147300000 reads so far
2011-05-19 20:48:25,807 - INFO - Processed 147400000 reads so far
2011-05-19 20:48:31,536 - INFO - Processed 147500000 reads so far
2011-05-19 20:48:52,945 - INFO - Processed 147600000 reads so far
2011-05-19 20:48:59,885 - INFO - Processed 147700000 reads so far
2011-05-19 20:49:04,313 - INFO - Processed 147800000 reads so far
2011-05-19 20:49:08,558 - INFO - Processed 147900000 reads so far
2011-05-19 20:49:15,026 - INFO - Processed 148000000 reads so far
2011-05-19 20:49:18,093 - INFO - Finished loading data. Outputting QC metrics
2011-05-19 20:49:38,978 - INFO - Finished outputting QC metrics
2011-05-19 20:49:39,054 - INFO - Finished generating QC metrics