2011-05-19 15:51:23,637 - INFO - Generating QC metrics for BAM File ['WTCHG_11823.bam']
2011-05-19 15:51:23,637 - INFO - Output will go to WTCHG_11823.qc.txt.tmp
2011-05-19 15:51:23,637 - INFO - Reading GC Map from file /data/Genomes/gcMap/Mouse37.gcMap.gz
2011-05-19 15:54:31,827 - INFO - Finished reading GC Map
2011-05-19 15:54:31,827 - INFO - Reading CDS from exon definition file /data/Genomes/annotation/Mouse37.refGene.txt.gz
2011-05-19 15:54:34,801 - INFO - Read 382138 exons (33804740 nucleotides) for 32 chromosomes
2011-05-19 15:54:34,803 - INFO - Computing coverage cut-off
2011-05-19 15:54:34,803 - INFO - Retrieving BAM file coverage info from samtools pileup
2011-05-19 15:54:39,194 - INFO - Processed 1000000 pile-up sites
2011-05-19 15:54:43,624 - INFO - Processed 2000000 pile-up sites
2011-05-19 15:54:48,207 - INFO - Processed 3000000 pile-up sites
2011-05-19 15:54:51,488 - INFO - Processed 4000000 pile-up sites
2011-05-19 15:54:56,093 - INFO - Processed 5000000 pile-up sites
2011-05-19 15:55:00,402 - INFO - Processed 6000000 pile-up sites
2011-05-19 15:55:04,766 - INFO - Processed 7000000 pile-up sites
2011-05-19 15:55:09,092 - INFO - Processed 8000000 pile-up sites
2011-05-19 15:55:13,461 - INFO - Processed 9000000 pile-up sites
2011-05-19 15:55:17,869 - INFO - Processed 10000000 pile-up sites
2011-05-19 15:55:24,066 - INFO - Processed 11000000 pile-up sites
2011-05-19 15:55:30,312 - INFO - Processed 12000000 pile-up sites
2011-05-19 15:55:35,088 - INFO - Processed 13000000 pile-up sites
2011-05-19 15:55:39,642 - INFO - Processed 14000000 pile-up sites
2011-05-19 15:55:43,912 - INFO - Processed 15000000 pile-up sites
2011-05-19 15:55:48,395 - INFO - Processed 16000000 pile-up sites
2011-05-19 15:55:53,357 - INFO - Processed 17000000 pile-up sites
2011-05-19 15:55:58,017 - INFO - Processed 18000000 pile-up sites
2011-05-19 15:56:02,570 - INFO - Processed 19000000 pile-up sites
2011-05-19 15:56:09,204 - INFO - Processed 20000000 pile-up sites
2011-05-19 15:56:13,886 - INFO - Processed 21000000 pile-up sites
2011-05-19 15:56:21,731 - INFO - Processed 22000000 pile-up sites
2011-05-19 15:56:26,301 - INFO - Processed 23000000 pile-up sites
2011-05-19 15:56:31,238 - INFO - Processed 24000000 pile-up sites
2011-05-19 15:56:35,363 - INFO - Processed 25000000 pile-up sites
2011-05-19 15:56:39,377 - INFO - Processed 26000000 pile-up sites
2011-05-19 15:56:44,815 - INFO - Processed 27000000 pile-up sites
2011-05-19 15:56:50,388 - INFO - Processed 28000000 pile-up sites
2011-05-19 15:56:54,907 - INFO - Processed 29000000 pile-up sites
2011-05-19 15:56:59,461 - INFO - Processed 30000000 pile-up sites
2011-05-19 15:57:03,975 - INFO - Processed 31000000 pile-up sites
2011-05-19 15:57:09,237 - INFO - Processed 32000000 pile-up sites
2011-05-19 15:57:14,277 - INFO - Processed 33000000 pile-up sites
2011-05-19 15:57:16,976 - INFO - Finished processing pile-up on 33582866 sites (200000003 nucleotides)
2011-05-19 15:57:16,977 - INFO - Coverage cut-off value is 29
2011-05-19 15:57:16,977 - INFO - Loading data into QC data manager
2011-05-19 15:57:17,224 - INFO - Reading data from BAM file WTCHG_11823.bam. All reads in file will be read
2011-05-19 15:57:17,267 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:2990005-23010005
2011-05-19 15:57:28,158 - INFO - Processed 100000 reads so far
2011-05-19 15:57:39,781 - INFO - Processed 200000 reads so far
2011-05-19 15:57:50,860 - INFO - Processed 300000 reads so far
2011-05-19 15:58:02,972 - INFO - Processed 400000 reads so far
2011-05-19 15:58:14,183 - INFO - Processed 500000 reads so far
2011-05-19 15:58:25,344 - INFO - Processed 600000 reads so far
2011-05-19 15:58:36,459 - INFO - Processed 700000 reads so far
2011-05-19 15:58:47,646 - INFO - Processed 800000 reads so far
2011-05-19 15:58:58,771 - INFO - Processed 900000 reads so far
2011-05-19 15:59:09,953 - INFO - Processed 1000000 reads so far
2011-05-19 15:59:21,245 - INFO - Processed 1100000 reads so far
2011-05-19 15:59:30,473 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:22990020-43010020
2011-05-19 15:59:31,628 - INFO - Processed 1200000 reads so far
2011-05-19 15:59:41,141 - INFO - Processed 1300000 reads so far
2011-05-19 15:59:51,696 - INFO - Processed 1400000 reads so far
2011-05-19 16:00:02,194 - INFO - Processed 1500000 reads so far
2011-05-19 16:00:12,658 - INFO - Processed 1600000 reads so far
2011-05-19 16:00:23,104 - INFO - Processed 1700000 reads so far
2011-05-19 16:00:33,721 - INFO - Processed 1800000 reads so far
2011-05-19 16:00:44,212 - INFO - Processed 1900000 reads so far
2011-05-19 16:00:56,325 - INFO - Processed 2000000 reads so far
2011-05-19 16:01:07,788 - INFO - Processed 2100000 reads so far
2011-05-19 16:01:23,375 - INFO - Processed 2200000 reads so far
2011-05-19 16:01:39,312 - INFO - Processed 2300000 reads so far
2011-05-19 16:01:42,536 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:42990082-63010082
2011-05-19 16:01:50,771 - INFO - Processed 2400000 reads so far
2011-05-19 16:02:01,630 - INFO - Processed 2500000 reads so far
2011-05-19 16:02:12,632 - INFO - Processed 2600000 reads so far
2011-05-19 16:02:24,960 - INFO - Processed 2700000 reads so far
2011-05-19 16:02:35,825 - INFO - Processed 2800000 reads so far
2011-05-19 16:02:47,094 - INFO - Processed 2900000 reads so far
2011-05-19 16:02:58,022 - INFO - Processed 3000000 reads so far
2011-05-19 16:03:09,453 - INFO - Processed 3100000 reads so far
2011-05-19 16:03:20,226 - INFO - Processed 3200000 reads so far
2011-05-19 16:03:32,141 - INFO - Processed 3300000 reads so far
2011-05-19 16:03:43,138 - INFO - Processed 3400000 reads so far
2011-05-19 16:03:51,251 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:62990084-83010084
2011-05-19 16:03:54,850 - INFO - Processed 3500000 reads so far
2011-05-19 16:04:08,941 - INFO - Processed 3600000 reads so far
2011-05-19 16:04:20,417 - INFO - Processed 3700000 reads so far
2011-05-19 16:04:30,951 - INFO - Processed 3800000 reads so far
2011-05-19 16:04:40,179 - INFO - Processed 3900000 reads so far
2011-05-19 16:04:51,281 - INFO - Processed 4000000 reads so far
2011-05-19 16:05:02,394 - INFO - Processed 4100000 reads so far
2011-05-19 16:05:13,965 - INFO - Processed 4200000 reads so far
2011-05-19 16:05:25,484 - INFO - Processed 4300000 reads so far
2011-05-19 16:05:35,983 - INFO - Processed 4400000 reads so far
2011-05-19 16:05:48,793 - INFO - Processed 4500000 reads so far
2011-05-19 16:05:59,975 - INFO - Processed 4600000 reads so far
2011-05-19 16:06:05,986 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:82990085-103010085
2011-05-19 16:06:09,541 - INFO - Processed 4700000 reads so far
2011-05-19 16:06:20,454 - INFO - Processed 4800000 reads so far
2011-05-19 16:06:31,730 - INFO - Processed 4900000 reads so far
2011-05-19 16:06:43,303 - INFO - Processed 5000000 reads so far
2011-05-19 16:06:54,638 - INFO - Processed 5100000 reads so far
2011-05-19 16:07:04,983 - INFO - Processed 5200000 reads so far
2011-05-19 16:07:15,306 - INFO - Processed 5300000 reads so far
2011-05-19 16:07:26,401 - INFO - Processed 5400000 reads so far
2011-05-19 16:07:35,196 - INFO - Processed 5500000 reads so far
2011-05-19 16:07:43,911 - INFO - Processed 5600000 reads so far
2011-05-19 16:07:52,278 - INFO - Processed 5700000 reads so far
2011-05-19 16:08:03,034 - INFO - Processed 5800000 reads so far
2011-05-19 16:08:07,074 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:102990104-123010104
2011-05-19 16:08:15,131 - INFO - Processed 5900000 reads so far
2011-05-19 16:08:29,292 - INFO - Processed 6000000 reads so far
2011-05-19 16:08:40,857 - INFO - Processed 6100000 reads so far
2011-05-19 16:09:12,949 - INFO - Processed 6200000 reads so far
2011-05-19 16:09:24,155 - INFO - Processed 6300000 reads so far
2011-05-19 16:09:35,733 - INFO - Processed 6400000 reads so far
2011-05-19 16:09:47,251 - INFO - Processed 6500000 reads so far
2011-05-19 16:09:58,516 - INFO - Processed 6600000 reads so far
2011-05-19 16:10:09,818 - INFO - Processed 6700000 reads so far
2011-05-19 16:10:21,194 - INFO - Processed 6800000 reads so far
2011-05-19 16:10:33,048 - INFO - Processed 6900000 reads so far
2011-05-19 16:10:39,802 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:122990114-143010114
2011-05-19 16:10:43,751 - INFO - Processed 7000000 reads so far
2011-05-19 16:10:54,632 - INFO - Processed 7100000 reads so far
2011-05-19 16:11:06,169 - INFO - Processed 7200000 reads so far
2011-05-19 16:11:16,884 - INFO - Processed 7300000 reads so far
2011-05-19 16:11:25,554 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:2990003-23010003
2011-05-19 16:11:29,641 - INFO - Processed 7400000 reads so far
2011-05-19 16:11:39,331 - INFO - Processed 7500000 reads so far
2011-05-19 16:11:50,005 - INFO - Processed 7600000 reads so far
2011-05-19 16:12:00,684 - INFO - Processed 7700000 reads so far
2011-05-19 16:12:11,641 - INFO - Processed 7800000 reads so far
2011-05-19 16:12:23,952 - INFO - Processed 7900000 reads so far
2011-05-19 16:12:34,602 - INFO - Processed 8000000 reads so far
2011-05-19 16:12:46,815 - INFO - Processed 8100000 reads so far
2011-05-19 16:12:59,504 - INFO - Processed 8200000 reads so far
2011-05-19 16:13:13,282 - INFO - Processed 8300000 reads so far
2011-05-19 16:13:24,346 - INFO - Processed 8400000 reads so far
2011-05-19 16:13:35,052 - INFO - Processed 8500000 reads so far
2011-05-19 16:13:45,804 - INFO - Processed 8600000 reads so far
2011-05-19 16:13:57,291 - INFO - Processed 8700000 reads so far
2011-05-19 16:13:59,705 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:22990048-43010048
2011-05-19 16:14:09,057 - INFO - Processed 8800000 reads so far
2011-05-19 16:14:19,600 - INFO - Processed 8900000 reads so far
2011-05-19 16:14:30,585 - INFO - Processed 9000000 reads so far
2011-05-19 16:14:41,528 - INFO - Processed 9100000 reads so far
2011-05-19 16:14:53,692 - INFO - Processed 9200000 reads so far
2011-05-19 16:15:05,248 - INFO - Processed 9300000 reads so far
2011-05-19 16:15:16,510 - INFO - Processed 9400000 reads so far
2011-05-19 16:15:27,547 - INFO - Processed 9500000 reads so far
2011-05-19 16:15:38,590 - INFO - Processed 9600000 reads so far
2011-05-19 16:15:51,651 - INFO - Processed 9700000 reads so far
2011-05-19 16:16:02,781 - INFO - Processed 9800000 reads so far
2011-05-19 16:16:10,265 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:42990061-63010061
2011-05-19 16:16:14,425 - INFO - Processed 9900000 reads so far
2011-05-19 16:16:25,925 - INFO - Processed 10000000 reads so far
2011-05-19 16:16:37,429 - INFO - Processed 10100000 reads so far
2011-05-19 16:17:15,748 - INFO - Processed 10200000 reads so far
2011-05-19 16:17:26,162 - INFO - Processed 10300000 reads so far
2011-05-19 16:17:37,157 - INFO - Processed 10400000 reads so far
2011-05-19 16:17:49,694 - INFO - Processed 10500000 reads so far
2011-05-19 16:18:00,941 - INFO - Processed 10600000 reads so far
2011-05-19 16:18:11,920 - INFO - Processed 10700000 reads so far
2011-05-19 16:18:22,686 - INFO - Processed 10800000 reads so far
2011-05-19 16:18:33,410 - INFO - Processed 10900000 reads so far
2011-05-19 16:18:48,133 - INFO - Processed 11000000 reads so far
2011-05-19 16:18:59,572 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:62990074-83010074
2011-05-19 16:18:59,744 - INFO - Processed 11100000 reads so far
2011-05-19 16:19:10,651 - INFO - Processed 11200000 reads so far
2011-05-19 16:19:22,098 - INFO - Processed 11300000 reads so far
2011-05-19 16:19:35,445 - INFO - Processed 11400000 reads so far
2011-05-19 16:19:48,335 - INFO - Processed 11500000 reads so far
2011-05-19 16:20:00,823 - INFO - Processed 11600000 reads so far
2011-05-19 16:20:11,099 - INFO - Processed 11700000 reads so far
2011-05-19 16:20:23,142 - INFO - Processed 11800000 reads so far
2011-05-19 16:20:35,373 - INFO - Processed 11900000 reads so far
2011-05-19 16:20:45,662 - INFO - Processed 12000000 reads so far
2011-05-19 16:20:58,256 - INFO - Processed 12100000 reads so far
2011-05-19 16:21:11,465 - INFO - Processed 12200000 reads so far
2011-05-19 16:21:22,455 - INFO - Processed 12300000 reads so far
2011-05-19 16:21:25,515 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:82990080-103010080
2011-05-19 16:21:34,197 - INFO - Processed 12400000 reads so far
2011-05-19 16:21:46,444 - INFO - Processed 12500000 reads so far
2011-05-19 16:21:56,535 - INFO - Processed 12600000 reads so far
2011-05-19 16:22:07,465 - INFO - Processed 12700000 reads so far
2011-05-19 16:22:19,365 - INFO - Processed 12800000 reads so far
2011-05-19 16:22:31,209 - INFO - Processed 12900000 reads so far
2011-05-19 16:22:44,767 - INFO - Processed 13000000 reads so far
2011-05-19 16:22:57,146 - INFO - Processed 13100000 reads so far
2011-05-19 16:23:09,035 - INFO - Processed 13200000 reads so far
2011-05-19 16:23:20,768 - INFO - Processed 13300000 reads so far
2011-05-19 16:23:32,823 - INFO - Processed 13400000 reads so far
2011-05-19 16:23:45,906 - INFO - Processed 13500000 reads so far
2011-05-19 16:23:46,196 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:102990085-123010085
2011-05-19 16:23:57,451 - INFO - Processed 13600000 reads so far
2011-05-19 16:24:10,000 - INFO - Processed 13700000 reads so far
2011-05-19 16:24:22,445 - INFO - Processed 13800000 reads so far
2011-05-19 16:24:33,186 - INFO - Processed 13900000 reads so far
2011-05-19 16:24:42,741 - INFO - Processed 14000000 reads so far
2011-05-19 16:24:54,512 - INFO - Processed 14100000 reads so far
2011-05-19 16:25:06,094 - INFO - Processed 14200000 reads so far
2011-05-19 16:25:18,394 - INFO - Processed 14300000 reads so far
2011-05-19 16:25:30,193 - INFO - Processed 14400000 reads so far
2011-05-19 16:25:40,516 - INFO - Processed 14500000 reads so far
2011-05-19 16:25:52,263 - INFO - Processed 14600000 reads so far
2011-05-19 16:26:01,870 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:2990074-23010074
2011-05-19 16:26:03,850 - INFO - Processed 14700000 reads so far
2011-05-19 16:26:12,752 - INFO - Processed 14800000 reads so far
2011-05-19 16:26:23,025 - INFO - Processed 14900000 reads so far
2011-05-19 16:26:34,179 - INFO - Processed 15000000 reads so far
2011-05-19 16:26:45,410 - INFO - Processed 15100000 reads so far
2011-05-19 16:26:56,881 - INFO - Processed 15200000 reads so far
2011-05-19 16:27:07,381 - INFO - Processed 15300000 reads so far
2011-05-19 16:27:19,251 - INFO - Processed 15400000 reads so far
2011-05-19 16:27:31,698 - INFO - Processed 15500000 reads so far
2011-05-19 16:27:44,324 - INFO - Processed 15600000 reads so far
2011-05-19 16:27:57,097 - INFO - Processed 15700000 reads so far
2011-05-19 16:28:08,625 - INFO - Processed 15800000 reads so far
2011-05-19 16:28:21,269 - INFO - Processed 15900000 reads so far
2011-05-19 16:28:39,508 - INFO - Processed 16000000 reads so far
2011-05-19 16:28:40,384 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:22990188-43010188
2011-05-19 16:28:51,845 - INFO - Processed 16100000 reads so far
2011-05-19 16:29:04,415 - INFO - Processed 16200000 reads so far
2011-05-19 16:29:15,841 - INFO - Processed 16300000 reads so far
2011-05-19 16:29:31,072 - INFO - Processed 16400000 reads so far
2011-05-19 16:29:46,034 - INFO - Processed 16500000 reads so far
2011-05-19 16:29:56,400 - INFO - Processed 16600000 reads so far
2011-05-19 16:30:09,213 - INFO - Processed 16700000 reads so far
2011-05-19 16:30:21,784 - INFO - Processed 16800000 reads so far
2011-05-19 16:30:35,062 - INFO - Processed 16900000 reads so far
2011-05-19 16:30:45,820 - INFO - Processed 17000000 reads so far
2011-05-19 16:30:58,851 - INFO - Processed 17100000 reads so far
2011-05-19 16:31:00,926 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:42990212-63010212
2011-05-19 16:31:10,796 - INFO - Processed 17200000 reads so far
2011-05-19 16:31:22,995 - INFO - Processed 17300000 reads so far
2011-05-19 16:31:42,437 - INFO - Processed 17400000 reads so far
2011-05-19 16:31:57,192 - INFO - Processed 17500000 reads so far
2011-05-19 16:32:13,163 - INFO - Processed 17600000 reads so far
2011-05-19 16:32:28,026 - INFO - Processed 17700000 reads so far
2011-05-19 16:32:42,486 - INFO - Processed 17800000 reads so far
2011-05-19 16:32:53,631 - INFO - Processed 17900000 reads so far
2011-05-19 16:33:04,967 - INFO - Processed 18000000 reads so far
2011-05-19 16:33:16,164 - INFO - Processed 18100000 reads so far
2011-05-19 16:33:25,428 - INFO - Processed 18200000 reads so far
2011-05-19 16:33:26,851 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:62990223-83010223
2011-05-19 16:33:37,323 - INFO - Processed 18300000 reads so far
2011-05-19 16:33:48,064 - INFO - Processed 18400000 reads so far
2011-05-19 16:34:00,089 - INFO - Processed 18500000 reads so far
2011-05-19 16:34:15,863 - INFO - Processed 18600000 reads so far
2011-05-19 16:34:28,288 - INFO - Processed 18700000 reads so far
2011-05-19 16:34:39,228 - INFO - Processed 18800000 reads so far
2011-05-19 16:34:52,700 - INFO - Processed 18900000 reads so far
2011-05-19 16:35:01,237 - INFO - Processed 19000000 reads so far
2011-05-19 16:35:11,668 - INFO - Processed 19100000 reads so far
2011-05-19 16:35:23,094 - INFO - Processed 19200000 reads so far
2011-05-19 16:35:34,986 - INFO - Processed 19300000 reads so far
2011-05-19 16:35:42,852 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:82990249-103010249
2011-05-19 16:35:50,115 - INFO - Processed 19400000 reads so far
2011-05-19 16:36:00,874 - INFO - Processed 19500000 reads so far
2011-05-19 16:36:12,514 - INFO - Processed 19600000 reads so far
2011-05-19 16:36:24,451 - INFO - Processed 19700000 reads so far
2011-05-19 16:36:34,846 - INFO - Processed 19800000 reads so far
2011-05-19 16:36:46,162 - INFO - Processed 19900000 reads so far
2011-05-19 16:36:57,412 - INFO - Processed 20000000 reads so far
2011-05-19 16:37:09,538 - INFO - Processed 20100000 reads so far
2011-05-19 16:37:23,730 - INFO - Processed 20200000 reads so far
2011-05-19 16:37:35,514 - INFO - Processed 20300000 reads so far
2011-05-19 16:37:48,270 - INFO - Processed 20400000 reads so far
2011-05-19 16:37:59,966 - INFO - Processed 20500000 reads so far
2011-05-19 16:38:00,810 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:102990256-123010256
2011-05-19 16:38:13,023 - INFO - Processed 20600000 reads so far
2011-05-19 16:38:25,299 - INFO - Processed 20700000 reads so far
2011-05-19 16:39:01,637 - INFO - Processed 20800000 reads so far
2011-05-19 16:40:20,919 - INFO - Processed 20900000 reads so far
2011-05-19 16:40:31,753 - INFO - Processed 21000000 reads so far
2011-05-19 16:40:42,563 - INFO - Processed 21100000 reads so far
2011-05-19 16:40:53,686 - INFO - Processed 21200000 reads so far
2011-05-19 16:41:02,641 - INFO - Processed 21300000 reads so far
2011-05-19 16:41:13,558 - INFO - Processed 21400000 reads so far
2011-05-19 16:41:22,189 - INFO - Processed 21500000 reads so far
2011-05-19 16:41:30,977 - INFO - Processed 21600000 reads so far
2011-05-19 16:41:39,172 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:2990088-23010088
2011-05-19 16:41:40,733 - INFO - Processed 21700000 reads so far
2011-05-19 16:41:50,366 - INFO - Processed 21800000 reads so far
2011-05-19 16:42:03,777 - INFO - Processed 21900000 reads so far
2011-05-19 16:42:15,996 - INFO - Processed 22000000 reads so far
2011-05-19 16:42:26,713 - INFO - Processed 22100000 reads so far
2011-05-19 16:42:37,509 - INFO - Processed 22200000 reads so far
2011-05-19 16:42:48,499 - INFO - Processed 22300000 reads so far
2011-05-19 16:43:01,734 - INFO - Processed 22400000 reads so far
2011-05-19 16:43:13,883 - INFO - Processed 22500000 reads so far
2011-05-19 16:43:26,749 - INFO - Processed 22600000 reads so far
2011-05-19 16:43:38,339 - INFO - Processed 22700000 reads so far
2011-05-19 16:43:50,096 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:22990148-43010148
2011-05-19 16:43:50,370 - INFO - Processed 22800000 reads so far
2011-05-19 16:44:04,561 - INFO - Processed 22900000 reads so far
2011-05-19 16:44:15,426 - INFO - Processed 23000000 reads so far
2011-05-19 16:44:26,836 - INFO - Processed 23100000 reads so far
2011-05-19 16:44:38,586 - INFO - Processed 23200000 reads so far
2011-05-19 16:44:54,653 - INFO - Processed 23300000 reads so far
2011-05-19 16:45:06,772 - INFO - Processed 23400000 reads so far
2011-05-19 16:45:19,548 - INFO - Processed 23500000 reads so far
2011-05-19 16:45:33,344 - INFO - Processed 23600000 reads so far
2011-05-19 16:45:45,322 - INFO - Processed 23700000 reads so far
2011-05-19 16:45:57,131 - INFO - Processed 23800000 reads so far
2011-05-19 16:46:10,162 - INFO - Processed 23900000 reads so far
2011-05-19 16:46:21,714 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:42990160-63010160
2011-05-19 16:46:26,350 - INFO - Processed 24000000 reads so far
2011-05-19 16:46:40,651 - INFO - Processed 24100000 reads so far
2011-05-19 16:46:52,539 - INFO - Processed 24200000 reads so far
2011-05-19 16:47:04,558 - INFO - Processed 24300000 reads so far
2011-05-19 16:47:16,662 - INFO - Processed 24400000 reads so far
2011-05-19 16:47:27,667 - INFO - Processed 24500000 reads so far
2011-05-19 16:47:39,982 - INFO - Processed 24600000 reads so far
2011-05-19 16:47:54,026 - INFO - Processed 24700000 reads so far
2011-05-19 16:48:10,121 - INFO - Processed 24800000 reads so far
2011-05-19 16:48:25,769 - INFO - Processed 24900000 reads so far
2011-05-19 16:48:37,253 - INFO - Processed 25000000 reads so far
2011-05-19 16:48:48,809 - INFO - Processed 25100000 reads so far
2011-05-19 16:49:00,268 - INFO - Processed 25200000 reads so far
2011-05-19 16:49:03,864 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:62990162-83010162
2011-05-19 16:49:13,626 - INFO - Processed 25300000 reads so far
2011-05-19 16:49:28,546 - INFO - Processed 25400000 reads so far
2011-05-19 16:49:39,753 - INFO - Processed 25500000 reads so far
2011-05-19 16:49:51,100 - INFO - Processed 25600000 reads so far
2011-05-19 16:50:02,495 - INFO - Processed 25700000 reads so far
2011-05-19 16:50:15,218 - INFO - Processed 25800000 reads so far
2011-05-19 16:50:27,919 - INFO - Processed 25900000 reads so far
2011-05-19 16:50:40,724 - INFO - Processed 26000000 reads so far
2011-05-19 16:50:52,658 - INFO - Processed 26100000 reads so far
2011-05-19 16:51:05,009 - INFO - Processed 26200000 reads so far
2011-05-19 16:51:17,513 - INFO - Processed 26300000 reads so far
2011-05-19 16:51:27,211 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:82990195-103010195
2011-05-19 16:51:28,594 - INFO - Processed 26400000 reads so far
2011-05-19 16:51:40,519 - INFO - Processed 26500000 reads so far
2011-05-19 16:51:53,379 - INFO - Processed 26600000 reads so far
2011-05-19 16:52:05,894 - INFO - Processed 26700000 reads so far
2011-05-19 16:52:15,141 - INFO - Processed 26800000 reads so far
2011-05-19 16:52:25,683 - INFO - Processed 26900000 reads so far
2011-05-19 16:52:39,693 - INFO - Processed 27000000 reads so far
2011-05-19 16:52:53,442 - INFO - Processed 27100000 reads so far
2011-05-19 16:53:05,430 - INFO - Processed 27200000 reads so far
2011-05-19 16:53:17,240 - INFO - Processed 27300000 reads so far
2011-05-19 16:53:28,214 - INFO - Processed 27400000 reads so far
2011-05-19 16:53:45,165 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:102990226-123010226
2011-05-19 16:53:45,670 - INFO - Processed 27500000 reads so far
2011-05-19 16:54:00,085 - INFO - Processed 27600000 reads so far
2011-05-19 16:54:14,461 - INFO - Processed 27700000 reads so far
2011-05-19 16:54:25,464 - INFO - Processed 27800000 reads so far
2011-05-19 16:54:37,344 - INFO - Processed 27900000 reads so far
2011-05-19 16:54:53,195 - INFO - Processed 28000000 reads so far
2011-05-19 16:55:04,547 - INFO - Processed 28100000 reads so far
2011-05-19 16:55:16,010 - INFO - Processed 28200000 reads so far
2011-05-19 16:55:27,298 - INFO - Processed 28300000 reads so far
2011-05-19 16:55:38,470 - INFO - Processed 28400000 reads so far
2011-05-19 16:55:49,490 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13_random:0-20010000
2011-05-19 16:55:50,816 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:2990017-23010017
2011-05-19 16:55:50,981 - INFO - Processed 28500000 reads so far
2011-05-19 16:56:03,575 - INFO - Processed 28600000 reads so far
2011-05-19 16:56:18,367 - INFO - Processed 28700000 reads so far
2011-05-19 16:56:31,522 - INFO - Processed 28800000 reads so far
2011-05-19 16:56:43,249 - INFO - Processed 28900000 reads so far
2011-05-19 16:56:56,439 - INFO - Processed 29000000 reads so far
2011-05-19 16:57:09,432 - INFO - Processed 29100000 reads so far
2011-05-19 16:57:22,353 - INFO - Processed 29200000 reads so far
2011-05-19 16:57:34,715 - INFO - Processed 29300000 reads so far
2011-05-19 16:57:49,053 - INFO - Processed 29400000 reads so far
2011-05-19 16:58:00,558 - INFO - Processed 29500000 reads so far
2011-05-19 16:58:08,182 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:22990058-43010058
2011-05-19 16:58:12,900 - INFO - Processed 29600000 reads so far
2011-05-19 16:58:24,732 - INFO - Processed 29700000 reads so far
2011-05-19 16:58:36,123 - INFO - Processed 29800000 reads so far
2011-05-19 16:58:47,036 - INFO - Processed 29900000 reads so far
2011-05-19 16:58:59,660 - INFO - Processed 30000000 reads so far
2011-05-19 16:59:13,444 - INFO - Processed 30100000 reads so far
2011-05-19 16:59:24,799 - INFO - Processed 30200000 reads so far
2011-05-19 16:59:39,192 - INFO - Processed 30300000 reads so far
2011-05-19 16:59:50,560 - INFO - Processed 30400000 reads so far
2011-05-19 17:00:04,461 - INFO - Processed 30500000 reads so far
2011-05-19 17:00:15,570 - INFO - Processed 30600000 reads so far
2011-05-19 17:00:26,663 - INFO - Processed 30700000 reads so far
2011-05-19 17:00:30,723 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:42990089-63010089
2011-05-19 17:00:39,336 - INFO - Processed 30800000 reads so far
2011-05-19 17:00:49,773 - INFO - Processed 30900000 reads so far
2011-05-19 17:01:02,775 - INFO - Processed 31000000 reads so far
2011-05-19 17:01:17,511 - INFO - Processed 31100000 reads so far
2011-05-19 17:01:33,664 - INFO - Processed 31200000 reads so far
2011-05-19 17:01:44,299 - INFO - Processed 31300000 reads so far
2011-05-19 17:01:57,205 - INFO - Processed 31400000 reads so far
2011-05-19 17:02:12,438 - INFO - Processed 31500000 reads so far
2011-05-19 17:02:24,441 - INFO - Processed 31600000 reads so far
2011-05-19 17:02:36,085 - INFO - Processed 31700000 reads so far
2011-05-19 17:02:47,206 - INFO - Processed 31800000 reads so far
2011-05-19 17:02:55,844 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:62990140-83010140
2011-05-19 17:02:56,836 - INFO - Processed 31900000 reads so far
2011-05-19 17:03:05,526 - INFO - Processed 32000000 reads so far
2011-05-19 17:03:14,969 - INFO - Processed 32100000 reads so far
2011-05-19 17:03:31,282 - INFO - Processed 32200000 reads so far
2011-05-19 17:03:44,305 - INFO - Processed 32300000 reads so far
2011-05-19 17:03:58,656 - INFO - Processed 32400000 reads so far
2011-05-19 17:04:11,085 - INFO - Processed 32500000 reads so far
2011-05-19 17:04:23,023 - INFO - Processed 32600000 reads so far
2011-05-19 17:04:35,381 - INFO - Processed 32700000 reads so far
2011-05-19 17:04:49,789 - INFO - Processed 32800000 reads so far
2011-05-19 17:05:01,856 - INFO - Processed 32900000 reads so far
2011-05-19 17:05:14,522 - INFO - Processed 33000000 reads so far
2011-05-19 17:05:25,045 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:82990182-103010182
2011-05-19 17:05:25,656 - INFO - Processed 33100000 reads so far
2011-05-19 17:05:39,109 - INFO - Processed 33200000 reads so far
2011-05-19 17:05:52,841 - INFO - Processed 33300000 reads so far
2011-05-19 17:06:04,454 - INFO - Processed 33400000 reads so far
2011-05-19 17:06:16,849 - INFO - Processed 33500000 reads so far
2011-05-19 17:06:30,681 - INFO - Processed 33600000 reads so far
2011-05-19 17:06:42,412 - INFO - Processed 33700000 reads so far
2011-05-19 17:06:55,689 - INFO - Processed 33800000 reads so far
2011-05-19 17:07:09,381 - INFO - Processed 33900000 reads so far
2011-05-19 17:07:23,068 - INFO - Processed 34000000 reads so far
2011-05-19 17:07:35,937 - INFO - Processed 34100000 reads so far
2011-05-19 17:07:39,713 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:102990194-123010194
2011-05-19 17:07:51,840 - INFO - Processed 34200000 reads so far
2011-05-19 17:08:01,611 - INFO - Processed 34300000 reads so far
2011-05-19 17:08:14,981 - INFO - Processed 34400000 reads so far
2011-05-19 17:08:28,126 - INFO - Processed 34500000 reads so far
2011-05-19 17:08:39,793 - INFO - Processed 34600000 reads so far
2011-05-19 17:08:51,152 - INFO - Processed 34700000 reads so far
2011-05-19 17:09:02,116 - INFO - Processed 34800000 reads so far
2011-05-19 17:09:15,163 - INFO - Processed 34900000 reads so far
2011-05-19 17:09:26,693 - INFO - Processed 35000000 reads so far
2011-05-19 17:09:37,945 - INFO - Processed 35100000 reads so far
2011-05-19 17:09:49,496 - INFO - Processed 35200000 reads so far
2011-05-19 17:09:51,283 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:122990212-143010212
2011-05-19 17:10:01,275 - INFO - Processed 35300000 reads so far
2011-05-19 17:10:04,849 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:2990012-23010012
2011-05-19 17:10:09,921 - INFO - Processed 35400000 reads so far
2011-05-19 17:10:19,956 - INFO - Processed 35500000 reads so far
2011-05-19 17:10:28,571 - INFO - Processed 35600000 reads so far
2011-05-19 17:10:38,951 - INFO - Processed 35700000 reads so far
2011-05-19 17:10:51,018 - INFO - Processed 35800000 reads so far
2011-05-19 17:11:03,684 - INFO - Processed 35900000 reads so far
2011-05-19 17:11:14,569 - INFO - Processed 36000000 reads so far
2011-05-19 17:11:25,378 - INFO - Processed 36100000 reads so far
2011-05-19 17:11:36,963 - INFO - Processed 36200000 reads so far
2011-05-19 17:11:48,146 - INFO - Processed 36300000 reads so far
2011-05-19 17:11:59,374 - INFO - Processed 36400000 reads so far
2011-05-19 17:12:03,714 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:22990029-43010029
2011-05-19 17:12:10,271 - INFO - Processed 36500000 reads so far
2011-05-19 17:12:21,583 - INFO - Processed 36600000 reads so far
2011-05-19 17:12:34,354 - INFO - Processed 36700000 reads so far
2011-05-19 17:12:45,290 - INFO - Processed 36800000 reads so far
2011-05-19 17:12:57,108 - INFO - Processed 36900000 reads so far
2011-05-19 17:13:10,143 - INFO - Processed 37000000 reads so far
2011-05-19 17:13:22,731 - INFO - Processed 37100000 reads so far
2011-05-19 17:13:37,511 - INFO - Processed 37200000 reads so far
2011-05-19 17:13:52,750 - INFO - Processed 37300000 reads so far
2011-05-19 17:14:05,697 - INFO - Processed 37400000 reads so far
2011-05-19 17:14:19,786 - INFO - Processed 37500000 reads so far
2011-05-19 17:14:32,640 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:42990045-63010045
2011-05-19 17:14:32,905 - INFO - Processed 37600000 reads so far
2011-05-19 17:14:45,048 - INFO - Processed 37700000 reads so far
2011-05-19 17:14:56,501 - INFO - Processed 37800000 reads so far
2011-05-19 17:15:11,014 - INFO - Processed 37900000 reads so far
2011-05-19 17:15:23,313 - INFO - Processed 38000000 reads so far
2011-05-19 17:15:35,335 - INFO - Processed 38100000 reads so far
2011-05-19 17:15:46,522 - INFO - Processed 38200000 reads so far
2011-05-19 17:15:57,626 - INFO - Processed 38300000 reads so far
2011-05-19 17:16:08,513 - INFO - Processed 38400000 reads so far
2011-05-19 17:16:19,370 - INFO - Processed 38500000 reads so far
2011-05-19 17:16:37,470 - INFO - Processed 38600000 reads so far
2011-05-19 17:16:50,150 - INFO - Processed 38700000 reads so far
2011-05-19 17:16:52,531 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:62990113-83010113
2011-05-19 17:17:03,171 - INFO - Processed 38800000 reads so far
2011-05-19 17:17:14,493 - INFO - Processed 38900000 reads so far
2011-05-19 17:17:25,837 - INFO - Processed 39000000 reads so far
2011-05-19 17:17:37,375 - INFO - Processed 39100000 reads so far
2011-05-19 17:17:50,135 - INFO - Processed 39200000 reads so far
2011-05-19 17:18:02,672 - INFO - Processed 39300000 reads so far
2011-05-19 17:18:19,509 - INFO - Processed 39400000 reads so far
2011-05-19 17:18:31,340 - INFO - Processed 39500000 reads so far
2011-05-19 17:18:45,713 - INFO - Processed 39600000 reads so far
2011-05-19 17:18:57,846 - INFO - Processed 39700000 reads so far
2011-05-19 17:19:09,358 - INFO - Processed 39800000 reads so far
2011-05-19 17:19:24,995 - INFO - Processed 39900000 reads so far
2011-05-19 17:19:33,537 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:82990133-103010133
2011-05-19 17:19:36,944 - INFO - Processed 40000000 reads so far
2011-05-19 17:19:48,251 - INFO - Processed 40100000 reads so far
2011-05-19 17:20:01,103 - INFO - Processed 40200000 reads so far
2011-05-19 17:20:12,133 - INFO - Processed 40300000 reads so far
2011-05-19 17:20:24,244 - INFO - Processed 40400000 reads so far
2011-05-19 17:20:41,205 - INFO - Processed 40500000 reads so far
2011-05-19 17:20:53,396 - INFO - Processed 40600000 reads so far
2011-05-19 17:21:07,122 - INFO - Processed 40700000 reads so far
2011-05-19 17:21:17,552 - INFO - Processed 40800000 reads so far
2011-05-19 17:21:29,004 - INFO - Processed 40900000 reads so far
2011-05-19 17:21:43,458 - INFO - Processed 41000000 reads so far
2011-05-19 17:21:57,438 - INFO - Processed 41100000 reads so far
2011-05-19 17:22:09,187 - INFO - Processed 41200000 reads so far
2011-05-19 17:22:10,539 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:102990138-123010138
2011-05-19 17:22:15,695 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:2990029-23010029
2011-05-19 17:22:21,453 - INFO - Processed 41300000 reads so far
2011-05-19 17:22:32,742 - INFO - Processed 41400000 reads so far
2011-05-19 17:22:45,209 - INFO - Processed 41500000 reads so far
2011-05-19 17:22:56,544 - INFO - Processed 41600000 reads so far
2011-05-19 17:23:12,352 - INFO - Processed 41700000 reads so far
2011-05-19 17:23:26,145 - INFO - Processed 41800000 reads so far
2011-05-19 17:23:37,351 - INFO - Processed 41900000 reads so far
2011-05-19 17:23:50,461 - INFO - Processed 42000000 reads so far
2011-05-19 17:24:04,062 - INFO - Processed 42100000 reads so far
2011-05-19 17:24:15,916 - INFO - Processed 42200000 reads so far
2011-05-19 17:24:27,682 - INFO - Processed 42300000 reads so far
2011-05-19 17:24:40,719 - INFO - Processed 42400000 reads so far
2011-05-19 17:24:52,079 - INFO - Processed 42500000 reads so far
2011-05-19 17:24:53,639 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:22990034-43010034
2011-05-19 17:25:02,713 - INFO - Processed 42600000 reads so far
2011-05-19 17:25:16,828 - INFO - Processed 42700000 reads so far
2011-05-19 17:25:29,031 - INFO - Processed 42800000 reads so far
2011-05-19 17:25:45,268 - INFO - Processed 42900000 reads so far
2011-05-19 17:25:59,235 - INFO - Processed 43000000 reads so far
2011-05-19 17:26:10,320 - INFO - Processed 43100000 reads so far
2011-05-19 17:26:21,524 - INFO - Processed 43200000 reads so far
2011-05-19 17:26:32,890 - INFO - Processed 43300000 reads so far
2011-05-19 17:26:45,918 - INFO - Processed 43400000 reads so far
2011-05-19 17:27:00,635 - INFO - Processed 43500000 reads so far
2011-05-19 17:27:10,582 - INFO - Processed 43600000 reads so far
2011-05-19 17:27:20,000 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:42990035-63010035
2011-05-19 17:27:21,712 - INFO - Processed 43700000 reads so far
2011-05-19 17:27:33,224 - INFO - Processed 43800000 reads so far
2011-05-19 17:27:44,643 - INFO - Processed 43900000 reads so far
2011-05-19 17:27:55,968 - INFO - Processed 44000000 reads so far
2011-05-19 17:28:08,670 - INFO - Processed 44100000 reads so far
2011-05-19 17:28:19,990 - INFO - Processed 44200000 reads so far
2011-05-19 17:28:33,634 - INFO - Processed 44300000 reads so far
2011-05-19 17:28:46,109 - INFO - Processed 44400000 reads so far
2011-05-19 17:28:57,413 - INFO - Processed 44500000 reads so far
2011-05-19 17:29:09,714 - INFO - Processed 44600000 reads so far
2011-05-19 17:29:24,042 - INFO - Processed 44700000 reads so far
2011-05-19 17:29:34,671 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:62990043-83010043
2011-05-19 17:29:35,500 - INFO - Processed 44800000 reads so far
2011-05-19 17:29:50,082 - INFO - Processed 44900000 reads so far
2011-05-19 17:30:03,553 - INFO - Processed 45000000 reads so far
2011-05-19 17:30:15,141 - INFO - Processed 45100000 reads so far
2011-05-19 17:30:30,656 - INFO - Processed 45200000 reads so far
2011-05-19 17:30:41,983 - INFO - Processed 45300000 reads so far
2011-05-19 17:30:53,526 - INFO - Processed 45400000 reads so far
2011-05-19 17:31:07,434 - INFO - Processed 45500000 reads so far
2011-05-19 17:31:19,207 - INFO - Processed 45600000 reads so far
2011-05-19 17:31:34,827 - INFO - Processed 45700000 reads so far
2011-05-19 17:31:45,883 - INFO - Processed 45800000 reads so far
2011-05-19 17:31:51,065 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:82990050-103010050
2011-05-19 17:31:57,251 - INFO - Processed 45900000 reads so far
2011-05-19 17:32:09,786 - INFO - Processed 46000000 reads so far
2011-05-19 17:32:20,716 - INFO - Processed 46100000 reads so far
2011-05-19 17:32:32,857 - INFO - Processed 46200000 reads so far
2011-05-19 17:32:47,894 - INFO - Processed 46300000 reads so far
2011-05-19 17:33:00,045 - INFO - Processed 46400000 reads so far
2011-05-19 17:33:11,284 - INFO - Processed 46500000 reads so far
2011-05-19 17:33:24,466 - INFO - Processed 46600000 reads so far
2011-05-19 17:33:36,965 - INFO - Processed 46700000 reads so far
2011-05-19 17:33:43,658 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16_random:0-20010088
2011-05-19 17:33:43,690 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:2989977-23009977
2011-05-19 17:33:50,399 - INFO - Processed 46800000 reads so far
2011-05-19 17:34:01,802 - INFO - Processed 46900000 reads so far
2011-05-19 17:34:16,120 - INFO - Processed 47000000 reads so far
2011-05-19 17:34:28,711 - INFO - Processed 47100000 reads so far
2011-05-19 17:34:41,249 - INFO - Processed 47200000 reads so far
2011-05-19 17:34:53,965 - INFO - Processed 47300000 reads so far
2011-05-19 17:35:06,764 - INFO - Processed 47400000 reads so far
2011-05-19 17:35:18,755 - INFO - Processed 47500000 reads so far
2011-05-19 17:35:29,686 - INFO - Processed 47600000 reads so far
2011-05-19 17:35:41,140 - INFO - Processed 47700000 reads so far
2011-05-19 17:35:52,683 - INFO - Processed 47800000 reads so far
2011-05-19 17:36:05,471 - INFO - Processed 47900000 reads so far
2011-05-19 17:36:14,569 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:22989993-43009993
2011-05-19 17:36:18,283 - INFO - Processed 48000000 reads so far
2011-05-19 17:36:27,473 - INFO - Processed 48100000 reads so far
2011-05-19 17:36:35,828 - INFO - Processed 48200000 reads so far
2011-05-19 17:36:46,078 - INFO - Processed 48300000 reads so far
2011-05-19 17:36:56,450 - INFO - Processed 48400000 reads so far
2011-05-19 17:37:07,516 - INFO - Processed 48500000 reads so far
2011-05-19 17:37:17,527 - INFO - Processed 48600000 reads so far
2011-05-19 17:37:30,927 - INFO - Processed 48700000 reads so far
2011-05-19 17:37:43,619 - INFO - Processed 48800000 reads so far
2011-05-19 17:37:54,567 - INFO - Processed 48900000 reads so far
2011-05-19 17:38:07,779 - INFO - Processed 49000000 reads so far
2011-05-19 17:38:19,025 - INFO - Processed 49100000 reads so far
2011-05-19 17:38:32,049 - INFO - Processed 49200000 reads so far
2011-05-19 17:38:41,612 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:42990001-63010001
2011-05-19 17:38:50,402 - INFO - Processed 49300000 reads so far
2011-05-19 17:39:02,633 - INFO - Processed 49400000 reads so far
2011-05-19 17:39:18,876 - INFO - Processed 49500000 reads so far
2011-05-19 17:39:30,932 - INFO - Processed 49600000 reads so far
2011-05-19 17:39:44,050 - INFO - Processed 49700000 reads so far
2011-05-19 17:39:55,418 - INFO - Processed 49800000 reads so far
2011-05-19 17:40:07,213 - INFO - Processed 49900000 reads so far
2011-05-19 17:40:18,893 - INFO - Processed 50000000 reads so far
2011-05-19 17:40:31,563 - INFO - Processed 50100000 reads so far
2011-05-19 17:40:41,537 - INFO - Processed 50200000 reads so far
2011-05-19 17:40:55,225 - INFO - Processed 50300000 reads so far
2011-05-19 17:41:04,840 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:62990010-83010010
2011-05-19 17:41:05,820 - INFO - Processed 50400000 reads so far
2011-05-19 17:41:16,521 - INFO - Processed 50500000 reads so far
2011-05-19 17:41:30,033 - INFO - Processed 50600000 reads so far
2011-05-19 17:41:40,836 - INFO - Processed 50700000 reads so far
2011-05-19 17:41:52,001 - INFO - Processed 50800000 reads so far
2011-05-19 17:42:04,290 - INFO - Processed 50900000 reads so far
2011-05-19 17:42:15,484 - INFO - Processed 51000000 reads so far
2011-05-19 17:42:27,573 - INFO - Processed 51100000 reads so far
2011-05-19 17:42:40,430 - INFO - Processed 51200000 reads so far
2011-05-19 17:42:51,152 - INFO - Processed 51300000 reads so far
2011-05-19 17:43:03,331 - INFO - Processed 51400000 reads so far
2011-05-19 17:43:16,353 - INFO - Processed 51500000 reads so far
2011-05-19 17:43:26,880 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:82990149-103010149
2011-05-19 17:43:30,939 - INFO - Processed 51600000 reads so far
2011-05-19 17:43:42,505 - INFO - Processed 51700000 reads so far
2011-05-19 17:43:54,309 - INFO - Processed 51800000 reads so far
2011-05-19 17:44:06,453 - INFO - Processed 51900000 reads so far
2011-05-19 17:44:19,205 - INFO - Processed 52000000 reads so far
2011-05-19 17:44:31,654 - INFO - Processed 52100000 reads so far
2011-05-19 17:44:43,248 - INFO - Processed 52200000 reads so far
2011-05-19 17:44:50,540 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17_random:0-20010046
2011-05-19 17:44:52,627 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:2989994-23009994
2011-05-19 17:44:54,555 - INFO - Processed 52300000 reads so far
2011-05-19 17:45:05,790 - INFO - Processed 52400000 reads so far
2011-05-19 17:45:17,136 - INFO - Processed 52500000 reads so far
2011-05-19 17:45:29,343 - INFO - Processed 52600000 reads so far
2011-05-19 17:45:41,183 - INFO - Processed 52700000 reads so far
2011-05-19 17:45:51,996 - INFO - Processed 52800000 reads so far
2011-05-19 17:46:01,892 - INFO - Processed 52900000 reads so far
2011-05-19 17:46:12,896 - INFO - Processed 53000000 reads so far
2011-05-19 17:46:25,546 - INFO - Processed 53100000 reads so far
2011-05-19 17:46:37,764 - INFO - Processed 53200000 reads so far
2011-05-19 17:46:49,208 - INFO - Processed 53300000 reads so far
2011-05-19 17:47:00,440 - INFO - Processed 53400000 reads so far
2011-05-19 17:47:10,283 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:22990000-43010000
2011-05-19 17:47:12,577 - INFO - Processed 53500000 reads so far
2011-05-19 17:47:24,536 - INFO - Processed 53600000 reads so far
2011-05-19 17:47:39,996 - INFO - Processed 53700000 reads so far
2011-05-19 17:47:51,706 - INFO - Processed 53800000 reads so far
2011-05-19 17:48:02,608 - INFO - Processed 53900000 reads so far
2011-05-19 17:48:14,418 - INFO - Processed 54000000 reads so far
2011-05-19 17:48:24,761 - INFO - Processed 54100000 reads so far
2011-05-19 17:48:35,828 - INFO - Processed 54200000 reads so far
2011-05-19 17:48:49,768 - INFO - Processed 54300000 reads so far
2011-05-19 17:49:00,793 - INFO - Processed 54400000 reads so far
2011-05-19 17:49:12,536 - INFO - Processed 54500000 reads so far
2011-05-19 17:49:25,055 - INFO - Processed 54600000 reads so far
2011-05-19 17:49:31,253 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:42990006-63010006
2011-05-19 17:49:35,668 - INFO - Processed 54700000 reads so far
2011-05-19 17:49:47,669 - INFO - Processed 54800000 reads so far
2011-05-19 17:50:02,044 - INFO - Processed 54900000 reads so far
2011-05-19 17:50:13,956 - INFO - Processed 55000000 reads so far
2011-05-19 17:50:26,772 - INFO - Processed 55100000 reads so far
2011-05-19 17:50:38,632 - INFO - Processed 55200000 reads so far
2011-05-19 17:50:51,307 - INFO - Processed 55300000 reads so far
2011-05-19 17:51:02,946 - INFO - Processed 55400000 reads so far
2011-05-19 17:51:16,822 - INFO - Processed 55500000 reads so far
2011-05-19 17:51:26,951 - INFO - Processed 55600000 reads so far
2011-05-19 17:51:36,137 - INFO - Processed 55700000 reads so far
2011-05-19 17:51:45,224 - INFO - Processed 55800000 reads so far
2011-05-19 17:51:47,108 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:62990018-83010018
2011-05-19 17:51:55,200 - INFO - Processed 55900000 reads so far
2011-05-19 17:52:01,883 - INFO - Processed 56000000 reads so far
2011-05-19 17:52:09,609 - INFO - Processed 56100000 reads so far
2011-05-19 17:52:17,078 - INFO - Processed 56200000 reads so far
2011-05-19 17:52:24,729 - INFO - Processed 56300000 reads so far
2011-05-19 17:52:33,422 - INFO - Processed 56400000 reads so far
2011-05-19 17:52:41,046 - INFO - Processed 56500000 reads so far
2011-05-19 17:52:49,196 - INFO - Processed 56600000 reads so far
2011-05-19 17:52:58,679 - INFO - Processed 56700000 reads so far
2011-05-19 17:53:06,087 - INFO - Processed 56800000 reads so far
2011-05-19 17:53:13,512 - INFO - Processed 56900000 reads so far
2011-05-19 17:53:20,819 - INFO - Processed 57000000 reads so far
2011-05-19 17:53:21,879 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:82990036-103010036
2011-05-19 17:53:28,177 - INFO - Processed 57100000 reads so far
2011-05-19 17:53:36,937 - INFO - Processed 57200000 reads so far
2011-05-19 17:53:43,806 - INFO - Processed 57300000 reads so far
2011-05-19 17:53:51,043 - INFO - Processed 57400000 reads so far
2011-05-19 17:53:54,728 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:2990020-23010020
2011-05-19 17:53:58,039 - INFO - Processed 57500000 reads so far
2011-05-19 17:54:04,902 - INFO - Processed 57600000 reads so far
2011-05-19 17:54:11,900 - INFO - Processed 57700000 reads so far
2011-05-19 17:54:22,535 - INFO - Processed 57800000 reads so far
2011-05-19 17:54:32,166 - INFO - Processed 57900000 reads so far
2011-05-19 17:54:40,905 - INFO - Processed 58000000 reads so far
2011-05-19 17:54:49,984 - INFO - Processed 58100000 reads so far
2011-05-19 17:54:57,790 - INFO - Processed 58200000 reads so far
2011-05-19 17:55:04,882 - INFO - Processed 58300000 reads so far
2011-05-19 17:55:11,816 - INFO - Processed 58400000 reads so far
2011-05-19 17:55:20,087 - INFO - Processed 58500000 reads so far
2011-05-19 17:55:29,847 - INFO - Processed 58600000 reads so far
2011-05-19 17:55:31,270 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:22990050-43010050
2011-05-19 17:55:36,727 - INFO - Processed 58700000 reads so far
2011-05-19 17:55:43,458 - INFO - Processed 58800000 reads so far
2011-05-19 17:55:53,417 - INFO - Processed 58900000 reads so far
2011-05-19 17:56:04,178 - INFO - Processed 59000000 reads so far
2011-05-19 17:56:15,104 - INFO - Processed 59100000 reads so far
2011-05-19 17:56:25,192 - INFO - Processed 59200000 reads so far
2011-05-19 17:56:37,620 - INFO - Processed 59300000 reads so far
2011-05-19 17:56:46,301 - INFO - Processed 59400000 reads so far
2011-05-19 17:56:56,411 - INFO - Processed 59500000 reads so far
2011-05-19 17:57:04,718 - INFO - Processed 59600000 reads so far
2011-05-19 17:57:14,770 - INFO - Processed 59700000 reads so far
2011-05-19 17:57:23,016 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:42990057-63010057
2011-05-19 17:57:23,655 - INFO - Processed 59800000 reads so far
2011-05-19 17:57:34,135 - INFO - Processed 59900000 reads so far
2011-05-19 17:57:42,424 - INFO - Processed 60000000 reads so far
2011-05-19 17:57:52,599 - INFO - Processed 60100000 reads so far
2011-05-19 17:57:59,343 - INFO - Processed 60200000 reads so far
2011-05-19 17:58:07,527 - INFO - Processed 60300000 reads so far
2011-05-19 17:58:15,885 - INFO - Processed 60400000 reads so far
2011-05-19 17:58:23,164 - INFO - Processed 60500000 reads so far
2011-05-19 17:58:33,334 - INFO - Processed 60600000 reads so far
2011-05-19 17:58:45,469 - INFO - Processed 60700000 reads so far
2011-05-19 17:58:54,859 - INFO - Processed 60800000 reads so far
2011-05-19 17:59:01,612 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:2989974-23009974
2011-05-19 17:59:01,846 - INFO - Processed 60900000 reads so far
2011-05-19 17:59:11,383 - INFO - Processed 61000000 reads so far
2011-05-19 17:59:25,742 - INFO - Processed 61100000 reads so far
2011-05-19 17:59:36,802 - INFO - Processed 61200000 reads so far
2011-05-19 17:59:51,213 - INFO - Processed 61300000 reads so far
2011-05-19 18:00:01,148 - INFO - Processed 61400000 reads so far
2011-05-19 18:00:10,884 - INFO - Processed 61500000 reads so far
2011-05-19 18:00:21,514 - INFO - Processed 61600000 reads so far
2011-05-19 18:00:31,276 - INFO - Processed 61700000 reads so far
2011-05-19 18:00:40,160 - INFO - Processed 61800000 reads so far
2011-05-19 18:00:50,141 - INFO - Processed 61900000 reads so far
2011-05-19 18:01:02,555 - INFO - Processed 62000000 reads so far
2011-05-19 18:01:05,200 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:22990027-43010027
2011-05-19 18:01:12,245 - INFO - Processed 62100000 reads so far
2011-05-19 18:01:21,251 - INFO - Processed 62200000 reads so far
2011-05-19 18:01:31,481 - INFO - Processed 62300000 reads so far
2011-05-19 18:01:41,143 - INFO - Processed 62400000 reads so far
2011-05-19 18:01:51,868 - INFO - Processed 62500000 reads so far
2011-05-19 18:02:03,226 - INFO - Processed 62600000 reads so far
2011-05-19 18:02:15,668 - INFO - Processed 62700000 reads so far
2011-05-19 18:02:26,890 - INFO - Processed 62800000 reads so far
2011-05-19 18:02:37,319 - INFO - Processed 62900000 reads so far
2011-05-19 18:02:46,590 - INFO - Processed 63000000 reads so far
2011-05-19 18:02:56,578 - INFO - Processed 63100000 reads so far
2011-05-19 18:03:04,788 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:42990032-63010032
2011-05-19 18:03:06,395 - INFO - Processed 63200000 reads so far
2011-05-19 18:03:16,260 - INFO - Processed 63300000 reads so far
2011-05-19 18:03:24,710 - INFO - Processed 63400000 reads so far
2011-05-19 18:03:33,736 - INFO - Processed 63500000 reads so far
2011-05-19 18:03:43,673 - INFO - Processed 63600000 reads so far
2011-05-19 18:03:53,154 - INFO - Processed 63700000 reads so far
2011-05-19 18:04:01,741 - INFO - Processed 63800000 reads so far
2011-05-19 18:04:10,469 - INFO - Processed 63900000 reads so far
2011-05-19 18:04:19,971 - INFO - Processed 64000000 reads so far
2011-05-19 18:04:35,474 - INFO - Processed 64100000 reads so far
2011-05-19 18:04:45,756 - INFO - Processed 64200000 reads so far
2011-05-19 18:05:00,170 - INFO - Processed 64300000 reads so far
2011-05-19 18:05:01,661 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:62990033-83010033
2011-05-19 18:05:11,115 - INFO - Processed 64400000 reads so far
2011-05-19 18:05:22,074 - INFO - Processed 64500000 reads so far
2011-05-19 18:05:34,345 - INFO - Processed 64600000 reads so far
2011-05-19 18:05:46,451 - INFO - Processed 64700000 reads so far
2011-05-19 18:05:57,022 - INFO - Processed 64800000 reads so far
2011-05-19 18:06:09,350 - INFO - Processed 64900000 reads so far
2011-05-19 18:06:17,951 - INFO - Processed 65000000 reads so far
2011-05-19 18:06:28,360 - INFO - Processed 65100000 reads so far
2011-05-19 18:06:41,580 - INFO - Processed 65200000 reads so far
2011-05-19 18:06:49,657 - INFO - Processed 65300000 reads so far
2011-05-19 18:06:58,051 - INFO - Processed 65400000 reads so far
2011-05-19 18:07:04,378 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:82990068-103010068
2011-05-19 18:07:07,714 - INFO - Processed 65500000 reads so far
2011-05-19 18:07:19,001 - INFO - Processed 65600000 reads so far
2011-05-19 18:07:27,894 - INFO - Processed 65700000 reads so far
2011-05-19 18:07:36,082 - INFO - Processed 65800000 reads so far
2011-05-19 18:07:46,086 - INFO - Processed 65900000 reads so far
2011-05-19 18:07:57,591 - INFO - Processed 66000000 reads so far
2011-05-19 18:08:07,682 - INFO - Processed 66100000 reads so far
2011-05-19 18:08:17,871 - INFO - Processed 66200000 reads so far
2011-05-19 18:08:32,051 - INFO - Processed 66300000 reads so far
2011-05-19 18:08:42,330 - INFO - Processed 66400000 reads so far
2011-05-19 18:08:53,044 - INFO - Processed 66500000 reads so far
2011-05-19 18:09:05,509 - INFO - Processed 66600000 reads so far
2011-05-19 18:09:17,462 - INFO - Processed 66700000 reads so far
2011-05-19 18:09:22,822 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:102990070-123010070
2011-05-19 18:09:28,572 - INFO - Processed 66800000 reads so far
2011-05-19 18:09:42,655 - INFO - Processed 66900000 reads so far
2011-05-19 18:09:51,958 - INFO - Processed 67000000 reads so far
2011-05-19 18:10:02,537 - INFO - Processed 67100000 reads so far
2011-05-19 18:10:15,261 - INFO - Processed 67200000 reads so far
2011-05-19 18:10:24,735 - INFO - Processed 67300000 reads so far
2011-05-19 18:10:33,186 - INFO - Processed 67400000 reads so far
2011-05-19 18:10:42,083 - INFO - Processed 67500000 reads so far
2011-05-19 18:10:55,194 - INFO - Processed 67600000 reads so far
2011-05-19 18:11:05,357 - INFO - Processed 67700000 reads so far
2011-05-19 18:11:14,862 - INFO - Processed 67800000 reads so far
2011-05-19 18:11:20,280 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:122990080-143010080
2011-05-19 18:11:25,147 - INFO - Processed 67900000 reads so far
2011-05-19 18:11:36,902 - INFO - Processed 68000000 reads so far
2011-05-19 18:11:46,039 - INFO - Processed 68100000 reads so far
2011-05-19 18:11:55,762 - INFO - Processed 68200000 reads so far
2011-05-19 18:12:08,402 - INFO - Processed 68300000 reads so far
2011-05-19 18:12:17,753 - INFO - Processed 68400000 reads so far
2011-05-19 18:12:25,611 - INFO - Processed 68500000 reads so far
2011-05-19 18:12:35,568 - INFO - Processed 68600000 reads so far
2011-05-19 18:12:50,929 - INFO - Processed 68700000 reads so far
2011-05-19 18:13:01,841 - INFO - Processed 68800000 reads so far
2011-05-19 18:13:15,376 - INFO - Processed 68900000 reads so far
2011-05-19 18:13:25,608 - INFO - Processed 69000000 reads so far
2011-05-19 18:13:31,142 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:142990121-163010121
2011-05-19 18:13:38,494 - INFO - Processed 69100000 reads so far
2011-05-19 18:13:50,162 - INFO - Processed 69200000 reads so far
2011-05-19 18:14:02,483 - INFO - Processed 69300000 reads so far
2011-05-19 18:14:10,793 - INFO - Processed 69400000 reads so far
2011-05-19 18:14:22,327 - INFO - Processed 69500000 reads so far
2011-05-19 18:14:36,441 - INFO - Processed 69600000 reads so far
2011-05-19 18:14:47,563 - INFO - Processed 69700000 reads so far
2011-05-19 18:14:57,021 - INFO - Processed 69800000 reads so far
2011-05-19 18:15:08,251 - INFO - Processed 69900000 reads so far
2011-05-19 18:15:19,945 - INFO - Processed 70000000 reads so far
2011-05-19 18:15:33,157 - INFO - Processed 70100000 reads so far
2011-05-19 18:15:39,721 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:162990138-183010138
2011-05-19 18:15:43,999 - INFO - Processed 70200000 reads so far
2011-05-19 18:15:56,263 - INFO - Processed 70300000 reads so far
2011-05-19 18:16:09,162 - INFO - Processed 70400000 reads so far
2011-05-19 18:16:20,455 - INFO - Processed 70500000 reads so far
2011-05-19 18:16:34,225 - INFO - Processed 70600000 reads so far
2011-05-19 18:16:46,023 - INFO - Processed 70700000 reads so far
2011-05-19 18:16:56,757 - INFO - Processed 70800000 reads so far
2011-05-19 18:17:06,699 - INFO - Processed 70900000 reads so far
2011-05-19 18:17:20,419 - INFO - Processed 71000000 reads so far
2011-05-19 18:17:33,600 - INFO - Processed 71100000 reads so far
2011-05-19 18:17:44,820 - INFO - Processed 71200000 reads so far
2011-05-19 18:17:55,184 - INFO - Processed 71300000 reads so far
2011-05-19 18:18:02,846 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:182990142-203010142
2011-05-19 18:18:05,187 - INFO - Processed 71400000 reads so far
2011-05-19 18:24:12,213 - INFO - Processed 71500000 reads so far
2011-05-19 18:24:21,957 - INFO - Processed 71600000 reads so far
2011-05-19 18:24:29,793 - INFO - Processed 71700000 reads so far
2011-05-19 18:24:37,238 - INFO - Processed 71800000 reads so far
2011-05-19 18:24:47,711 - INFO - Processed 71900000 reads so far
2011-05-19 18:24:56,624 - INFO - Processed 72000000 reads so far
2011-05-19 18:25:07,452 - INFO - Processed 72100000 reads so far
2011-05-19 18:25:16,472 - INFO - Processed 72200000 reads so far
2011-05-19 18:25:20,406 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1_random:0-20010007
2011-05-19 18:25:25,617 - INFO - Processed 72300000 reads so far
2011-05-19 18:25:31,551 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:2990066-23010066
2011-05-19 18:25:32,121 - INFO - Processed 72400000 reads so far
2011-05-19 18:25:40,397 - INFO - Processed 72500000 reads so far
2011-05-19 18:25:49,485 - INFO - Processed 72600000 reads so far
2011-05-19 18:25:58,933 - INFO - Processed 72700000 reads so far
2011-05-19 18:26:07,906 - INFO - Processed 72800000 reads so far
2011-05-19 18:26:17,805 - INFO - Processed 72900000 reads so far
2011-05-19 18:26:26,644 - INFO - Processed 73000000 reads so far
2011-05-19 18:26:35,615 - INFO - Processed 73100000 reads so far
2011-05-19 18:26:45,158 - INFO - Processed 73200000 reads so far
2011-05-19 18:26:54,273 - INFO - Processed 73300000 reads so far
2011-05-19 18:27:05,557 - INFO - Processed 73400000 reads so far
2011-05-19 18:27:14,202 - INFO - Processed 73500000 reads so far
2011-05-19 18:27:22,617 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:22990067-43010067
2011-05-19 18:27:25,875 - INFO - Processed 73600000 reads so far
2011-05-19 18:27:37,329 - INFO - Processed 73700000 reads so far
2011-05-19 18:27:48,061 - INFO - Processed 73800000 reads so far
2011-05-19 18:27:58,437 - INFO - Processed 73900000 reads so far
2011-05-19 18:28:07,041 - INFO - Processed 74000000 reads so far
2011-05-19 18:28:18,437 - INFO - Processed 74100000 reads so far
2011-05-19 18:28:29,780 - INFO - Processed 74200000 reads so far
2011-05-19 18:28:41,318 - INFO - Processed 74300000 reads so far
2011-05-19 18:28:53,489 - INFO - Processed 74400000 reads so far
2011-05-19 18:29:07,249 - INFO - Processed 74500000 reads so far
2011-05-19 18:29:17,174 - INFO - Processed 74600000 reads so far
2011-05-19 18:29:25,041 - INFO - Processed 74700000 reads so far
2011-05-19 18:29:36,993 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:42990074-63010074
2011-05-19 18:29:37,443 - INFO - Processed 74800000 reads so far
2011-05-19 18:29:44,733 - INFO - Processed 74900000 reads so far
2011-05-19 18:29:52,310 - INFO - Processed 75000000 reads so far
2011-05-19 18:30:02,577 - INFO - Processed 75100000 reads so far
2011-05-19 18:30:14,867 - INFO - Processed 75200000 reads so far
2011-05-19 18:30:24,979 - INFO - Processed 75300000 reads so far
2011-05-19 18:30:39,392 - INFO - Processed 75400000 reads so far
2011-05-19 18:30:50,486 - INFO - Processed 75500000 reads so far
2011-05-19 18:31:01,470 - INFO - Processed 75600000 reads so far
2011-05-19 18:31:09,535 - INFO - Processed 75700000 reads so far
2011-05-19 18:31:18,560 - INFO - Processed 75800000 reads so far
2011-05-19 18:31:31,779 - INFO - Processed 75900000 reads so far
2011-05-19 18:31:33,024 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:62990105-83010105
2011-05-19 18:31:42,943 - INFO - Processed 76000000 reads so far
2011-05-19 18:31:56,549 - INFO - Processed 76100000 reads so far
2011-05-19 18:32:09,902 - INFO - Processed 76200000 reads so far
2011-05-19 18:32:21,350 - INFO - Processed 76300000 reads so far
2011-05-19 18:32:32,675 - INFO - Processed 76400000 reads so far
2011-05-19 18:32:42,319 - INFO - Processed 76500000 reads so far
2011-05-19 18:32:50,601 - INFO - Processed 76600000 reads so far
2011-05-19 18:32:59,420 - INFO - Processed 76700000 reads so far
2011-05-19 18:33:06,790 - INFO - Processed 76800000 reads so far
2011-05-19 18:33:16,403 - INFO - Processed 76900000 reads so far
2011-05-19 18:33:23,763 - INFO - Processed 77000000 reads so far
2011-05-19 18:33:29,031 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:82990117-103010117
2011-05-19 18:33:37,313 - INFO - Processed 77100000 reads so far
2011-05-19 18:33:47,701 - INFO - Processed 77200000 reads so far
2011-05-19 18:33:56,913 - INFO - Processed 77300000 reads so far
2011-05-19 18:34:11,854 - INFO - Processed 77400000 reads so far
2011-05-19 18:34:23,514 - INFO - Processed 77500000 reads so far
2011-05-19 18:34:35,024 - INFO - Processed 77600000 reads so far
2011-05-19 18:34:48,750 - INFO - Processed 77700000 reads so far
2011-05-19 18:34:59,351 - INFO - Processed 77800000 reads so far
2011-05-19 18:35:06,905 - INFO - Processed 77900000 reads so far
2011-05-19 18:35:15,146 - INFO - Processed 78000000 reads so far
2011-05-19 18:35:24,023 - INFO - Processed 78100000 reads so far
2011-05-19 18:35:32,327 - INFO - Processed 78200000 reads so far
2011-05-19 18:35:40,944 - INFO - Processed 78300000 reads so far
2011-05-19 18:35:50,393 - INFO - Processed 78400000 reads so far
2011-05-19 18:36:04,369 - INFO - Processed 78500000 reads so far
2011-05-19 18:36:15,001 - INFO - Processed 78600000 reads so far
2011-05-19 18:36:29,251 - INFO - Processed 78700000 reads so far
2011-05-19 18:36:38,984 - INFO - Processed 78800000 reads so far
2011-05-19 18:36:46,578 - INFO - Processed 78900000 reads so far
2011-05-19 18:36:55,368 - INFO - Processed 79000000 reads so far
2011-05-19 18:37:04,502 - INFO - Processed 79100000 reads so far
2011-05-19 18:37:12,092 - INFO - Processed 79200000 reads so far
2011-05-19 18:37:20,245 - INFO - Processed 79300000 reads so far
2011-05-19 18:37:28,876 - INFO - Processed 79400000 reads so far
2011-05-19 18:37:39,226 - INFO - Processed 79500000 reads so far
2011-05-19 18:37:46,542 - INFO - Processed 79600000 reads so far
2011-05-19 18:37:56,604 - INFO - Processed 79700000 reads so far
2011-05-19 18:38:06,378 - INFO - Processed 79800000 reads so far
2011-05-19 18:38:16,870 - INFO - Processed 79900000 reads so far
2011-05-19 18:38:24,726 - INFO - Processed 80000000 reads so far
2011-05-19 18:38:31,624 - INFO - Processed 80100000 reads so far
2011-05-19 18:38:39,584 - INFO - Processed 80200000 reads so far
2011-05-19 18:38:45,989 - INFO - Processed 80300000 reads so far
2011-05-19 18:38:59,994 - INFO - Processed 80400000 reads so far
2011-05-19 18:39:11,297 - INFO - Processed 80500000 reads so far
2011-05-19 18:39:21,151 - INFO - Processed 80600000 reads so far
2011-05-19 18:39:32,304 - INFO - Processed 80700000 reads so far
2011-05-19 18:39:42,347 - INFO - Processed 80800000 reads so far
2011-05-19 18:39:51,436 - INFO - Processed 80900000 reads so far
2011-05-19 18:40:02,447 - INFO - Processed 81000000 reads so far
2011-05-19 18:40:11,873 - INFO - Processed 81100000 reads so far
2011-05-19 18:40:20,870 - INFO - Processed 81200000 reads so far
2011-05-19 18:40:27,560 - INFO - Processed 81300000 reads so far
2011-05-19 18:40:35,174 - INFO - Processed 81400000 reads so far
2011-05-19 18:40:43,030 - INFO - Processed 81500000 reads so far
2011-05-19 18:40:51,618 - INFO - Processed 81600000 reads so far
2011-05-19 18:41:00,807 - INFO - Processed 81700000 reads so far
2011-05-19 18:41:14,357 - INFO - Processed 81800000 reads so far
2011-05-19 18:41:23,688 - INFO - Processed 81900000 reads so far
2011-05-19 18:41:32,445 - INFO - Processed 82000000 reads so far
2011-05-19 18:41:39,179 - INFO - Processed 82100000 reads so far
2011-05-19 18:41:46,482 - INFO - Processed 82200000 reads so far
2011-05-19 18:41:52,389 - INFO - Processed 82300000 reads so far
2011-05-19 18:41:58,611 - INFO - Processed 82400000 reads so far
2011-05-19 18:42:04,303 - INFO - Processed 82500000 reads so far
2011-05-19 18:42:11,368 - INFO - Processed 82600000 reads so far
2011-05-19 18:42:19,982 - INFO - Processed 82700000 reads so far
2011-05-19 18:42:26,189 - INFO - Processed 82800000 reads so far
2011-05-19 18:42:32,482 - INFO - Processed 82900000 reads so far
2011-05-19 18:42:38,897 - INFO - Processed 83000000 reads so far
2011-05-19 18:42:44,345 - INFO - Processed 83100000 reads so far
2011-05-19 18:42:51,500 - INFO - Processed 83200000 reads so far
2011-05-19 18:42:59,244 - INFO - Processed 83300000 reads so far
2011-05-19 18:43:08,068 - INFO - Processed 83400000 reads so far
2011-05-19 18:43:17,027 - INFO - Processed 83500000 reads so far
2011-05-19 18:43:24,561 - INFO - Processed 83600000 reads so far
2011-05-19 18:43:33,317 - INFO - Processed 83700000 reads so far
2011-05-19 18:43:42,267 - INFO - Processed 83800000 reads so far
2011-05-19 18:43:51,921 - INFO - Processed 83900000 reads so far
2011-05-19 18:44:00,525 - INFO - Processed 84000000 reads so far
2011-05-19 18:44:11,534 - INFO - Processed 84100000 reads so far
2011-05-19 18:44:20,412 - INFO - Processed 84200000 reads so far
2011-05-19 18:44:28,256 - INFO - Processed 84300000 reads so far
2011-05-19 18:44:36,396 - INFO - Processed 84400000 reads so far
2011-05-19 18:44:48,495 - INFO - Processed 84500000 reads so far
2011-05-19 18:44:58,536 - INFO - Processed 84600000 reads so far
2011-05-19 18:45:05,674 - INFO - Processed 84700000 reads so far
2011-05-19 18:45:12,466 - INFO - Processed 84800000 reads so far
2011-05-19 18:45:22,405 - INFO - Processed 84900000 reads so far
2011-05-19 18:45:29,896 - INFO - Processed 85000000 reads so far
2011-05-19 18:45:37,824 - INFO - Processed 85100000 reads so far
2011-05-19 18:45:44,689 - INFO - Processed 85200000 reads so far
2011-05-19 18:45:54,416 - INFO - Processed 85300000 reads so far
2011-05-19 18:46:03,355 - INFO - Processed 85400000 reads so far
2011-05-19 18:46:12,122 - INFO - Processed 85500000 reads so far
2011-05-19 18:46:21,069 - INFO - Processed 85600000 reads so far
2011-05-19 18:46:32,103 - INFO - Processed 85700000 reads so far
2011-05-19 18:46:42,340 - INFO - Processed 85800000 reads so far
2011-05-19 18:46:52,160 - INFO - Processed 85900000 reads so far
2011-05-19 18:47:02,710 - INFO - Processed 86000000 reads so far
2011-05-19 18:47:11,804 - INFO - Processed 86100000 reads so far
2011-05-19 18:47:21,834 - INFO - Processed 86200000 reads so far
2011-05-19 18:47:29,758 - INFO - Processed 86300000 reads so far
2011-05-19 18:47:39,548 - INFO - Processed 86400000 reads so far
2011-05-19 18:47:48,401 - INFO - Processed 86500000 reads so far
2011-05-19 18:47:56,968 - INFO - Processed 86600000 reads so far
2011-05-19 18:48:07,166 - INFO - Processed 86700000 reads so far
2011-05-19 18:48:16,632 - INFO - Processed 86800000 reads so far
2011-05-19 18:48:25,008 - INFO - Processed 86900000 reads so far
2011-05-19 18:48:33,781 - INFO - Processed 87000000 reads so far
2011-05-19 18:48:43,896 - INFO - Processed 87100000 reads so far
2011-05-19 18:48:53,322 - INFO - Processed 87200000 reads so far
2011-05-19 18:49:02,334 - INFO - Processed 87300000 reads so far
2011-05-19 18:49:11,966 - INFO - Processed 87400000 reads so far
2011-05-19 18:49:20,545 - INFO - Processed 87500000 reads so far
2011-05-19 18:49:29,700 - INFO - Processed 87600000 reads so far
2011-05-19 18:49:42,880 - INFO - Processed 87700000 reads so far
2011-05-19 18:49:51,517 - INFO - Processed 87800000 reads so far
2011-05-19 18:50:04,310 - INFO - Processed 87900000 reads so far
2011-05-19 18:50:14,515 - INFO - Processed 88000000 reads so far
2011-05-19 18:50:23,783 - INFO - Processed 88100000 reads so far
2011-05-19 18:50:34,844 - INFO - Processed 88200000 reads so far
2011-05-19 18:50:44,138 - INFO - Processed 88300000 reads so far
2011-05-19 18:50:52,297 - INFO - Processed 88400000 reads so far
2011-05-19 18:51:02,009 - INFO - Processed 88500000 reads so far
2011-05-19 18:51:11,324 - INFO - Processed 88600000 reads so far
2011-05-19 18:51:20,317 - INFO - Processed 88700000 reads so far
2011-05-19 18:51:29,748 - INFO - Processed 88800000 reads so far
2011-05-19 18:51:39,183 - INFO - Processed 88900000 reads so far
2011-05-19 18:51:48,394 - INFO - Processed 89000000 reads so far
2011-05-19 18:51:59,534 - INFO - Processed 89100000 reads so far
2011-05-19 18:52:10,767 - INFO - Processed 89200000 reads so far
2011-05-19 18:52:24,997 - INFO - Processed 89300000 reads so far
2011-05-19 18:52:25,915 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:102990183-123010183
2011-05-19 18:52:37,240 - INFO - Processed 89400000 reads so far
2011-05-19 18:52:49,825 - INFO - Processed 89500000 reads so far
2011-05-19 18:53:00,844 - INFO - Processed 89600000 reads so far
2011-05-19 18:53:11,209 - INFO - Processed 89700000 reads so far
2011-05-19 18:53:24,819 - INFO - Processed 89800000 reads so far
2011-05-19 18:53:36,762 - INFO - Processed 89900000 reads so far
2011-05-19 18:53:49,370 - INFO - Processed 90000000 reads so far
2011-05-19 18:53:59,561 - INFO - Processed 90100000 reads so far
2011-05-19 18:54:09,081 - INFO - Processed 90200000 reads so far
2011-05-19 18:54:55,319 - INFO - Processed 90300000 reads so far
2011-05-19 18:55:06,256 - INFO - Processed 90400000 reads so far
2011-05-19 18:55:11,232 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:122990237-143010237
2011-05-19 18:55:14,741 - INFO - Processed 90500000 reads so far
2011-05-19 18:55:27,270 - INFO - Processed 90600000 reads so far
2011-05-19 18:55:38,513 - INFO - Processed 90700000 reads so far
2011-05-19 18:55:49,281 - INFO - Processed 90800000 reads so far
2011-05-19 18:56:02,033 - INFO - Processed 90900000 reads so far
2011-05-19 18:56:11,235 - INFO - Processed 91000000 reads so far
2011-05-19 18:56:22,273 - INFO - Processed 91100000 reads so far
2011-05-19 18:56:35,943 - INFO - Processed 91200000 reads so far
2011-05-19 18:56:48,346 - INFO - Processed 91300000 reads so far
2011-05-19 18:57:00,747 - INFO - Processed 91400000 reads so far
2011-05-19 18:57:13,111 - INFO - Processed 91500000 reads so far
2011-05-19 18:57:23,255 - INFO - Processed 91600000 reads so far
2011-05-19 18:57:27,035 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:142990244-163010244
2011-05-19 18:57:34,083 - INFO - Processed 91700000 reads so far
2011-05-19 18:57:46,295 - INFO - Processed 91800000 reads so far
2011-05-19 18:57:55,764 - INFO - Processed 91900000 reads so far
2011-05-19 18:58:05,797 - INFO - Processed 92000000 reads so far
2011-05-19 18:58:15,230 - INFO - Processed 92100000 reads so far
2011-05-19 18:58:26,531 - INFO - Processed 92200000 reads so far
2011-05-19 18:58:36,781 - INFO - Processed 92300000 reads so far
2011-05-19 18:58:47,121 - INFO - Processed 92400000 reads so far
2011-05-19 18:58:56,375 - INFO - Processed 92500000 reads so far
2011-05-19 18:59:09,453 - INFO - Processed 92600000 reads so far
2011-05-19 18:59:18,386 - INFO - Processed 92700000 reads so far
2011-05-19 18:59:27,933 - INFO - Processed 92800000 reads so far
2011-05-19 18:59:33,193 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:162990266-183010266
2011-05-19 18:59:36,355 - INFO - Processed 92900000 reads so far
2011-05-19 18:59:48,042 - INFO - Processed 93000000 reads so far
2011-05-19 18:59:57,267 - INFO - Processed 93100000 reads so far
2011-05-19 19:00:07,131 - INFO - Processed 93200000 reads so far
2011-05-19 19:00:17,715 - INFO - Processed 93300000 reads so far
2011-05-19 19:00:29,697 - INFO - Processed 93400000 reads so far
2011-05-19 19:00:40,833 - INFO - Processed 93500000 reads so far
2011-05-19 19:00:51,900 - INFO - Processed 93600000 reads so far
2011-05-19 19:01:03,847 - INFO - Processed 93700000 reads so far
2011-05-19 19:01:18,396 - INFO - Processed 93800000 reads so far
2011-05-19 19:01:30,439 - INFO - Processed 93900000 reads so far
2011-05-19 19:01:43,547 - INFO - Processed 94000000 reads so far
2011-05-19 19:01:51,912 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:2990000-23010000
2011-05-19 19:01:52,378 - INFO - Processed 94100000 reads so far
2011-05-19 19:02:03,835 - INFO - Processed 94200000 reads so far
2011-05-19 19:02:17,455 - INFO - Processed 94300000 reads so far
2011-05-19 19:02:28,962 - INFO - Processed 94400000 reads so far
2011-05-19 19:02:39,984 - INFO - Processed 94500000 reads so far
2011-05-19 19:02:52,544 - INFO - Processed 94600000 reads so far
2011-05-19 19:03:05,225 - INFO - Processed 94700000 reads so far
2011-05-19 19:03:16,133 - INFO - Processed 94800000 reads so far
2011-05-19 19:03:28,115 - INFO - Processed 94900000 reads so far
2011-05-19 19:03:36,885 - INFO - Processed 95000000 reads so far
2011-05-19 19:03:48,635 - INFO - Processed 95100000 reads so far
2011-05-19 19:03:58,774 - INFO - Processed 95200000 reads so far
2011-05-19 19:03:59,145 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:22990069-43010069
2011-05-19 19:04:09,880 - INFO - Processed 95300000 reads so far
2011-05-19 19:04:20,073 - INFO - Processed 95400000 reads so far
2011-05-19 19:04:29,538 - INFO - Processed 95500000 reads so far
2011-05-19 19:04:39,596 - INFO - Processed 95600000 reads so far
2011-05-19 19:04:49,215 - INFO - Processed 95700000 reads so far
2011-05-19 19:05:01,693 - INFO - Processed 95800000 reads so far
2011-05-19 19:05:12,316 - INFO - Processed 95900000 reads so far
2011-05-19 19:05:22,828 - INFO - Processed 96000000 reads so far
2011-05-19 19:05:36,350 - INFO - Processed 96100000 reads so far
2011-05-19 19:05:47,176 - INFO - Processed 96200000 reads so far
2011-05-19 19:05:58,403 - INFO - Processed 96300000 reads so far
2011-05-19 19:06:06,223 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:42990079-63010079
2011-05-19 19:06:10,265 - INFO - Processed 96400000 reads so far
2011-05-19 19:06:23,009 - INFO - Processed 96500000 reads so far
2011-05-19 19:06:36,784 - INFO - Processed 96600000 reads so far
2011-05-19 19:06:47,352 - INFO - Processed 96700000 reads so far
2011-05-19 19:06:58,132 - INFO - Processed 96800000 reads so far
2011-05-19 19:07:11,353 - INFO - Processed 96900000 reads so far
2011-05-19 19:07:22,404 - INFO - Processed 97000000 reads so far
2011-05-19 19:07:32,655 - INFO - Processed 97100000 reads so far
2011-05-19 19:07:42,388 - INFO - Processed 97200000 reads so far
2011-05-19 19:07:54,080 - INFO - Processed 97300000 reads so far
2011-05-19 19:08:02,003 - INFO - Processed 97400000 reads so far
2011-05-19 19:08:08,092 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:62990132-83010132
2011-05-19 19:08:12,746 - INFO - Processed 97500000 reads so far
2011-05-19 19:08:23,455 - INFO - Processed 97600000 reads so far
2011-05-19 19:08:33,814 - INFO - Processed 97700000 reads so far
2011-05-19 19:08:42,648 - INFO - Processed 97800000 reads so far
2011-05-19 19:08:54,042 - INFO - Processed 97900000 reads so far
2011-05-19 19:09:01,725 - INFO - Processed 98000000 reads so far
2011-05-19 19:09:12,268 - INFO - Processed 98100000 reads so far
2011-05-19 19:09:22,816 - INFO - Processed 98200000 reads so far
2011-05-19 19:09:31,666 - INFO - Processed 98300000 reads so far
2011-05-19 19:09:41,595 - INFO - Processed 98400000 reads so far
2011-05-19 19:09:51,665 - INFO - Processed 98500000 reads so far
2011-05-19 19:10:01,157 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:82990148-103010148
2011-05-19 19:10:04,578 - INFO - Processed 98600000 reads so far
2011-05-19 19:10:24,232 - INFO - Processed 98700000 reads so far
2011-05-19 19:10:57,069 - INFO - Processed 98800000 reads so far
2011-05-19 19:11:33,795 - INFO - Processed 98900000 reads so far
2011-05-19 19:11:45,047 - INFO - Processed 99000000 reads so far
2011-05-19 19:11:57,382 - INFO - Processed 99100000 reads so far
2011-05-19 19:12:04,599 - INFO - Processed 99200000 reads so far
2011-05-19 19:12:13,342 - INFO - Processed 99300000 reads so far
2011-05-19 19:12:23,874 - INFO - Processed 99400000 reads so far
2011-05-19 19:12:30,560 - INFO - Processed 99500000 reads so far
2011-05-19 19:12:37,297 - INFO - Processed 99600000 reads so far
2011-05-19 19:12:45,457 - INFO - Processed 99700000 reads so far
2011-05-19 19:12:51,164 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:102990156-123010156
2011-05-19 19:12:52,324 - INFO - Processed 99800000 reads so far
2011-05-19 19:12:59,630 - INFO - Processed 99900000 reads so far
2011-05-19 19:13:09,534 - INFO - Processed 100000000 reads so far
2011-05-19 19:13:18,144 - INFO - Processed 100100000 reads so far
2011-05-19 19:13:28,990 - INFO - Processed 100200000 reads so far
2011-05-19 19:13:37,378 - INFO - Processed 100300000 reads so far
2011-05-19 19:13:48,101 - INFO - Processed 100400000 reads so far
2011-05-19 19:13:59,903 - INFO - Processed 100500000 reads so far
2011-05-19 19:14:11,003 - INFO - Processed 100600000 reads so far
2011-05-19 19:14:20,300 - INFO - Processed 100700000 reads so far
2011-05-19 19:14:30,021 - INFO - Processed 100800000 reads so far
2011-05-19 19:14:40,373 - INFO - Processed 100900000 reads so far
2011-05-19 19:14:42,815 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:122990159-143010159
2011-05-19 19:14:49,830 - INFO - Processed 101000000 reads so far
2011-05-19 19:15:01,826 - INFO - Processed 101100000 reads so far
2011-05-19 19:15:10,434 - INFO - Processed 101200000 reads so far
2011-05-19 19:15:19,814 - INFO - Processed 101300000 reads so far
2011-05-19 19:15:30,816 - INFO - Processed 101400000 reads so far
2011-05-19 19:15:45,192 - INFO - Processed 101500000 reads so far
2011-05-19 19:15:54,268 - INFO - Processed 101600000 reads so far
2011-05-19 19:16:02,514 - INFO - Processed 101700000 reads so far
2011-05-19 19:16:15,212 - INFO - Processed 101800000 reads so far
2011-05-19 19:16:24,054 - INFO - Processed 101900000 reads so far
2011-05-19 19:16:37,969 - INFO - Processed 102000000 reads so far
2011-05-19 19:16:43,419 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:142990178-163010178
2011-05-19 19:16:47,418 - INFO - Processed 102100000 reads so far
2011-05-19 19:16:54,259 - INFO - Processed 102200000 reads so far
2011-05-19 19:17:02,577 - INFO - Processed 102300000 reads so far
2011-05-19 19:17:11,801 - INFO - Processed 102400000 reads so far
2011-05-19 19:17:19,055 - INFO - Processed 102500000 reads so far
2011-05-19 19:17:28,681 - INFO - Processed 102600000 reads so far
2011-05-19 19:17:38,799 - INFO - Processed 102700000 reads so far
2011-05-19 19:17:48,291 - INFO - Processed 102800000 reads so far
2011-05-19 19:17:57,789 - INFO - Processed 102900000 reads so far
2011-05-19 19:18:08,318 - INFO - Processed 103000000 reads so far
2011-05-19 19:18:12,601 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3_random:0-20010100
2011-05-19 19:18:12,696 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:2989985-23009985
2011-05-19 19:18:18,390 - INFO - Processed 103100000 reads so far
2011-05-19 19:18:27,468 - INFO - Processed 103200000 reads so far
2011-05-19 19:18:35,475 - INFO - Processed 103300000 reads so far
2011-05-19 19:18:42,560 - INFO - Processed 103400000 reads so far
2011-05-19 19:18:51,049 - INFO - Processed 103500000 reads so far
2011-05-19 19:19:01,447 - INFO - Processed 103600000 reads so far
2011-05-19 19:19:12,309 - INFO - Processed 103700000 reads so far
2011-05-19 19:19:21,234 - INFO - Processed 103800000 reads so far
2011-05-19 19:19:28,996 - INFO - Processed 103900000 reads so far
2011-05-19 19:19:42,628 - INFO - Processed 104000000 reads so far
2011-05-19 19:19:56,701 - INFO - Processed 104100000 reads so far
2011-05-19 19:20:07,592 - INFO - Processed 104200000 reads so far
2011-05-19 19:20:08,605 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:22990014-43010014
2011-05-19 19:20:19,002 - INFO - Processed 104300000 reads so far
2011-05-19 19:20:30,124 - INFO - Processed 104400000 reads so far
2011-05-19 19:20:41,559 - INFO - Processed 104500000 reads so far
2011-05-19 19:20:53,836 - INFO - Processed 104600000 reads so far
2011-05-19 19:21:04,879 - INFO - Processed 104700000 reads so far
2011-05-19 19:21:15,301 - INFO - Processed 104800000 reads so far
2011-05-19 19:21:23,859 - INFO - Processed 104900000 reads so far
2011-05-19 19:21:34,463 - INFO - Processed 105000000 reads so far
2011-05-19 19:21:42,153 - INFO - Processed 105100000 reads so far
2011-05-19 19:21:48,932 - INFO - Processed 105200000 reads so far
2011-05-19 19:21:57,523 - INFO - Processed 105300000 reads so far
2011-05-19 19:21:59,242 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:42990019-63010019
2011-05-19 19:22:11,023 - INFO - Processed 105400000 reads so far
2011-05-19 19:22:22,038 - INFO - Processed 105500000 reads so far
2011-05-19 19:22:32,999 - INFO - Processed 105600000 reads so far
2011-05-19 19:22:44,751 - INFO - Processed 105700000 reads so far
2011-05-19 19:22:55,852 - INFO - Processed 105800000 reads so far
2011-05-19 19:23:07,347 - INFO - Processed 105900000 reads so far
2011-05-19 19:23:22,366 - INFO - Processed 106000000 reads so far
2011-05-19 19:23:32,781 - INFO - Processed 106100000 reads so far
2011-05-19 19:23:41,584 - INFO - Processed 106200000 reads so far
2011-05-19 19:23:50,400 - INFO - Processed 106300000 reads so far
2011-05-19 19:24:00,485 - INFO - Processed 106400000 reads so far
2011-05-19 19:24:09,425 - INFO - Processed 106500000 reads so far
2011-05-19 19:24:13,238 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:62990020-83010020
2011-05-19 19:24:18,712 - INFO - Processed 106600000 reads so far
2011-05-19 19:24:31,914 - INFO - Processed 106700000 reads so far
2011-05-19 19:24:41,907 - INFO - Processed 106800000 reads so far
2011-05-19 19:24:50,636 - INFO - Processed 106900000 reads so far
2011-05-19 19:24:58,448 - INFO - Processed 107000000 reads so far
2011-05-19 19:25:08,808 - INFO - Processed 107100000 reads so far
2011-05-19 19:25:20,541 - INFO - Processed 107200000 reads so far
2011-05-19 19:25:31,732 - INFO - Processed 107300000 reads so far
2011-05-19 19:25:43,242 - INFO - Processed 107400000 reads so far
2011-05-19 19:25:57,328 - INFO - Processed 107500000 reads so far
2011-05-19 19:26:06,103 - INFO - Processed 107600000 reads so far
2011-05-19 19:26:14,780 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:82990045-103010045
2011-05-19 19:26:18,575 - INFO - Processed 107700000 reads so far
2011-05-19 19:26:29,046 - INFO - Processed 107800000 reads so far
2011-05-19 19:26:38,618 - INFO - Processed 107900000 reads so far
2011-05-19 19:26:48,115 - INFO - Processed 108000000 reads so far
2011-05-19 19:26:59,746 - INFO - Processed 108100000 reads so far
2011-05-19 19:27:09,075 - INFO - Processed 108200000 reads so far
2011-05-19 19:27:18,383 - INFO - Processed 108300000 reads so far
2011-05-19 19:27:31,833 - INFO - Processed 108400000 reads so far
2011-05-19 19:27:41,124 - INFO - Processed 108500000 reads so far
2011-05-19 19:27:50,722 - INFO - Processed 108600000 reads so far
2011-05-19 19:28:04,411 - INFO - Processed 108700000 reads so far
2011-05-19 19:28:13,774 - INFO - Processed 108800000 reads so far
2011-05-19 19:28:17,860 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:102990054-123010054
2011-05-19 19:28:26,330 - INFO - Processed 108900000 reads so far
2011-05-19 19:28:38,777 - INFO - Processed 109000000 reads so far
2011-05-19 19:28:47,425 - INFO - Processed 109100000 reads so far
2011-05-19 19:28:55,814 - INFO - Processed 109200000 reads so far
2011-05-19 19:29:03,429 - INFO - Processed 109300000 reads so far
2011-05-19 19:29:15,476 - INFO - Processed 109400000 reads so far
2011-05-19 19:29:24,514 - INFO - Processed 109500000 reads so far
2011-05-19 19:29:32,965 - INFO - Processed 109600000 reads so far
2011-05-19 19:29:41,813 - INFO - Processed 109700000 reads so far
2011-05-19 19:29:51,360 - INFO - Processed 109800000 reads so far
2011-05-19 19:30:00,682 - INFO - Processed 109900000 reads so far
2011-05-19 19:30:04,591 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:122990093-143010093
2011-05-19 19:30:09,062 - INFO - Processed 110000000 reads so far
2011-05-19 19:30:16,849 - INFO - Processed 110100000 reads so far
2011-05-19 19:30:28,104 - INFO - Processed 110200000 reads so far
2011-05-19 19:30:36,101 - INFO - Processed 110300000 reads so far
2011-05-19 19:30:45,527 - INFO - Processed 110400000 reads so far
2011-05-19 19:30:54,493 - INFO - Processed 110500000 reads so far
2011-05-19 19:31:05,253 - INFO - Processed 110600000 reads so far
2011-05-19 19:31:13,529 - INFO - Processed 110700000 reads so far
2011-05-19 19:31:22,301 - INFO - Processed 110800000 reads so far
2011-05-19 19:31:36,315 - INFO - Processed 110900000 reads so far
2011-05-19 19:31:45,513 - INFO - Processed 111000000 reads so far
2011-05-19 19:31:56,660 - INFO - Processed 111100000 reads so far
2011-05-19 19:32:09,598 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:142990094-163010094
2011-05-19 19:32:10,289 - INFO - Processed 111200000 reads so far
2011-05-19 19:32:21,697 - INFO - Processed 111300000 reads so far
2011-05-19 19:32:29,866 - INFO - Processed 111400000 reads so far
2011-05-19 19:32:38,687 - INFO - Processed 111500000 reads so far
2011-05-19 19:32:52,160 - INFO - Processed 111600000 reads so far
2011-05-19 19:33:02,016 - INFO - Processed 111700000 reads so far
2011-05-19 19:33:12,783 - INFO - Processed 111800000 reads so far
2011-05-19 19:33:25,414 - INFO - Processed 111900000 reads so far
2011-05-19 19:33:36,220 - INFO - Processed 112000000 reads so far
2011-05-19 19:33:44,523 - INFO - Processed 112100000 reads so far
2011-05-19 19:33:52,773 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4_random:0-20010000
2011-05-19 19:33:53,422 - INFO - Processed 112200000 reads so far
2011-05-19 19:33:53,616 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:2990004-23010004
2011-05-19 19:34:02,526 - INFO - Processed 112300000 reads so far
2011-05-19 19:34:11,211 - INFO - Processed 112400000 reads so far
2011-05-19 19:34:20,339 - INFO - Processed 112500000 reads so far
2011-05-19 19:34:29,445 - INFO - Processed 112600000 reads so far
2011-05-19 19:34:39,024 - INFO - Processed 112700000 reads so far
2011-05-19 19:34:47,438 - INFO - Processed 112800000 reads so far
2011-05-19 19:34:56,626 - INFO - Processed 112900000 reads so far
2011-05-19 19:35:06,891 - INFO - Processed 113000000 reads so far
2011-05-19 19:35:15,011 - INFO - Processed 113100000 reads so far
2011-05-19 19:35:24,353 - INFO - Processed 113200000 reads so far
2011-05-19 19:35:34,615 - INFO - Processed 113300000 reads so far
2011-05-19 19:35:38,462 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:22990015-43010015
2011-05-19 19:35:45,872 - INFO - Processed 113400000 reads so far
2011-05-19 19:35:55,283 - INFO - Processed 113500000 reads so far
2011-05-19 19:36:04,792 - INFO - Processed 113600000 reads so far
2011-05-19 19:36:13,967 - INFO - Processed 113700000 reads so far
2011-05-19 19:36:26,467 - INFO - Processed 113800000 reads so far
2011-05-19 19:36:38,441 - INFO - Processed 113900000 reads so far
2011-05-19 19:36:47,851 - INFO - Processed 114000000 reads so far
2011-05-19 19:36:56,912 - INFO - Processed 114100000 reads so far
2011-05-19 19:37:07,498 - INFO - Processed 114200000 reads so far
2011-05-19 19:37:18,896 - INFO - Processed 114300000 reads so far
2011-05-19 19:37:28,071 - INFO - Processed 114400000 reads so far
2011-05-19 19:37:36,790 - INFO - Processed 114500000 reads so far
2011-05-19 19:37:41,086 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:42990026-63010026
2011-05-19 19:37:47,202 - INFO - Processed 114600000 reads so far
2011-05-19 19:37:58,754 - INFO - Processed 114700000 reads so far
2011-05-19 19:38:11,412 - INFO - Processed 114800000 reads so far
2011-05-19 19:38:20,984 - INFO - Processed 114900000 reads so far
2011-05-19 19:38:33,192 - INFO - Processed 115000000 reads so far
2011-05-19 19:38:43,825 - INFO - Processed 115100000 reads so far
2011-05-19 19:38:54,463 - INFO - Processed 115200000 reads so far
2011-05-19 19:39:05,391 - INFO - Processed 115300000 reads so far
2011-05-19 19:39:16,402 - INFO - Processed 115400000 reads so far
2011-05-19 19:39:29,249 - INFO - Processed 115500000 reads so far
2011-05-19 19:39:39,831 - INFO - Processed 115600000 reads so far
2011-05-19 19:39:43,733 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:62990070-83010070
2011-05-19 19:39:50,953 - INFO - Processed 115700000 reads so far
2011-05-19 19:40:00,519 - INFO - Processed 115800000 reads so far
2011-05-19 19:40:40,097 - INFO - Processed 115900000 reads so far
2011-05-19 19:40:51,718 - INFO - Processed 116000000 reads so far
2011-05-19 19:41:00,882 - INFO - Processed 116100000 reads so far
2011-05-19 19:41:10,824 - INFO - Processed 116200000 reads so far
2011-05-19 19:41:20,805 - INFO - Processed 116300000 reads so far
2011-05-19 19:41:32,062 - INFO - Processed 116400000 reads so far
2011-05-19 19:41:43,677 - INFO - Processed 116500000 reads so far
2011-05-19 19:41:53,770 - INFO - Processed 116600000 reads so far
2011-05-19 19:42:03,208 - INFO - Processed 116700000 reads so far
2011-05-19 19:42:12,233 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:82990085-103010085
2011-05-19 19:42:15,998 - INFO - Processed 116800000 reads so far
2011-05-19 19:42:28,435 - INFO - Processed 116900000 reads so far
2011-05-19 19:42:40,104 - INFO - Processed 117000000 reads so far
2011-05-19 19:42:56,533 - INFO - Processed 117100000 reads so far
2011-05-19 19:43:07,322 - INFO - Processed 117200000 reads so far
2011-05-19 19:43:15,672 - INFO - Processed 117300000 reads so far
2011-05-19 19:43:27,081 - INFO - Processed 117400000 reads so far
2011-05-19 19:43:37,953 - INFO - Processed 117500000 reads so far
2011-05-19 19:43:48,923 - INFO - Processed 117600000 reads so far
2011-05-19 19:44:03,189 - INFO - Processed 117700000 reads so far
2011-05-19 19:44:16,055 - INFO - Processed 117800000 reads so far
2011-05-19 19:44:20,311 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:102990087-123010087
2011-05-19 19:44:27,186 - INFO - Processed 117900000 reads so far
2011-05-19 19:44:40,430 - INFO - Processed 118000000 reads so far
2011-05-19 19:44:51,248 - INFO - Processed 118100000 reads so far
2011-05-19 19:45:01,887 - INFO - Processed 118200000 reads so far
2011-05-19 19:45:15,951 - INFO - Processed 118300000 reads so far
2011-05-19 19:45:26,311 - INFO - Processed 118400000 reads so far
2011-05-19 19:45:35,486 - INFO - Processed 118500000 reads so far
2011-05-19 19:45:46,275 - INFO - Processed 118600000 reads so far
2011-05-19 19:45:55,090 - INFO - Processed 118700000 reads so far
2011-05-19 19:46:04,562 - INFO - Processed 118800000 reads so far
2011-05-19 19:46:15,933 - INFO - Processed 118900000 reads so far
2011-05-19 19:46:28,091 - INFO - Processed 119000000 reads so far
2011-05-19 19:46:39,053 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:122990092-143010092
2011-05-19 19:46:40,842 - INFO - Processed 119100000 reads so far
2011-05-19 19:46:52,174 - INFO - Processed 119200000 reads so far
2011-05-19 19:47:01,718 - INFO - Processed 119300000 reads so far
2011-05-19 19:47:11,243 - INFO - Processed 119400000 reads so far
2011-05-19 19:47:22,578 - INFO - Processed 119500000 reads so far
2011-05-19 19:47:32,462 - INFO - Processed 119600000 reads so far
2011-05-19 19:47:41,373 - INFO - Processed 119700000 reads so far
2011-05-19 19:47:51,665 - INFO - Processed 119800000 reads so far
2011-05-19 19:48:04,134 - INFO - Processed 119900000 reads so far
2011-05-19 19:48:16,685 - INFO - Processed 120000000 reads so far
2011-05-19 19:48:27,953 - INFO - Processed 120100000 reads so far
2011-05-19 19:48:40,289 - INFO - Processed 120200000 reads so far
2011-05-19 19:48:51,097 - INFO - Processed 120300000 reads so far
2011-05-19 19:48:53,006 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:142990115-163010115
2011-05-19 19:49:02,345 - INFO - Processed 120400000 reads so far
2011-05-19 19:49:13,189 - INFO - Processed 120500000 reads so far
2011-05-19 19:49:23,265 - INFO - Processed 120600000 reads so far
2011-05-19 19:49:35,190 - INFO - Processed 120700000 reads so far
2011-05-19 19:49:49,601 - INFO - Processed 120800000 reads so far
2011-05-19 19:49:59,979 - INFO - Processed 120900000 reads so far
2011-05-19 19:50:01,005 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5_random:0-20010038
2011-05-19 19:50:01,292 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:2989984-23009984
2011-05-19 19:50:10,162 - INFO - Processed 121000000 reads so far
2011-05-19 19:50:20,098 - INFO - Processed 121100000 reads so far
2011-05-19 19:50:28,080 - INFO - Processed 121200000 reads so far
2011-05-19 19:50:37,556 - INFO - Processed 121300000 reads so far
2011-05-19 19:50:48,203 - INFO - Processed 121400000 reads so far
2011-05-19 19:50:57,585 - INFO - Processed 121500000 reads so far
2011-05-19 19:51:11,054 - INFO - Processed 121600000 reads so far
2011-05-19 19:51:20,766 - INFO - Processed 121700000 reads so far
2011-05-19 19:51:31,427 - INFO - Processed 121800000 reads so far
2011-05-19 19:51:41,541 - INFO - Processed 121900000 reads so far
2011-05-19 19:51:53,925 - INFO - Processed 122000000 reads so far
2011-05-19 19:51:56,099 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:22990055-43010055
2011-05-19 19:52:04,409 - INFO - Processed 122100000 reads so far
2011-05-19 19:52:15,762 - INFO - Processed 122200000 reads so far
2011-05-19 19:52:25,800 - INFO - Processed 122300000 reads so far
2011-05-19 19:52:37,094 - INFO - Processed 122400000 reads so far
2011-05-19 19:52:47,508 - INFO - Processed 122500000 reads so far
2011-05-19 19:52:58,693 - INFO - Processed 122600000 reads so far
2011-05-19 19:53:12,486 - INFO - Processed 122700000 reads so far
2011-05-19 19:53:22,557 - INFO - Processed 122800000 reads so far
2011-05-19 19:53:31,979 - INFO - Processed 122900000 reads so far
2011-05-19 19:53:41,556 - INFO - Processed 123000000 reads so far
2011-05-19 19:53:51,850 - INFO - Processed 123100000 reads so far
2011-05-19 19:54:01,320 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:42990079-63010079
2011-05-19 19:54:01,590 - INFO - Processed 123200000 reads so far
2011-05-19 19:54:10,550 - INFO - Processed 123300000 reads so far
2011-05-19 19:54:19,271 - INFO - Processed 123400000 reads so far
2011-05-19 19:54:32,859 - INFO - Processed 123500000 reads so far
2011-05-19 19:54:43,358 - INFO - Processed 123600000 reads so far
2011-05-19 19:54:52,869 - INFO - Processed 123700000 reads so far
2011-05-19 19:55:03,909 - INFO - Processed 123800000 reads so far
2011-05-19 19:55:13,407 - INFO - Processed 123900000 reads so far
2011-05-19 19:55:23,366 - INFO - Processed 124000000 reads so far
2011-05-19 19:55:34,612 - INFO - Processed 124100000 reads so far
2011-05-19 19:55:45,119 - INFO - Processed 124200000 reads so far
2011-05-19 19:55:54,813 - INFO - Processed 124300000 reads so far
2011-05-19 19:56:01,779 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:62990131-83010131
2011-05-19 19:56:07,372 - INFO - Processed 124400000 reads so far
2011-05-19 19:56:18,156 - INFO - Processed 124500000 reads so far
2011-05-19 19:56:27,405 - INFO - Processed 124600000 reads so far
2011-05-19 19:56:36,136 - INFO - Processed 124700000 reads so far
2011-05-19 19:56:45,484 - INFO - Processed 124800000 reads so far
2011-05-19 19:56:54,084 - INFO - Processed 124900000 reads so far
2011-05-19 19:57:04,262 - INFO - Processed 125000000 reads so far
2011-05-19 19:57:15,038 - INFO - Processed 125100000 reads so far
2011-05-19 19:57:25,887 - INFO - Processed 125200000 reads so far
2011-05-19 19:57:35,928 - INFO - Processed 125300000 reads so far
2011-05-19 19:57:45,970 - INFO - Processed 125400000 reads so far
2011-05-19 19:57:51,045 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:82990134-103010134
2011-05-19 19:57:58,125 - INFO - Processed 125500000 reads so far
2011-05-19 19:58:07,550 - INFO - Processed 125600000 reads so far
2011-05-19 19:58:17,642 - INFO - Processed 125700000 reads so far
2011-05-19 19:58:26,463 - INFO - Processed 125800000 reads so far
2011-05-19 19:58:39,502 - INFO - Processed 125900000 reads so far
2011-05-19 19:58:49,494 - INFO - Processed 126000000 reads so far
2011-05-19 19:59:02,790 - INFO - Processed 126100000 reads so far
2011-05-19 19:59:16,138 - INFO - Processed 126200000 reads so far
2011-05-19 19:59:27,297 - INFO - Processed 126300000 reads so far
2011-05-19 19:59:43,140 - INFO - Processed 126400000 reads so far
2011-05-19 19:59:55,156 - INFO - Processed 126500000 reads so far
2011-05-19 20:00:07,036 - INFO - Processed 126600000 reads so far
2011-05-19 20:00:16,803 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:102990153-123010153
2011-05-19 20:00:19,230 - INFO - Processed 126700000 reads so far
2011-05-19 20:00:29,680 - INFO - Processed 126800000 reads so far
2011-05-19 20:00:40,749 - INFO - Processed 126900000 reads so far
2011-05-19 20:00:51,147 - INFO - Processed 127000000 reads so far
2011-05-19 20:01:00,655 - INFO - Processed 127100000 reads so far
2011-05-19 20:01:10,595 - INFO - Processed 127200000 reads so far
2011-05-19 20:01:21,708 - INFO - Processed 127300000 reads so far
2011-05-19 20:01:29,987 - INFO - Processed 127400000 reads so far
2011-05-19 20:01:45,201 - INFO - Processed 127500000 reads so far
2011-05-19 20:01:53,463 - INFO - Processed 127600000 reads so far
2011-05-19 20:02:03,549 - INFO - Processed 127700000 reads so far
2011-05-19 20:02:12,953 - INFO - Processed 127800000 reads so far
2011-05-19 20:02:22,926 - INFO - Processed 127900000 reads so far
2011-05-19 20:02:36,897 - INFO - Processed 128000000 reads so far
2011-05-19 20:02:47,897 - INFO - Processed 128100000 reads so far
2011-05-19 20:03:00,423 - INFO - Processed 128200000 reads so far
2011-05-19 20:03:13,352 - INFO - Processed 128300000 reads so far
2011-05-19 20:03:27,849 - INFO - Processed 128400000 reads so far
2011-05-19 20:03:40,694 - INFO - Processed 128500000 reads so far
2011-05-19 20:03:53,947 - INFO - Processed 128600000 reads so far
2011-05-19 20:04:05,150 - INFO - Processed 128700000 reads so far
2011-05-19 20:04:15,714 - INFO - Processed 128800000 reads so far
2011-05-19 20:04:28,706 - INFO - Processed 128900000 reads so far
2011-05-19 20:04:39,622 - INFO - Processed 129000000 reads so far
2011-05-19 20:04:41,074 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:122990167-143010167
2011-05-19 20:04:50,446 - INFO - Processed 129100000 reads so far
2011-05-19 20:05:01,802 - INFO - Processed 129200000 reads so far
2011-05-19 20:05:13,200 - INFO - Processed 129300000 reads so far
2011-05-19 20:05:22,943 - INFO - Processed 129400000 reads so far
2011-05-19 20:05:36,265 - INFO - Processed 129500000 reads so far
2011-05-19 20:05:46,831 - INFO - Processed 129600000 reads so far
2011-05-19 20:05:57,240 - INFO - Processed 129700000 reads so far
2011-05-19 20:06:07,797 - INFO - Processed 129800000 reads so far
2011-05-19 20:06:16,922 - INFO - Processed 129900000 reads so far
2011-05-19 20:06:27,799 - INFO - Processed 130000000 reads so far
2011-05-19 20:06:40,480 - INFO - Processed 130100000 reads so far
2011-05-19 20:06:49,940 - INFO - Processed 130200000 reads so far
2011-05-19 20:06:51,348 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:142990177-163010177
2011-05-19 20:06:59,720 - INFO - Processed 130300000 reads so far
2011-05-19 20:07:09,851 - INFO - Processed 130400000 reads so far
2011-05-19 20:07:20,879 - INFO - Processed 130500000 reads so far
2011-05-19 20:07:31,842 - INFO - Processed 130600000 reads so far
2011-05-19 20:07:33,079 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:2990081-23010081
2011-05-19 20:07:43,082 - INFO - Processed 130700000 reads so far
2011-05-19 20:07:54,306 - INFO - Processed 130800000 reads so far
2011-05-19 20:08:03,696 - INFO - Processed 130900000 reads so far
2011-05-19 20:08:13,965 - INFO - Processed 131000000 reads so far
2011-05-19 20:08:25,781 - INFO - Processed 131100000 reads so far
2011-05-19 20:08:36,862 - INFO - Processed 131200000 reads so far
2011-05-19 20:08:49,420 - INFO - Processed 131300000 reads so far
2011-05-19 20:09:02,704 - INFO - Processed 131400000 reads so far
2011-05-19 20:09:12,349 - INFO - Processed 131500000 reads so far
2011-05-19 20:09:22,927 - INFO - Processed 131600000 reads so far
2011-05-19 20:09:25,231 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:22990103-43010103
2011-05-19 20:09:33,985 - INFO - Processed 131700000 reads so far
2011-05-19 20:09:44,300 - INFO - Processed 131800000 reads so far
2011-05-19 20:09:53,499 - INFO - Processed 131900000 reads so far
2011-05-19 20:10:04,282 - INFO - Processed 132000000 reads so far
2011-05-19 20:10:14,893 - INFO - Processed 132100000 reads so far
2011-05-19 20:10:23,212 - INFO - Processed 132200000 reads so far
2011-05-19 20:10:33,863 - INFO - Processed 132300000 reads so far
2011-05-19 20:10:45,554 - INFO - Processed 132400000 reads so far
2011-05-19 20:10:59,140 - INFO - Processed 132500000 reads so far
2011-05-19 20:11:01,691 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:46348172-66368172
2011-05-19 20:11:10,755 - INFO - Processed 132600000 reads so far
2011-05-19 20:11:21,911 - INFO - Processed 132700000 reads so far
2011-05-19 20:11:31,776 - INFO - Processed 132800000 reads so far
2011-05-19 20:11:43,119 - INFO - Processed 132900000 reads so far
2011-05-19 20:11:54,874 - INFO - Processed 133000000 reads so far
2011-05-19 20:12:04,604 - INFO - Processed 133100000 reads so far
2011-05-19 20:12:14,388 - INFO - Processed 133200000 reads so far
2011-05-19 20:12:24,625 - INFO - Processed 133300000 reads so far
2011-05-19 20:12:34,181 - INFO - Processed 133400000 reads so far
2011-05-19 20:12:44,962 - INFO - Processed 133500000 reads so far
2011-05-19 20:12:56,049 - INFO - Processed 133600000 reads so far
2011-05-19 20:13:10,983 - INFO - Processed 133700000 reads so far
2011-05-19 20:13:11,104 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:66348188-86368188
2011-05-19 20:13:21,180 - INFO - Processed 133800000 reads so far
2011-05-19 20:13:31,787 - INFO - Processed 133900000 reads so far
2011-05-19 20:13:43,582 - INFO - Processed 134000000 reads so far
2011-05-19 20:13:54,541 - INFO - Processed 134100000 reads so far
2011-05-19 20:14:03,848 - INFO - Processed 134200000 reads so far
2011-05-19 20:14:15,996 - INFO - Processed 134300000 reads so far
2011-05-19 20:14:25,880 - INFO - Processed 134400000 reads so far
2011-05-19 20:14:38,154 - INFO - Processed 134500000 reads so far
2011-05-19 20:14:48,935 - INFO - Processed 134600000 reads so far
2011-05-19 20:14:58,859 - INFO - Processed 134700000 reads so far
2011-05-19 20:15:09,006 - INFO - Processed 134800000 reads so far
2011-05-19 20:15:20,962 - INFO - Processed 134900000 reads so far
2011-05-19 20:15:21,708 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:86348208-106368208
2011-05-19 20:15:30,982 - INFO - Processed 135000000 reads so far
2011-05-19 20:15:40,452 - INFO - Processed 135100000 reads so far
2011-05-19 20:15:57,922 - INFO - Processed 135200000 reads so far
2011-05-19 20:16:07,742 - INFO - Processed 135300000 reads so far
2011-05-19 20:16:19,224 - INFO - Processed 135400000 reads so far
2011-05-19 20:16:33,998 - INFO - Processed 135500000 reads so far
2011-05-19 20:16:45,803 - INFO - Processed 135600000 reads so far
2011-05-19 20:16:56,928 - INFO - Processed 135700000 reads so far
2011-05-19 20:17:08,320 - INFO - Processed 135800000 reads so far
2011-05-19 20:17:19,334 - INFO - Processed 135900000 reads so far
2011-05-19 20:17:30,649 - INFO - Processed 136000000 reads so far
2011-05-19 20:17:38,367 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:106348213-126368213
2011-05-19 20:17:41,917 - INFO - Processed 136100000 reads so far
2011-05-19 20:17:55,427 - INFO - Processed 136200000 reads so far
2011-05-19 20:18:08,594 - INFO - Processed 136300000 reads so far
2011-05-19 20:18:21,407 - INFO - Processed 136400000 reads so far
2011-05-19 20:18:34,269 - INFO - Processed 136500000 reads so far
2011-05-19 20:18:45,137 - INFO - Processed 136600000 reads so far
2011-05-19 20:18:54,172 - INFO - Processed 136700000 reads so far
2011-05-19 20:19:03,121 - INFO - Processed 136800000 reads so far
2011-05-19 20:19:11,885 - INFO - Processed 136900000 reads so far
2011-05-19 20:19:19,102 - INFO - Processed 137000000 reads so far
2011-05-19 20:19:29,937 - INFO - Processed 137100000 reads so far
2011-05-19 20:19:39,543 - INFO - Processed 137200000 reads so far
2011-05-19 20:19:46,547 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:126348222-146368222
2011-05-19 20:19:49,659 - INFO - Processed 137300000 reads so far
2011-05-19 20:20:01,332 - INFO - Processed 137400000 reads so far
2011-05-19 20:20:11,730 - INFO - Processed 137500000 reads so far
2011-05-19 20:20:21,647 - INFO - Processed 137600000 reads so far
2011-05-19 20:20:34,056 - INFO - Processed 137700000 reads so far
2011-05-19 20:20:45,444 - INFO - Processed 137800000 reads so far
2011-05-19 20:20:57,176 - INFO - Processed 137900000 reads so far
2011-05-19 20:21:17,078 - INFO - Processed 138000000 reads so far
2011-05-19 20:21:28,306 - INFO - Processed 138100000 reads so far
2011-05-19 20:21:38,910 - INFO - Processed 138200000 reads so far
2011-05-19 20:21:52,609 - INFO - Processed 138300000 reads so far
2011-05-19 20:22:02,060 - INFO - Processed 138400000 reads so far
2011-05-19 20:22:11,932 - INFO - Processed 138500000 reads so far
2011-05-19 20:22:15,177 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:146348241-166368241
2011-05-19 20:22:21,330 - INFO - Processed 138600000 reads so far
2011-05-19 20:22:31,104 - INFO - Processed 138700000 reads so far
2011-05-19 20:22:39,595 - INFO - Processed 138800000 reads so far
2011-05-19 20:22:48,406 - INFO - Processed 138900000 reads so far
2011-05-19 20:22:56,950 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7_random:0-20010020
2011-05-19 20:22:58,123 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:2990010-23010010
2011-05-19 20:23:02,691 - INFO - Processed 139000000 reads so far
2011-05-19 20:23:11,271 - INFO - Processed 139100000 reads so far
2011-05-19 20:23:19,851 - INFO - Processed 139200000 reads so far
2011-05-19 20:23:28,240 - INFO - Processed 139300000 reads so far
2011-05-19 20:23:37,901 - INFO - Processed 139400000 reads so far
2011-05-19 20:23:46,684 - INFO - Processed 139500000 reads so far
2011-05-19 20:23:54,786 - INFO - Processed 139600000 reads so far
2011-05-19 20:24:08,111 - INFO - Processed 139700000 reads so far
2011-05-19 20:24:17,003 - INFO - Processed 139800000 reads so far
2011-05-19 20:24:27,243 - INFO - Processed 139900000 reads so far
2011-05-19 20:24:39,051 - INFO - Processed 140000000 reads so far
2011-05-19 20:24:46,399 - INFO - Processed 140100000 reads so far
2011-05-19 20:24:55,369 - INFO - Processed 140200000 reads so far
2011-05-19 20:25:02,211 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:22990022-43010022
2011-05-19 20:25:06,354 - INFO - Processed 140300000 reads so far
2011-05-19 20:25:17,189 - INFO - Processed 140400000 reads so far
2011-05-19 20:25:27,689 - INFO - Processed 140500000 reads so far
2011-05-19 20:25:36,190 - INFO - Processed 140600000 reads so far
2011-05-19 20:25:45,705 - INFO - Processed 140700000 reads so far
2011-05-19 20:25:54,582 - INFO - Processed 140800000 reads so far
2011-05-19 20:26:03,608 - INFO - Processed 140900000 reads so far
2011-05-19 20:26:15,781 - INFO - Processed 141000000 reads so far
2011-05-19 20:26:25,039 - INFO - Processed 141100000 reads so far
2011-05-19 20:26:37,813 - INFO - Processed 141200000 reads so far
2011-05-19 20:26:50,708 - INFO - Processed 141300000 reads so far
2011-05-19 20:27:00,236 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:42990073-63010073
2011-05-19 20:27:00,326 - INFO - Processed 141400000 reads so far
2011-05-19 20:27:10,212 - INFO - Processed 141500000 reads so far
2011-05-19 20:27:23,682 - INFO - Processed 141600000 reads so far
2011-05-19 20:27:33,263 - INFO - Processed 141700000 reads so far
2011-05-19 20:27:42,804 - INFO - Processed 141800000 reads so far
2011-05-19 20:27:59,263 - INFO - Processed 141900000 reads so far
2011-05-19 20:28:10,862 - INFO - Processed 142000000 reads so far
2011-05-19 20:28:20,123 - INFO - Processed 142100000 reads so far
2011-05-19 20:28:30,944 - INFO - Processed 142200000 reads so far
2011-05-19 20:28:41,448 - INFO - Processed 142300000 reads so far
2011-05-19 20:28:53,576 - INFO - Processed 142400000 reads so far
2011-05-19 20:28:54,007 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:62990085-83010085
2011-05-19 20:29:03,822 - INFO - Processed 142500000 reads so far
2011-05-19 20:29:12,739 - INFO - Processed 142600000 reads so far
2011-05-19 20:29:21,596 - INFO - Processed 142700000 reads so far
2011-05-19 20:29:30,334 - INFO - Processed 142800000 reads so far
2011-05-19 20:29:38,866 - INFO - Processed 142900000 reads so far
2011-05-19 20:29:47,017 - INFO - Processed 143000000 reads so far
2011-05-19 20:29:56,676 - INFO - Processed 143100000 reads so far
2011-05-19 20:30:05,862 - INFO - Processed 143200000 reads so far
2011-05-19 20:30:15,449 - INFO - Processed 143300000 reads so far
2011-05-19 20:30:24,763 - INFO - Processed 143400000 reads so far
2011-05-19 20:30:33,339 - INFO - Processed 143500000 reads so far
2011-05-19 20:30:42,143 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:82990187-103010187
2011-05-19 20:30:44,328 - INFO - Processed 143600000 reads so far
2011-05-19 20:30:53,055 - INFO - Processed 143700000 reads so far
2011-05-19 20:31:01,584 - INFO - Processed 143800000 reads so far
2011-05-19 20:31:09,752 - INFO - Processed 143900000 reads so far
2011-05-19 20:31:19,454 - INFO - Processed 144000000 reads so far
2011-05-19 20:31:30,572 - INFO - Processed 144100000 reads so far
2011-05-19 20:31:42,286 - INFO - Processed 144200000 reads so far
2011-05-19 20:31:56,848 - INFO - Processed 144300000 reads so far
2011-05-19 20:32:08,128 - INFO - Processed 144400000 reads so far
2011-05-19 20:32:17,483 - INFO - Processed 144500000 reads so far
2011-05-19 20:32:27,369 - INFO - Processed 144600000 reads so far
2011-05-19 20:32:35,970 - INFO - Processed 144700000 reads so far
2011-05-19 20:32:41,008 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:102990189-123010189
2011-05-19 20:32:45,530 - INFO - Processed 144800000 reads so far
2011-05-19 20:32:55,914 - INFO - Processed 144900000 reads so far
2011-05-19 20:33:06,386 - INFO - Processed 145000000 reads so far
2011-05-19 20:33:18,579 - INFO - Processed 145100000 reads so far
2011-05-19 20:33:28,093 - INFO - Processed 145200000 reads so far
2011-05-19 20:33:37,281 - INFO - Processed 145300000 reads so far
2011-05-19 20:33:47,918 - INFO - Processed 145400000 reads so far
2011-05-19 20:33:56,685 - INFO - Processed 145500000 reads so far
2011-05-19 20:34:06,439 - INFO - Processed 145600000 reads so far
2011-05-19 20:34:16,443 - INFO - Processed 145700000 reads so far
2011-05-19 20:34:26,428 - INFO - Processed 145800000 reads so far
2011-05-19 20:34:37,841 - INFO - Processed 145900000 reads so far
2011-05-19 20:34:44,560 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:122990195-143010195
2011-05-19 20:34:48,760 - INFO - Processed 146000000 reads so far
2011-05-19 20:35:01,949 - INFO - Processed 146100000 reads so far
2011-05-19 20:35:12,461 - INFO - Processed 146200000 reads so far
2011-05-19 20:35:23,745 - INFO - Processed 146300000 reads so far
2011-05-19 20:35:33,565 - INFO - Processed 146400000 reads so far
2011-05-19 20:35:41,957 - INFO - Processed 146500000 reads so far
2011-05-19 20:35:44,269 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8_random:0-20010000
2011-05-19 20:35:50,955 - INFO - Processed 146600000 reads so far
2011-05-19 20:35:59,044 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:2989968-23009968
2011-05-19 20:36:00,032 - INFO - Processed 146700000 reads so far
2011-05-19 20:36:09,413 - INFO - Processed 146800000 reads so far
2011-05-19 20:36:15,304 - INFO - Processed 146900000 reads so far
2011-05-19 20:36:22,525 - INFO - Processed 147000000 reads so far
2011-05-19 20:36:29,280 - INFO - Processed 147100000 reads so far
2011-05-19 20:36:36,039 - INFO - Processed 147200000 reads so far
2011-05-19 20:36:43,233 - INFO - Processed 147300000 reads so far
2011-05-19 20:36:49,897 - INFO - Processed 147400000 reads so far
2011-05-19 20:36:56,463 - INFO - Processed 147500000 reads so far
2011-05-19 20:37:03,387 - INFO - Processed 147600000 reads so far
2011-05-19 20:37:11,280 - INFO - Processed 147700000 reads so far
2011-05-19 20:37:18,889 - INFO - Processed 147800000 reads so far
2011-05-19 20:37:26,713 - INFO - Processed 147900000 reads so far
2011-05-19 20:37:35,268 - INFO - Processed 148000000 reads so far
2011-05-19 20:37:42,271 - INFO - Processed 148100000 reads so far
2011-05-19 20:37:48,994 - INFO - Processed 148200000 reads so far
2011-05-19 20:37:56,413 - INFO - Processed 148300000 reads so far
2011-05-19 20:38:02,479 - INFO - Processed 148400000 reads so far
2011-05-19 20:38:09,138 - INFO - Processed 148500000 reads so far
2011-05-19 20:38:17,088 - INFO - Processed 148600000 reads so far
2011-05-19 20:38:22,855 - INFO - Processed 148700000 reads so far
2011-05-19 20:38:29,718 - INFO - Processed 148800000 reads so far
2011-05-19 20:38:38,199 - INFO - Processed 148900000 reads so far
2011-05-19 20:38:45,586 - INFO - Processed 149000000 reads so far
2011-05-19 20:38:51,602 - INFO - Processed 149100000 reads so far
2011-05-19 20:38:58,493 - INFO - Processed 149200000 reads so far
2011-05-19 20:39:04,758 - INFO - Processed 149300000 reads so far
2011-05-19 20:39:13,503 - INFO - Processed 149400000 reads so far
2011-05-19 20:39:20,745 - INFO - Processed 149500000 reads so far
2011-05-19 20:39:27,843 - INFO - Processed 149600000 reads so far
2011-05-19 20:39:34,655 - INFO - Processed 149700000 reads so far
2011-05-19 20:39:43,476 - INFO - Processed 149800000 reads so far
2011-05-19 20:39:50,861 - INFO - Processed 149900000 reads so far
2011-05-19 20:39:57,137 - INFO - Processed 150000000 reads so far
2011-05-19 20:40:04,578 - INFO - Processed 150100000 reads so far
2011-05-19 20:40:10,076 - INFO - Processed 150200000 reads so far
2011-05-19 20:40:17,790 - INFO - Processed 150300000 reads so far
2011-05-19 20:40:26,212 - INFO - Processed 150400000 reads so far
2011-05-19 20:40:32,796 - INFO - Processed 150500000 reads so far
2011-05-19 20:40:41,075 - INFO - Processed 150600000 reads so far
2011-05-19 20:40:49,707 - INFO - Processed 150700000 reads so far
2011-05-19 20:41:01,337 - INFO - Processed 150800000 reads so far
2011-05-19 20:41:10,049 - INFO - Processed 150900000 reads so far
2011-05-19 20:41:18,718 - INFO - Processed 151000000 reads so far
2011-05-19 20:41:26,951 - INFO - Processed 151100000 reads so far
2011-05-19 20:41:35,504 - INFO - Processed 151200000 reads so far
2011-05-19 20:41:41,943 - INFO - Processed 151300000 reads so far
2011-05-19 20:41:50,035 - INFO - Processed 151400000 reads so far
2011-05-19 20:41:57,787 - INFO - Processed 151500000 reads so far
2011-05-19 20:42:03,081 - INFO - Processed 151600000 reads so far
2011-05-19 20:42:09,433 - INFO - Processed 151700000 reads so far
2011-05-19 20:42:17,928 - INFO - Processed 151800000 reads so far
2011-05-19 20:42:25,187 - INFO - Processed 151900000 reads so far
2011-05-19 20:42:31,852 - INFO - Processed 152000000 reads so far
2011-05-19 20:42:39,325 - INFO - Processed 152100000 reads so far
2011-05-19 20:42:45,310 - INFO - Processed 152200000 reads so far
2011-05-19 20:42:52,442 - INFO - Processed 152300000 reads so far
2011-05-19 20:43:00,526 - INFO - Processed 152400000 reads so far
2011-05-19 20:43:08,235 - INFO - Processed 152500000 reads so far
2011-05-19 20:43:15,221 - INFO - Processed 152600000 reads so far
2011-05-19 20:43:24,887 - INFO - Processed 152700000 reads so far
2011-05-19 20:43:32,295 - INFO - Processed 152800000 reads so far
2011-05-19 20:43:40,824 - INFO - Processed 152900000 reads so far
2011-05-19 20:43:47,497 - INFO - Processed 153000000 reads so far
2011-05-19 20:44:00,078 - INFO - Processed 153100000 reads so far
2011-05-19 20:44:07,246 - INFO - Processed 153200000 reads so far
2011-05-19 20:44:16,107 - INFO - Processed 153300000 reads so far
2011-05-19 20:44:24,206 - INFO - Processed 153400000 reads so far
2011-05-19 20:44:34,645 - INFO - Processed 153500000 reads so far
2011-05-19 20:44:42,860 - INFO - Processed 153600000 reads so far
2011-05-19 20:44:53,079 - INFO - Processed 153700000 reads so far
2011-05-19 20:45:00,938 - INFO - Processed 153800000 reads so far
2011-05-19 20:45:07,397 - INFO - Processed 153900000 reads so far
2011-05-19 20:45:16,410 - INFO - Processed 154000000 reads so far
2011-05-19 20:45:24,937 - INFO - Processed 154100000 reads so far
2011-05-19 20:45:32,584 - INFO - Processed 154200000 reads so far
2011-05-19 20:45:41,234 - INFO - Processed 154300000 reads so far
2011-05-19 20:45:49,757 - INFO - Processed 154400000 reads so far
2011-05-19 20:46:00,889 - INFO - Processed 154500000 reads so far
2011-05-19 20:46:11,556 - INFO - Processed 154600000 reads so far
2011-05-19 20:46:22,652 - INFO - Processed 154700000 reads so far
2011-05-19 20:46:33,558 - INFO - Processed 154800000 reads so far
2011-05-19 20:46:43,256 - INFO - Processed 154900000 reads so far
2011-05-19 20:46:56,084 - INFO - Processed 155000000 reads so far
2011-05-19 20:47:05,912 - INFO - Processed 155100000 reads so far
2011-05-19 20:47:15,842 - INFO - Processed 155200000 reads so far
2011-05-19 20:47:25,595 - INFO - Processed 155300000 reads so far
2011-05-19 20:47:35,670 - INFO - Processed 155400000 reads so far
2011-05-19 20:47:45,690 - INFO - Processed 155500000 reads so far
2011-05-19 20:47:46,577 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:22989978-43009978
2011-05-19 20:47:54,337 - INFO - Processed 155600000 reads so far
2011-05-19 20:48:03,567 - INFO - Processed 155700000 reads so far
2011-05-19 20:48:13,832 - INFO - Processed 155800000 reads so far
2011-05-19 20:48:23,950 - INFO - Processed 155900000 reads so far
2011-05-19 20:48:35,331 - INFO - Processed 156000000 reads so far
2011-05-19 20:49:00,000 - INFO - Processed 156100000 reads so far
2011-05-19 20:49:08,427 - INFO - Processed 156200000 reads so far
2011-05-19 20:49:19,474 - INFO - Processed 156300000 reads so far
2011-05-19 20:49:29,222 - INFO - Processed 156400000 reads so far
2011-05-19 20:49:40,594 - INFO - Processed 156500000 reads so far
2011-05-19 20:49:52,208 - INFO - Processed 156600000 reads so far
2011-05-19 20:50:03,577 - INFO - Processed 156700000 reads so far
2011-05-19 20:50:15,342 - INFO - Processed 156800000 reads so far
2011-05-19 20:50:22,145 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:42989994-63009994
2011-05-19 20:50:26,989 - INFO - Processed 156900000 reads so far
2011-05-19 20:50:41,173 - INFO - Processed 157000000 reads so far
2011-05-19 20:50:51,518 - INFO - Processed 157100000 reads so far
2011-05-19 20:51:02,147 - INFO - Processed 157200000 reads so far
2011-05-19 20:51:13,309 - INFO - Processed 157300000 reads so far
2011-05-19 20:51:27,537 - INFO - Processed 157400000 reads so far
2011-05-19 20:51:39,646 - INFO - Processed 157500000 reads so far
2011-05-19 20:51:51,972 - INFO - Processed 157600000 reads so far
2011-05-19 20:52:03,820 - INFO - Processed 157700000 reads so far
2011-05-19 20:52:16,880 - INFO - Processed 157800000 reads so far
2011-05-19 20:52:27,195 - INFO - Processed 157900000 reads so far
2011-05-19 20:52:36,501 - INFO - Processed 158000000 reads so far
2011-05-19 20:52:47,815 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:62989996-83009996
2011-05-19 20:52:48,494 - INFO - Processed 158100000 reads so far
2011-05-19 20:52:59,560 - INFO - Processed 158200000 reads so far
2011-05-19 20:53:10,956 - INFO - Processed 158300000 reads so far
2011-05-19 20:53:22,783 - INFO - Processed 158400000 reads so far
2011-05-19 20:53:34,966 - INFO - Processed 158500000 reads so far
2011-05-19 20:53:46,636 - INFO - Processed 158600000 reads so far
2011-05-19 20:53:55,658 - INFO - Processed 158700000 reads so far
2011-05-19 20:54:06,595 - INFO - Processed 158800000 reads so far
2011-05-19 20:54:17,960 - INFO - Processed 158900000 reads so far
2011-05-19 20:54:29,720 - INFO - Processed 159000000 reads so far
2011-05-19 20:54:39,848 - INFO - Processed 159100000 reads so far
2011-05-19 20:54:49,545 - INFO - Processed 159200000 reads so far
2011-05-19 20:54:55,867 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:82990008-103010008
2011-05-19 20:54:58,606 - INFO - Processed 159300000 reads so far
2011-05-19 20:55:07,317 - INFO - Processed 159400000 reads so far
2011-05-19 20:55:15,761 - INFO - Processed 159500000 reads so far
2011-05-19 20:55:26,324 - INFO - Processed 159600000 reads so far
2011-05-19 20:55:36,577 - INFO - Processed 159700000 reads so far
2011-05-19 20:55:47,268 - INFO - Processed 159800000 reads so far
2011-05-19 20:55:57,754 - INFO - Processed 159900000 reads so far
2011-05-19 20:56:06,809 - INFO - Processed 160000000 reads so far
2011-05-19 20:56:17,182 - INFO - Processed 160100000 reads so far
2011-05-19 20:56:27,327 - INFO - Processed 160200000 reads so far
2011-05-19 20:56:37,565 - INFO - Processed 160300000 reads so far
2011-05-19 20:56:49,764 - INFO - Processed 160400000 reads so far
2011-05-19 20:56:52,671 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:102990016-123010016
2011-05-19 20:57:01,478 - INFO - Processed 160500000 reads so far
2011-05-19 20:57:09,351 - INFO - Processed 160600000 reads so far
2011-05-19 20:57:22,069 - INFO - Processed 160700000 reads so far
2011-05-19 20:57:33,725 - INFO - Processed 160800000 reads so far
2011-05-19 20:57:42,868 - INFO - Processed 160900000 reads so far
2011-05-19 20:57:54,692 - INFO - Processed 161000000 reads so far
2011-05-19 20:58:06,172 - INFO - Processed 161100000 reads so far
2011-05-19 20:58:17,079 - INFO - Processed 161200000 reads so far
2011-05-19 20:58:28,196 - INFO - Processed 161300000 reads so far
2011-05-19 20:58:38,978 - INFO - Processed 161400000 reads so far
2011-05-19 20:58:50,892 - INFO - Processed 161500000 reads so far
2011-05-19 20:59:02,649 - INFO - Processed 161600000 reads so far
2011-05-19 20:59:11,432 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:122990019-143010019
2011-05-19 20:59:14,858 - INFO - Processed 161700000 reads so far
2011-05-19 20:59:18,837 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9_random:0-20010008
2011-05-19 20:59:23,079 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrM:0-20010000
2011-05-19 20:59:26,123 - INFO - Processed 161800000 reads so far
2011-05-19 20:59:28,433 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrUn_random:0-20010000
2011-05-19 20:59:37,662 - INFO - Processed 161900000 reads so far
2011-05-19 20:59:47,621 - INFO - Processed 162000000 reads so far
2011-05-19 20:59:57,523 - INFO - Processed 162100000 reads so far
2011-05-19 21:00:07,214 - INFO - Processed 162200000 reads so far
2011-05-19 21:00:14,169 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:2990016-23010016
2011-05-19 21:00:20,859 - INFO - Processed 162300000 reads so far
2011-05-19 21:00:31,231 - INFO - Processed 162400000 reads so far
2011-05-19 21:00:45,370 - INFO - Processed 162500000 reads so far
2011-05-19 21:00:57,334 - INFO - Processed 162600000 reads so far
2011-05-19 21:01:09,555 - INFO - Processed 162700000 reads so far
2011-05-19 21:01:22,447 - INFO - Processed 162800000 reads so far
2011-05-19 21:01:36,893 - INFO - Processed 162900000 reads so far
2011-05-19 21:01:45,128 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:22990061-43010061
2011-05-19 21:01:48,034 - INFO - Processed 163000000 reads so far
2011-05-19 21:02:01,403 - INFO - Processed 163100000 reads so far
2011-05-19 21:02:12,326 - INFO - Processed 163200000 reads so far
2011-05-19 21:02:23,771 - INFO - Processed 163300000 reads so far
2011-05-19 21:02:35,935 - INFO - Processed 163400000 reads so far
2011-05-19 21:02:48,842 - INFO - Processed 163500000 reads so far
2011-05-19 21:03:01,332 - INFO - Processed 163600000 reads so far
2011-05-19 21:03:12,912 - INFO - Processed 163700000 reads so far
2011-05-19 21:03:13,342 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:42990090-63010090
2011-05-19 21:03:22,957 - INFO - Processed 163800000 reads so far
2011-05-19 21:03:35,331 - INFO - Processed 163900000 reads so far
2011-05-19 21:03:48,372 - INFO - Processed 164000000 reads so far
2011-05-19 21:04:01,395 - INFO - Processed 164100000 reads so far
2011-05-19 21:04:13,761 - INFO - Processed 164200000 reads so far
2011-05-19 21:04:29,269 - INFO - Processed 164300000 reads so far
2011-05-19 21:04:30,510 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:62990111-83010111
2011-05-19 21:04:41,795 - INFO - Processed 164400000 reads so far
2011-05-19 21:04:54,005 - INFO - Processed 164500000 reads so far
2011-05-19 21:05:06,403 - INFO - Processed 164600000 reads so far
2011-05-19 21:05:19,828 - INFO - Processed 164700000 reads so far
2011-05-19 21:05:31,776 - INFO - Processed 164800000 reads so far
2011-05-19 21:05:44,865 - INFO - Processed 164900000 reads so far
2011-05-19 21:05:45,934 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:82990151-103010151
2011-05-19 21:05:56,938 - INFO - Processed 165000000 reads so far
2011-05-19 21:06:08,423 - INFO - Processed 165100000 reads so far
2011-05-19 21:06:21,738 - INFO - Processed 165200000 reads so far
2011-05-19 21:06:34,236 - INFO - Processed 165300000 reads so far
2011-05-19 21:06:47,571 - INFO - Processed 165400000 reads so far
2011-05-19 21:07:00,177 - INFO - Processed 165500000 reads so far
2011-05-19 21:07:00,536 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:102990248-123010248
2011-05-19 21:07:12,289 - INFO - Processed 165600000 reads so far
2011-05-19 21:07:25,017 - INFO - Processed 165700000 reads so far
2011-05-19 21:07:37,885 - INFO - Processed 165800000 reads so far
2011-05-19 21:07:49,887 - INFO - Processed 165900000 reads so far
2011-05-19 21:08:02,637 - INFO - Processed 166000000 reads so far
2011-05-19 21:08:13,192 - INFO - Processed 166100000 reads so far
2011-05-19 21:08:23,185 - INFO - Processed 166200000 reads so far
2011-05-19 21:08:23,908 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:122990259-143010259
2011-05-19 21:08:34,760 - INFO - Processed 166300000 reads so far
2011-05-19 21:08:45,659 - INFO - Processed 166400000 reads so far
2011-05-19 21:08:56,771 - INFO - Processed 166500000 reads so far
2011-05-19 21:09:08,912 - INFO - Processed 166600000 reads so far
2011-05-19 21:09:16,273 - INFO - Processed 166700000 reads so far
2011-05-19 21:09:26,872 - INFO - Processed 166800000 reads so far
2011-05-19 21:09:32,446 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:142990285-163010285
2011-05-19 21:09:37,860 - INFO - Processed 166900000 reads so far
2011-05-19 21:10:10,000 - INFO - Processed 167000000 reads so far
2011-05-19 21:10:33,976 - INFO - Processed 167100000 reads so far
2011-05-19 21:10:56,921 - INFO - Processed 167200000 reads so far
2011-05-19 21:11:15,582 - INFO - Processed 167300000 reads so far
2011-05-19 21:11:25,747 - INFO - Processed 167400000 reads so far
2011-05-19 21:11:29,504 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:162990287-183010287
2011-05-19 21:11:39,435 - INFO - Processed 167500000 reads so far
2011-05-19 21:11:51,323 - INFO - Processed 167600000 reads so far
2011-05-19 21:11:53,126 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX_random:0-20010000
2011-05-19 21:11:59,946 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY:0-20010000
2011-05-19 21:12:03,095 - INFO - Processed 167700000 reads so far
2011-05-19 21:12:08,733 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:0-20011756
2011-05-19 21:12:13,532 - INFO - Processed 167800000 reads so far
2011-05-19 21:12:24,958 - INFO - Processed 167900000 reads so far
2011-05-19 21:12:35,552 - INFO - Processed 168000000 reads so far
2011-05-19 21:12:46,699 - INFO - Processed 168100000 reads so far
2011-05-19 21:12:59,079 - INFO - Processed 168200000 reads so far
2011-05-19 21:13:11,899 - INFO - Processed 168300000 reads so far
2011-05-19 21:13:22,511 - INFO - Processed 168400000 reads so far
2011-05-19 21:13:32,817 - INFO - Processed 168500000 reads so far
2011-05-19 21:13:44,473 - INFO - Processed 168600000 reads so far
2011-05-19 21:13:46,710 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:19991940-40011940
2011-05-19 21:13:56,465 - INFO - Processed 168700000 reads so far
2011-05-19 21:14:08,170 - INFO - Processed 168800000 reads so far
2011-05-19 21:14:20,840 - INFO - Processed 168900000 reads so far
2011-05-19 21:14:31,375 - INFO - Processed 169000000 reads so far
2011-05-19 21:14:36,693 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:39992073-60012073
2011-05-19 21:14:38,989 - INFO - Processed 169100000 reads so far
2011-05-19 21:14:47,050 - INFO - Processed 169200000 reads so far
2011-05-19 21:14:55,968 - INFO - Processed 169300000 reads so far
2011-05-19 21:15:06,045 - INFO - Processed 169400000 reads so far
2011-05-19 21:15:16,119 - INFO - Processed 169500000 reads so far
2011-05-19 21:15:26,950 - INFO - Processed 169600000 reads so far
2011-05-19 21:15:36,629 - INFO - Processed 169700000 reads so far
2011-05-19 21:15:39,834 - INFO - Processed 169800000 reads so far
2011-05-19 21:15:47,148 - INFO - Processed 169900000 reads so far
2011-05-19 21:15:52,542 - INFO - Processed 170000000 reads so far
2011-05-19 21:15:56,960 - INFO - Processed 170100000 reads so far
2011-05-19 21:16:02,043 - INFO - Processed 170200000 reads so far
2011-05-19 21:16:07,201 - INFO - Processed 170300000 reads so far
2011-05-19 21:16:11,454 - INFO - Processed 170400000 reads so far
2011-05-19 21:16:16,623 - INFO - Processed 170500000 reads so far
2011-05-19 21:16:24,058 - INFO - Processed 170600000 reads so far
2011-05-19 21:16:29,529 - INFO - Processed 170700000 reads so far
2011-05-19 21:16:32,222 - INFO - Processed 170800000 reads so far
2011-05-19 21:16:41,259 - INFO - Processed 170900000 reads so far
2011-05-19 21:16:44,925 - INFO - Processed 171000000 reads so far
2011-05-19 21:16:50,126 - INFO - Processed 171100000 reads so far
2011-05-19 21:16:55,512 - INFO - Processed 171200000 reads so far
2011-05-19 21:16:58,449 - INFO - Finished loading data. Outputting QC metrics
2011-05-19 21:17:27,286 - INFO - Finished outputting QC metrics
2011-05-19 21:17:27,388 - INFO - Finished generating QC metrics