2011-05-19 20:40:29,750 - INFO - Generating QC metrics for BAM File ['WTCHG_11729.bam']
2011-05-19 20:40:29,751 - INFO - Output will go to WTCHG_11729.qc.txt.tmp
2011-05-19 20:40:29,751 - INFO - Reading GC Map from file /data/Genomes/gcMap/Mouse37.gcMap.gz
2011-05-19 20:43:35,301 - INFO - Finished reading GC Map
2011-05-19 20:43:35,301 - INFO - Reading CDS from exon definition file /data/Genomes/annotation/Mouse37.refGene.txt.gz
2011-05-19 20:43:38,113 - INFO - Read 382138 exons (33804740 nucleotides) for 32 chromosomes
2011-05-19 20:43:38,114 - INFO - Computing coverage cut-off
2011-05-19 20:43:38,114 - INFO - Retrieving BAM file coverage info from samtools pileup
2011-05-19 20:43:42,379 - INFO - Processed 1000000 pile-up sites
2011-05-19 20:43:46,692 - INFO - Processed 2000000 pile-up sites
2011-05-19 20:43:54,159 - INFO - Processed 3000000 pile-up sites
2011-05-19 20:43:57,166 - INFO - Processed 4000000 pile-up sites
2011-05-19 20:44:01,137 - INFO - Processed 5000000 pile-up sites
2011-05-19 20:44:05,545 - INFO - Processed 6000000 pile-up sites
2011-05-19 20:44:09,826 - INFO - Processed 7000000 pile-up sites
2011-05-19 20:44:13,902 - INFO - Processed 8000000 pile-up sites
2011-05-19 20:44:17,158 - INFO - Processed 9000000 pile-up sites
2011-05-19 20:44:20,898 - INFO - Processed 10000000 pile-up sites
2011-05-19 20:44:24,920 - INFO - Processed 11000000 pile-up sites
2011-05-19 20:44:29,850 - INFO - Processed 12000000 pile-up sites
2011-05-19 20:44:33,700 - INFO - Processed 13000000 pile-up sites
2011-05-19 20:44:37,735 - INFO - Processed 14000000 pile-up sites
2011-05-19 20:44:41,764 - INFO - Processed 15000000 pile-up sites
2011-05-19 20:44:47,006 - INFO - Processed 16000000 pile-up sites
2011-05-19 20:44:50,900 - INFO - Processed 17000000 pile-up sites
2011-05-19 20:44:55,006 - INFO - Processed 18000000 pile-up sites
2011-05-19 20:44:59,410 - INFO - Processed 19000000 pile-up sites
2011-05-19 20:45:03,541 - INFO - Processed 20000000 pile-up sites
2011-05-19 20:45:07,394 - INFO - Processed 21000000 pile-up sites
2011-05-19 20:45:11,402 - INFO - Processed 22000000 pile-up sites
2011-05-19 20:45:16,122 - INFO - Processed 23000000 pile-up sites
2011-05-19 20:45:20,907 - INFO - Processed 24000000 pile-up sites
2011-05-19 20:45:25,447 - INFO - Processed 25000000 pile-up sites
2011-05-19 20:45:29,473 - INFO - Processed 26000000 pile-up sites
2011-05-19 20:45:32,752 - INFO - Processed 27000000 pile-up sites
2011-05-19 20:45:38,101 - INFO - Processed 28000000 pile-up sites
2011-05-19 20:45:42,463 - INFO - Processed 29000000 pile-up sites
2011-05-19 20:45:46,266 - INFO - Processed 30000000 pile-up sites
2011-05-19 20:45:50,553 - INFO - Processed 31000000 pile-up sites
2011-05-19 20:45:54,678 - INFO - Processed 32000000 pile-up sites
2011-05-19 20:45:58,556 - INFO - Processed 33000000 pile-up sites
2011-05-19 20:46:02,496 - INFO - Processed 34000000 pile-up sites
2011-05-19 20:46:05,141 - INFO - Processed 35000000 pile-up sites
2011-05-19 20:46:07,952 - INFO - Finished processing pile-up on 35901208 sites (200000002 nucleotides)
2011-05-19 20:46:07,952 - INFO - Coverage cut-off value is 33
2011-05-19 20:46:07,952 - INFO - Loading data into QC data manager
2011-05-19 20:46:08,118 - WARNING - Found RG tag 'SM' (value: 231) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,118 - WARNING - Found RG tag 'ID' (value: WTCHG_11729) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,118 - WARNING - Found RG tag 'SM' (value: 231) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,119 - WARNING - Found RG tag 'ID' (value: WTCHG_11729) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,119 - WARNING - Found RG tag 'SM' (value: 231) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,119 - WARNING - Found RG tag 'ID' (value: WTCHG_11729) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,119 - WARNING - Found RG tag 'SM' (value: 231) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,119 - WARNING - Found RG tag 'ID' (value: WTCHG_11729) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,175 - WARNING - Found RG tag 'SM' (value: 231) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,175 - WARNING - Found RG tag 'ID' (value: WTCHG_11729) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,175 - WARNING - Found RG tag 'SM' (value: 231) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,175 - WARNING - Found RG tag 'ID' (value: WTCHG_11729) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,175 - WARNING - Found RG tag 'SM' (value: 231) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,175 - WARNING - Found RG tag 'ID' (value: WTCHG_11729) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,175 - WARNING - Found RG tag 'SM' (value: 231) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,175 - WARNING - Found RG tag 'ID' (value: WTCHG_11729) duplicated in CO field (value: 036/11) -- ignoring CO value
2011-05-19 20:46:08,185 - INFO - Reading data from BAM file WTCHG_11729.bam. All reads in file will be read
2011-05-19 20:46:08,274 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:2990004-23010004
2011-05-19 20:46:19,535 - INFO - Processed 100000 reads so far
2011-05-19 20:46:30,948 - INFO - Processed 200000 reads so far
2011-05-19 20:46:42,243 - INFO - Processed 300000 reads so far
2011-05-19 20:46:55,260 - INFO - Processed 400000 reads so far
2011-05-19 20:47:06,739 - INFO - Processed 500000 reads so far
2011-05-19 20:47:15,546 - INFO - Processed 600000 reads so far
2011-05-19 20:47:22,978 - INFO - Processed 700000 reads so far
2011-05-19 20:47:34,459 - INFO - Processed 800000 reads so far
2011-05-19 20:47:41,301 - INFO - Processed 900000 reads so far
2011-05-19 20:47:50,152 - INFO - Processed 1000000 reads so far
2011-05-19 20:47:57,826 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:22990024-43010024
2011-05-19 20:47:58,127 - INFO - Processed 1100000 reads so far
2011-05-19 20:48:09,354 - INFO - Processed 1200000 reads so far
2011-05-19 20:48:18,112 - INFO - Processed 1300000 reads so far
2011-05-19 20:48:27,097 - INFO - Processed 1400000 reads so far
2011-05-19 20:48:34,898 - INFO - Processed 1500000 reads so far
2011-05-19 20:48:53,271 - INFO - Processed 1600000 reads so far
2011-05-19 20:49:04,936 - INFO - Processed 1700000 reads so far
2011-05-19 20:49:14,547 - INFO - Processed 1800000 reads so far
2011-05-19 20:49:24,364 - INFO - Processed 1900000 reads so far
2011-05-19 20:49:35,466 - INFO - Processed 2000000 reads so far
2011-05-19 20:49:45,920 - INFO - Processed 2100000 reads so far
2011-05-19 20:49:53,351 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:42990026-63010026
2011-05-19 20:49:57,293 - INFO - Processed 2200000 reads so far
2011-05-19 20:50:06,950 - INFO - Processed 2300000 reads so far
2011-05-19 20:50:16,682 - INFO - Processed 2400000 reads so far
2011-05-19 20:50:25,619 - INFO - Processed 2500000 reads so far
2011-05-19 20:50:38,670 - INFO - Processed 2600000 reads so far
2011-05-19 20:50:51,349 - INFO - Processed 2700000 reads so far
2011-05-19 20:51:02,550 - INFO - Processed 2800000 reads so far
2011-05-19 20:51:14,166 - INFO - Processed 2900000 reads so far
2011-05-19 20:51:28,309 - INFO - Processed 3000000 reads so far
2011-05-19 20:51:42,707 - INFO - Processed 3100000 reads so far
2011-05-19 20:51:54,428 - INFO - Processed 3200000 reads so far
2011-05-19 20:51:56,926 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:62990039-83010039
2011-05-19 20:52:05,479 - INFO - Processed 3300000 reads so far
2011-05-19 20:52:18,673 - INFO - Processed 3400000 reads so far
2011-05-19 20:52:28,800 - INFO - Processed 3500000 reads so far
2011-05-19 20:52:39,315 - INFO - Processed 3600000 reads so far
2011-05-19 20:52:51,032 - INFO - Processed 3700000 reads so far
2011-05-19 20:53:02,055 - INFO - Processed 3800000 reads so far
2011-05-19 20:53:13,478 - INFO - Processed 3900000 reads so far
2011-05-19 20:53:26,263 - INFO - Processed 4000000 reads so far
2011-05-19 20:53:39,247 - INFO - Processed 4100000 reads so far
2011-05-19 20:53:50,050 - INFO - Processed 4200000 reads so far
2011-05-19 20:54:01,002 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:82990046-103010046
2011-05-19 20:54:01,991 - INFO - Processed 4300000 reads so far
2011-05-19 20:54:12,020 - INFO - Processed 4400000 reads so far
2011-05-19 20:54:22,864 - INFO - Processed 4500000 reads so far
2011-05-19 20:54:34,740 - INFO - Processed 4600000 reads so far
2011-05-19 20:54:47,302 - INFO - Processed 4700000 reads so far
2011-05-19 20:54:58,881 - INFO - Processed 4800000 reads so far
2011-05-19 20:55:10,744 - INFO - Processed 4900000 reads so far
2011-05-19 20:55:22,075 - INFO - Processed 5000000 reads so far
2011-05-19 20:55:33,320 - INFO - Processed 5100000 reads so far
2011-05-19 20:55:45,481 - INFO - Processed 5200000 reads so far
2011-05-19 20:55:57,014 - INFO - Processed 5300000 reads so far
2011-05-19 20:56:02,608 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:102990111-123010111
2011-05-19 20:56:08,705 - INFO - Processed 5400000 reads so far
2011-05-19 20:56:19,902 - INFO - Processed 5500000 reads so far
2011-05-19 20:56:31,161 - INFO - Processed 5600000 reads so far
2011-05-19 20:56:42,178 - INFO - Processed 5700000 reads so far
2011-05-19 20:56:54,131 - INFO - Processed 5800000 reads so far
2011-05-19 20:57:05,662 - INFO - Processed 5900000 reads so far
2011-05-19 20:57:18,892 - INFO - Processed 6000000 reads so far
2011-05-19 20:57:28,032 - INFO - Processed 6100000 reads so far
2011-05-19 20:57:37,016 - INFO - Processed 6200000 reads so far
2011-05-19 20:57:49,288 - INFO - Processed 6300000 reads so far
2011-05-19 20:57:58,341 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:122990118-143010118
2011-05-19 20:58:00,609 - INFO - Processed 6400000 reads so far
2011-05-19 20:58:11,767 - INFO - Processed 6500000 reads so far
2011-05-19 20:58:22,452 - INFO - Processed 6600000 reads so far
2011-05-19 20:58:32,484 - INFO - Processed 6700000 reads so far
2011-05-19 20:58:37,742 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:2990002-23010002
2011-05-19 20:58:44,468 - INFO - Processed 6800000 reads so far
2011-05-19 20:58:54,215 - INFO - Processed 6900000 reads so far
2011-05-19 20:59:06,321 - INFO - Processed 7000000 reads so far
2011-05-19 20:59:19,379 - INFO - Processed 7100000 reads so far
2011-05-19 20:59:30,974 - INFO - Processed 7200000 reads so far
2011-05-19 20:59:40,162 - INFO - Processed 7300000 reads so far
2011-05-19 20:59:48,322 - INFO - Processed 7400000 reads so far
2011-05-19 20:59:56,379 - INFO - Processed 7500000 reads so far
2011-05-19 21:00:05,728 - INFO - Processed 7600000 reads so far
2011-05-19 21:00:18,950 - INFO - Processed 7700000 reads so far
2011-05-19 21:00:28,238 - INFO - Processed 7800000 reads so far
2011-05-19 21:00:40,522 - INFO - Processed 7900000 reads so far
2011-05-19 21:00:49,859 - INFO - Processed 8000000 reads so far
2011-05-19 21:00:51,861 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:22990024-43010024
2011-05-19 21:00:56,862 - INFO - Processed 8100000 reads so far
2011-05-19 21:01:05,954 - INFO - Processed 8200000 reads so far
2011-05-19 21:01:14,709 - INFO - Processed 8300000 reads so far
2011-05-19 21:01:26,651 - INFO - Processed 8400000 reads so far
2011-05-19 21:01:37,849 - INFO - Processed 8500000 reads so far
2011-05-19 21:01:47,780 - INFO - Processed 8600000 reads so far
2011-05-19 21:01:59,196 - INFO - Processed 8700000 reads so far
2011-05-19 21:02:10,000 - INFO - Processed 8800000 reads so far
2011-05-19 21:02:22,350 - INFO - Processed 8900000 reads so far
2011-05-19 21:02:35,051 - INFO - Processed 9000000 reads so far
2011-05-19 21:02:46,885 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:42990034-63010034
2011-05-19 21:02:48,000 - INFO - Processed 9100000 reads so far
2011-05-19 21:03:00,474 - INFO - Processed 9200000 reads so far
2011-05-19 21:03:13,031 - INFO - Processed 9300000 reads so far
2011-05-19 21:03:24,710 - INFO - Processed 9400000 reads so far
2011-05-19 21:03:36,821 - INFO - Processed 9500000 reads so far
2011-05-19 21:03:49,086 - INFO - Processed 9600000 reads so far
2011-05-19 21:04:00,397 - INFO - Processed 9700000 reads so far
2011-05-19 21:04:12,929 - INFO - Processed 9800000 reads so far
2011-05-19 21:04:23,065 - INFO - Processed 9900000 reads so far
2011-05-19 21:04:37,634 - INFO - Processed 10000000 reads so far
2011-05-19 21:04:49,881 - INFO - Processed 10100000 reads so far
2011-05-19 21:04:56,910 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:62990052-83010052
2011-05-19 21:05:01,771 - INFO - Processed 10200000 reads so far
2011-05-19 21:05:14,260 - INFO - Processed 10300000 reads so far
2011-05-19 21:05:25,537 - INFO - Processed 10400000 reads so far
2011-05-19 21:05:37,541 - INFO - Processed 10500000 reads so far
2011-05-19 21:05:49,023 - INFO - Processed 10600000 reads so far
2011-05-19 21:06:00,094 - INFO - Processed 10700000 reads so far
2011-05-19 21:06:13,294 - INFO - Processed 10800000 reads so far
2011-05-19 21:06:25,697 - INFO - Processed 10900000 reads so far
2011-05-19 21:06:37,153 - INFO - Processed 11000000 reads so far
2011-05-19 21:06:50,534 - INFO - Processed 11100000 reads so far
2011-05-19 21:07:00,568 - INFO - Processed 11200000 reads so far
2011-05-19 21:07:02,915 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:82990058-103010058
2011-05-19 21:07:11,954 - INFO - Processed 11300000 reads so far
2011-05-19 21:07:22,827 - INFO - Processed 11400000 reads so far
2011-05-19 21:07:35,731 - INFO - Processed 11500000 reads so far
2011-05-19 21:07:47,252 - INFO - Processed 11600000 reads so far
2011-05-19 21:07:57,208 - INFO - Processed 11700000 reads so far
2011-05-19 21:08:08,559 - INFO - Processed 11800000 reads so far
2011-05-19 21:08:20,025 - INFO - Processed 11900000 reads so far
2011-05-19 21:08:32,010 - INFO - Processed 12000000 reads so far
2011-05-19 21:08:43,570 - INFO - Processed 12100000 reads so far
2011-05-19 21:08:54,662 - INFO - Processed 12200000 reads so far
2011-05-19 21:09:00,052 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:102990064-123010064
2011-05-19 21:09:06,038 - INFO - Processed 12300000 reads so far
2011-05-19 21:09:18,727 - INFO - Processed 12400000 reads so far
2011-05-19 21:09:30,971 - INFO - Processed 12500000 reads so far
2011-05-19 21:09:47,385 - INFO - Processed 12600000 reads so far
2011-05-19 21:10:14,513 - INFO - Processed 12700000 reads so far
2011-05-19 21:10:43,180 - INFO - Processed 12800000 reads so far
2011-05-19 21:11:01,043 - INFO - Processed 12900000 reads so far
2011-05-19 21:11:18,011 - INFO - Processed 13000000 reads so far
2011-05-19 21:11:26,823 - INFO - Processed 13100000 reads so far
2011-05-19 21:11:38,581 - INFO - Processed 13200000 reads so far
2011-05-19 21:11:46,693 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:2990037-23010037
2011-05-19 21:11:49,379 - INFO - Processed 13300000 reads so far
2011-05-19 21:11:58,208 - INFO - Processed 13400000 reads so far
2011-05-19 21:12:08,775 - INFO - Processed 13500000 reads so far
2011-05-19 21:12:17,094 - INFO - Processed 13600000 reads so far
2011-05-19 21:12:25,352 - INFO - Processed 13700000 reads so far
2011-05-19 21:12:34,822 - INFO - Processed 13800000 reads so far
2011-05-19 21:12:44,153 - INFO - Processed 13900000 reads so far
2011-05-19 21:12:55,116 - INFO - Processed 14000000 reads so far
2011-05-19 21:13:06,308 - INFO - Processed 14100000 reads so far
2011-05-19 21:13:15,026 - INFO - Processed 14200000 reads so far
2011-05-19 21:13:24,598 - INFO - Processed 14300000 reads so far
2011-05-19 21:13:33,788 - INFO - Processed 14400000 reads so far
2011-05-19 21:13:40,583 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:22990192-43010192
2011-05-19 21:13:44,621 - INFO - Processed 14500000 reads so far
2011-05-19 21:13:54,981 - INFO - Processed 14600000 reads so far
2011-05-19 21:14:04,872 - INFO - Processed 14700000 reads so far
2011-05-19 21:14:18,161 - INFO - Processed 14800000 reads so far
2011-05-19 21:14:30,493 - INFO - Processed 14900000 reads so far
2011-05-19 21:14:39,351 - INFO - Processed 15000000 reads so far
2011-05-19 21:14:51,260 - INFO - Processed 15100000 reads so far
2011-05-19 21:15:04,130 - INFO - Processed 15200000 reads so far
2011-05-19 21:15:15,740 - INFO - Processed 15300000 reads so far
2011-05-19 21:15:26,543 - INFO - Processed 15400000 reads so far
2011-05-19 21:15:32,408 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:42990217-63010217
2011-05-19 21:15:37,876 - INFO - Processed 15500000 reads so far
2011-05-19 21:15:51,458 - INFO - Processed 15600000 reads so far
2011-05-19 21:16:03,052 - INFO - Processed 15700000 reads so far
2011-05-19 21:16:13,264 - INFO - Processed 15800000 reads so far
2011-05-19 21:16:27,492 - INFO - Processed 15900000 reads so far
2011-05-19 21:16:40,423 - INFO - Processed 16000000 reads so far
2011-05-19 21:16:49,762 - INFO - Processed 16100000 reads so far
2011-05-19 21:17:00,226 - INFO - Processed 16200000 reads so far
2011-05-19 21:17:11,674 - INFO - Processed 16300000 reads so far
2011-05-19 21:17:20,661 - INFO - Processed 16400000 reads so far
2011-05-19 21:17:28,735 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:62990283-83010283
2011-05-19 21:17:30,071 - INFO - Processed 16500000 reads so far
2011-05-19 21:17:42,245 - INFO - Processed 16600000 reads so far
2011-05-19 21:17:50,870 - INFO - Processed 16700000 reads so far
2011-05-19 21:17:59,734 - INFO - Processed 16800000 reads so far
2011-05-19 21:18:08,247 - INFO - Processed 16900000 reads so far
2011-05-19 21:18:18,288 - INFO - Processed 17000000 reads so far
2011-05-19 21:18:26,724 - INFO - Processed 17100000 reads so far
2011-05-19 21:18:34,308 - INFO - Processed 17200000 reads so far
2011-05-19 21:18:43,332 - INFO - Processed 17300000 reads so far
2011-05-19 21:18:52,088 - INFO - Processed 17400000 reads so far
2011-05-19 21:19:01,866 - INFO - Processed 17500000 reads so far
2011-05-19 21:19:07,871 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:82990309-103010309
2011-05-19 21:19:14,051 - INFO - Processed 17600000 reads so far
2011-05-19 21:19:23,872 - INFO - Processed 17700000 reads so far
2011-05-19 21:19:32,667 - INFO - Processed 17800000 reads so far
2011-05-19 21:19:42,581 - INFO - Processed 17900000 reads so far
2011-05-19 21:19:54,609 - INFO - Processed 18000000 reads so far
2011-05-19 21:20:03,606 - INFO - Processed 18100000 reads so far
2011-05-19 21:20:12,755 - INFO - Processed 18200000 reads so far
2011-05-19 21:20:21,163 - INFO - Processed 18300000 reads so far
2011-05-19 21:20:30,401 - INFO - Processed 18400000 reads so far
2011-05-19 21:20:45,507 - INFO - Processed 18500000 reads so far
2011-05-19 21:20:55,422 - INFO - Processed 18600000 reads so far
2011-05-19 21:20:57,408 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:102990311-123010311
2011-05-19 21:21:04,124 - INFO - Processed 18700000 reads so far
2011-05-19 21:21:13,106 - INFO - Processed 18800000 reads so far
2011-05-19 21:21:23,917 - INFO - Processed 18900000 reads so far
2011-05-19 21:21:32,920 - INFO - Processed 19000000 reads so far
2011-05-19 21:21:42,941 - INFO - Processed 19100000 reads so far
2011-05-19 21:21:51,388 - INFO - Processed 19200000 reads so far
2011-05-19 21:22:01,633 - INFO - Processed 19300000 reads so far
2011-05-19 21:22:10,483 - INFO - Processed 19400000 reads so far
2011-05-19 21:22:18,388 - INFO - Processed 19500000 reads so far
2011-05-19 21:22:27,224 - INFO - Processed 19600000 reads so far
2011-05-19 21:22:36,399 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:2990025-23010025
2011-05-19 21:22:37,971 - INFO - Processed 19700000 reads so far
2011-05-19 21:22:47,140 - INFO - Processed 19800000 reads so far
2011-05-19 21:22:55,952 - INFO - Processed 19900000 reads so far
2011-05-19 21:23:04,612 - INFO - Processed 20000000 reads so far
2011-05-19 21:23:13,108 - INFO - Processed 20100000 reads so far
2011-05-19 21:23:23,251 - INFO - Processed 20200000 reads so far
2011-05-19 21:23:32,150 - INFO - Processed 20300000 reads so far
2011-05-19 21:23:41,189 - INFO - Processed 20400000 reads so far
2011-05-19 21:23:51,820 - INFO - Processed 20500000 reads so far
2011-05-19 21:24:00,064 - INFO - Processed 20600000 reads so far
2011-05-19 21:24:10,278 - INFO - Processed 20700000 reads so far
2011-05-19 21:24:13,326 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:22990062-43010062
2011-05-19 21:24:21,555 - INFO - Processed 20800000 reads so far
2011-05-19 21:24:33,119 - INFO - Processed 20900000 reads so far
2011-05-19 21:24:43,994 - INFO - Processed 21000000 reads so far
2011-05-19 21:24:55,733 - INFO - Processed 21100000 reads so far
2011-05-19 21:25:07,090 - INFO - Processed 21200000 reads so far
2011-05-19 21:25:19,145 - INFO - Processed 21300000 reads so far
2011-05-19 21:25:29,839 - INFO - Processed 21400000 reads so far
2011-05-19 21:25:40,611 - INFO - Processed 21500000 reads so far
2011-05-19 21:25:49,928 - INFO - Processed 21600000 reads so far
2011-05-19 21:25:57,940 - INFO - Processed 21700000 reads so far
2011-05-19 21:26:09,543 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:42990111-63010111
2011-05-19 21:26:10,122 - INFO - Processed 21800000 reads so far
2011-05-19 21:26:18,579 - INFO - Processed 21900000 reads so far
2011-05-19 21:26:25,696 - INFO - Processed 22000000 reads so far
2011-05-19 21:26:34,123 - INFO - Processed 22100000 reads so far
2011-05-19 21:26:42,621 - INFO - Processed 22200000 reads so far
2011-05-19 21:26:53,211 - INFO - Processed 22300000 reads so far
2011-05-19 21:27:04,303 - INFO - Processed 22400000 reads so far
2011-05-19 21:27:15,082 - INFO - Processed 22500000 reads so far
2011-05-19 21:27:23,730 - INFO - Processed 22600000 reads so far
2011-05-19 21:27:30,916 - INFO - Processed 22700000 reads so far
2011-05-19 21:27:37,775 - INFO - Processed 22800000 reads so far
2011-05-19 21:27:42,743 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:62990121-83010121
2011-05-19 21:27:44,869 - INFO - Processed 22900000 reads so far
2011-05-19 21:27:52,814 - INFO - Processed 23000000 reads so far
2011-05-19 21:28:00,365 - INFO - Processed 23100000 reads so far
2011-05-19 21:28:10,000 - INFO - Processed 23200000 reads so far
2011-05-19 21:28:20,325 - INFO - Processed 23300000 reads so far
2011-05-19 21:28:27,954 - INFO - Processed 23400000 reads so far
2011-05-19 21:28:34,806 - INFO - Processed 23500000 reads so far
2011-05-19 21:28:42,940 - INFO - Processed 23600000 reads so far
2011-05-19 21:28:51,963 - INFO - Processed 23700000 reads so far
2011-05-19 21:29:02,339 - INFO - Processed 23800000 reads so far
2011-05-19 21:29:12,080 - INFO - Processed 23900000 reads so far
2011-05-19 21:29:14,805 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:82990135-103010135
2011-05-19 21:29:19,971 - INFO - Processed 24000000 reads so far
2011-05-19 21:29:31,777 - INFO - Processed 24100000 reads so far
2011-05-19 21:29:39,741 - INFO - Processed 24200000 reads so far
2011-05-19 21:29:48,857 - INFO - Processed 24300000 reads so far
2011-05-19 21:29:59,841 - INFO - Processed 24400000 reads so far
2011-05-19 21:30:07,650 - INFO - Processed 24500000 reads so far
2011-05-19 21:30:16,211 - INFO - Processed 24600000 reads so far
2011-05-19 21:30:24,287 - INFO - Processed 24700000 reads so far
2011-05-19 21:30:31,547 - INFO - Processed 24800000 reads so far
2011-05-19 21:30:40,467 - INFO - Processed 24900000 reads so far
2011-05-19 21:30:44,703 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:102990167-123010167
2011-05-19 21:30:49,772 - INFO - Processed 25000000 reads so far
2011-05-19 21:31:00,484 - INFO - Processed 25100000 reads so far
2011-05-19 21:31:14,088 - INFO - Processed 25200000 reads so far
2011-05-19 21:31:25,656 - INFO - Processed 25300000 reads so far
2011-05-19 21:31:37,218 - INFO - Processed 25400000 reads so far
2011-05-19 21:31:48,563 - INFO - Processed 25500000 reads so far
2011-05-19 21:31:58,968 - INFO - Processed 25600000 reads so far
2011-05-19 21:32:07,995 - INFO - Processed 25700000 reads so far
2011-05-19 21:32:18,859 - INFO - Processed 25800000 reads so far
2011-05-19 21:32:28,212 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13_random:0-20010000
2011-05-19 21:32:29,452 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:2990015-23010015
2011-05-19 21:32:31,926 - INFO - Processed 25900000 reads so far
2011-05-19 21:32:43,091 - INFO - Processed 26000000 reads so far
2011-05-19 21:32:53,738 - INFO - Processed 26100000 reads so far
2011-05-19 21:33:01,350 - INFO - Processed 26200000 reads so far
2011-05-19 21:33:09,759 - INFO - Processed 26300000 reads so far
2011-05-19 21:33:18,143 - INFO - Processed 26400000 reads so far
2011-05-19 21:33:29,033 - INFO - Processed 26500000 reads so far
2011-05-19 21:33:38,029 - INFO - Processed 26600000 reads so far
2011-05-19 21:33:46,187 - INFO - Processed 26700000 reads so far
2011-05-19 21:33:55,634 - INFO - Processed 26800000 reads so far
2011-05-19 21:34:08,979 - INFO - Processed 26900000 reads so far
2011-05-19 21:34:16,181 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:22990062-43010062
2011-05-19 21:34:16,906 - INFO - Processed 27000000 reads so far
2011-05-19 21:34:31,192 - INFO - Processed 27100000 reads so far
2011-05-19 21:34:46,855 - INFO - Processed 27200000 reads so far
2011-05-19 21:34:58,181 - INFO - Processed 27300000 reads so far
2011-05-19 21:35:08,483 - INFO - Processed 27400000 reads so far
2011-05-19 21:35:16,967 - INFO - Processed 27500000 reads so far
2011-05-19 21:35:26,944 - INFO - Processed 27600000 reads so far
2011-05-19 21:35:37,108 - INFO - Processed 27700000 reads so far
2011-05-19 21:35:49,266 - INFO - Processed 27800000 reads so far
2011-05-19 21:36:01,632 - INFO - Processed 27900000 reads so far
2011-05-19 21:36:12,714 - INFO - Processed 28000000 reads so far
2011-05-19 21:36:19,086 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:42990129-63010129
2011-05-19 21:36:21,119 - INFO - Processed 28100000 reads so far
2011-05-19 21:36:30,891 - INFO - Processed 28200000 reads so far
2011-05-19 21:36:42,287 - INFO - Processed 28300000 reads so far
2011-05-19 21:36:54,282 - INFO - Processed 28400000 reads so far
2011-05-19 21:37:04,630 - INFO - Processed 28500000 reads so far
2011-05-19 21:37:12,700 - INFO - Processed 28600000 reads so far
2011-05-19 21:37:21,405 - INFO - Processed 28700000 reads so far
2011-05-19 21:37:31,270 - INFO - Processed 28800000 reads so far
2011-05-19 21:37:43,806 - INFO - Processed 28900000 reads so far
2011-05-19 21:37:56,178 - INFO - Processed 29000000 reads so far
2011-05-19 21:38:06,869 - INFO - Processed 29100000 reads so far
2011-05-19 21:38:14,424 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:62990143-83010143
2011-05-19 21:38:17,229 - INFO - Processed 29200000 reads so far
2011-05-19 21:38:27,947 - INFO - Processed 29300000 reads so far
2011-05-19 21:38:39,013 - INFO - Processed 29400000 reads so far
2011-05-19 21:38:52,029 - INFO - Processed 29500000 reads so far
2011-05-19 21:39:02,382 - INFO - Processed 29600000 reads so far
2011-05-19 21:39:13,391 - INFO - Processed 29700000 reads so far
2011-05-19 21:39:25,884 - INFO - Processed 29800000 reads so far
2011-05-19 21:39:38,138 - INFO - Processed 29900000 reads so far
2011-05-19 21:39:49,272 - INFO - Processed 30000000 reads so far
2011-05-19 21:40:00,025 - INFO - Processed 30100000 reads so far
2011-05-19 21:40:08,149 - INFO - Processed 30200000 reads so far
2011-05-19 21:40:12,740 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:82990144-103010144
2011-05-19 21:40:19,227 - INFO - Processed 30300000 reads so far
2011-05-19 21:40:26,602 - INFO - Processed 30400000 reads so far
2011-05-19 21:40:38,713 - INFO - Processed 30500000 reads so far
2011-05-19 21:40:49,990 - INFO - Processed 30600000 reads so far
2011-05-19 21:41:01,957 - INFO - Processed 30700000 reads so far
2011-05-19 21:41:12,977 - INFO - Processed 30800000 reads so far
2011-05-19 21:41:26,148 - INFO - Processed 30900000 reads so far
2011-05-19 21:41:36,240 - INFO - Processed 31000000 reads so far
2011-05-19 21:41:44,734 - INFO - Processed 31100000 reads so far
2011-05-19 21:41:52,970 - INFO - Processed 31200000 reads so far
2011-05-19 21:41:57,821 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:102990169-123010169
2011-05-19 21:42:01,649 - INFO - Processed 31300000 reads so far
2011-05-19 21:42:10,501 - INFO - Processed 31400000 reads so far
2011-05-19 21:42:20,764 - INFO - Processed 31500000 reads so far
2011-05-19 21:42:28,918 - INFO - Processed 31600000 reads so far
2011-05-19 21:42:37,316 - INFO - Processed 31700000 reads so far
2011-05-19 21:42:45,865 - INFO - Processed 31800000 reads so far
2011-05-19 21:42:55,867 - INFO - Processed 31900000 reads so far
2011-05-19 21:43:07,715 - INFO - Processed 32000000 reads so far
2011-05-19 21:43:19,279 - INFO - Processed 32100000 reads so far
2011-05-19 21:43:30,153 - INFO - Processed 32200000 reads so far
2011-05-19 21:43:39,969 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:122990170-143010170
2011-05-19 21:43:40,436 - INFO - Processed 32300000 reads so far
2011-05-19 21:43:49,784 - INFO - Processed 32400000 reads so far
2011-05-19 21:43:50,788 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:2990009-23010009
2011-05-19 21:43:59,208 - INFO - Processed 32500000 reads so far
2011-05-19 21:44:08,237 - INFO - Processed 32600000 reads so far
2011-05-19 21:44:17,669 - INFO - Processed 32700000 reads so far
2011-05-19 21:44:28,433 - INFO - Processed 32800000 reads so far
2011-05-19 21:44:38,505 - INFO - Processed 32900000 reads so far
2011-05-19 21:44:46,788 - INFO - Processed 33000000 reads so far
2011-05-19 21:44:54,741 - INFO - Processed 33100000 reads so far
2011-05-19 21:45:03,476 - INFO - Processed 33200000 reads so far
2011-05-19 21:45:13,821 - INFO - Processed 33300000 reads so far
2011-05-19 21:45:22,002 - INFO - Processed 33400000 reads so far
2011-05-19 21:45:28,105 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:22990028-43010028
2011-05-19 21:45:32,179 - INFO - Processed 33500000 reads so far
2011-05-19 21:45:42,027 - INFO - Processed 33600000 reads so far
2011-05-19 21:45:50,141 - INFO - Processed 33700000 reads so far
2011-05-19 21:45:59,310 - INFO - Processed 33800000 reads so far
2011-05-19 21:46:10,416 - INFO - Processed 33900000 reads so far
2011-05-19 21:46:19,227 - INFO - Processed 34000000 reads so far
2011-05-19 21:46:27,815 - INFO - Processed 34100000 reads so far
2011-05-19 21:46:37,324 - INFO - Processed 34200000 reads so far
2011-05-19 21:46:45,060 - INFO - Processed 34300000 reads so far
2011-05-19 21:46:53,106 - INFO - Processed 34400000 reads so far
2011-05-19 21:47:00,537 - INFO - Processed 34500000 reads so far
2011-05-19 21:47:02,462 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:42990059-63010059
2011-05-19 21:47:10,217 - INFO - Processed 34600000 reads so far
2011-05-19 21:47:21,514 - INFO - Processed 34700000 reads so far
2011-05-19 21:47:31,616 - INFO - Processed 34800000 reads so far
2011-05-19 21:47:39,806 - INFO - Processed 34900000 reads so far
2011-05-19 21:47:46,622 - INFO - Processed 35000000 reads so far
2011-05-19 21:47:53,392 - INFO - Processed 35100000 reads so far
2011-05-19 21:48:00,695 - INFO - Processed 35200000 reads so far
2011-05-19 21:48:11,398 - INFO - Processed 35300000 reads so far
2011-05-19 21:48:20,475 - INFO - Processed 35400000 reads so far
2011-05-19 21:48:31,189 - INFO - Processed 35500000 reads so far
2011-05-19 21:48:40,126 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:62990083-83010083
2011-05-19 21:48:42,010 - INFO - Processed 35600000 reads so far
2011-05-19 21:48:49,482 - INFO - Processed 35700000 reads so far
2011-05-19 21:48:58,060 - INFO - Processed 35800000 reads so far
2011-05-19 21:49:09,648 - INFO - Processed 35900000 reads so far
2011-05-19 21:49:19,845 - INFO - Processed 36000000 reads so far
2011-05-19 21:49:27,442 - INFO - Processed 36100000 reads so far
2011-05-19 21:49:35,336 - INFO - Processed 36200000 reads so far
2011-05-19 21:49:42,561 - INFO - Processed 36300000 reads so far
2011-05-19 21:49:53,706 - INFO - Processed 36400000 reads so far
2011-05-19 21:50:03,272 - INFO - Processed 36500000 reads so far
2011-05-19 21:50:14,525 - INFO - Processed 36600000 reads so far
2011-05-19 21:50:25,840 - INFO - Processed 36700000 reads so far
2011-05-19 21:50:25,962 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:82990113-103010113
2011-05-19 21:50:34,728 - INFO - Processed 36800000 reads so far
2011-05-19 21:50:45,654 - INFO - Processed 36900000 reads so far
2011-05-19 21:50:57,633 - INFO - Processed 37000000 reads so far
2011-05-19 21:51:09,672 - INFO - Processed 37100000 reads so far
2011-05-19 21:51:21,008 - INFO - Processed 37200000 reads so far
2011-05-19 21:51:32,533 - INFO - Processed 37300000 reads so far
2011-05-19 21:51:43,862 - INFO - Processed 37400000 reads so far
2011-05-19 21:51:53,718 - INFO - Processed 37500000 reads so far
2011-05-19 21:52:04,978 - INFO - Processed 37600000 reads so far
2011-05-19 21:52:16,132 - INFO - Processed 37700000 reads so far
2011-05-19 21:52:24,703 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:102990119-123010119
2011-05-19 21:52:27,592 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:2990204-23010204
2011-05-19 21:52:27,948 - INFO - Processed 37800000 reads so far
2011-05-19 21:52:41,311 - INFO - Processed 37900000 reads so far
2011-05-19 21:52:52,896 - INFO - Processed 38000000 reads so far
2011-05-19 21:53:04,242 - INFO - Processed 38100000 reads so far
2011-05-19 21:53:16,096 - INFO - Processed 38200000 reads so far
2011-05-19 21:53:27,336 - INFO - Processed 38300000 reads so far
2011-05-19 21:53:38,687 - INFO - Processed 38400000 reads so far
2011-05-19 21:53:50,969 - INFO - Processed 38500000 reads so far
2011-05-19 21:54:02,356 - INFO - Processed 38600000 reads so far
2011-05-19 21:54:13,807 - INFO - Processed 38700000 reads so far
2011-05-19 21:54:25,260 - INFO - Processed 38800000 reads so far
2011-05-19 21:54:37,593 - INFO - Processed 38900000 reads so far
2011-05-19 21:54:40,762 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:22990217-43010217
2011-05-19 21:54:48,931 - INFO - Processed 39000000 reads so far
2011-05-19 21:55:00,493 - INFO - Processed 39100000 reads so far
2011-05-19 21:55:11,544 - INFO - Processed 39200000 reads so far
2011-05-19 21:55:23,145 - INFO - Processed 39300000 reads so far
2011-05-19 21:55:34,420 - INFO - Processed 39400000 reads so far
2011-05-19 21:55:45,953 - INFO - Processed 39500000 reads so far
2011-05-19 21:55:57,240 - INFO - Processed 39600000 reads so far
2011-05-19 21:56:10,088 - INFO - Processed 39700000 reads so far
2011-05-19 21:56:21,724 - INFO - Processed 39800000 reads so far
2011-05-19 21:56:35,017 - INFO - Processed 39900000 reads so far
2011-05-19 21:56:46,372 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:42990246-63010246
2011-05-19 21:56:48,180 - INFO - Processed 40000000 reads so far
2011-05-19 21:56:57,821 - INFO - Processed 40100000 reads so far
2011-05-19 21:57:06,276 - INFO - Processed 40200000 reads so far
2011-05-19 21:57:14,691 - INFO - Processed 40300000 reads so far
2011-05-19 21:57:25,013 - INFO - Processed 40400000 reads so far
2011-05-19 21:57:36,325 - INFO - Processed 40500000 reads so far
2011-05-19 21:57:44,945 - INFO - Processed 40600000 reads so far
2011-05-19 21:57:58,167 - INFO - Processed 40700000 reads so far
2011-05-19 21:58:06,464 - INFO - Processed 40800000 reads so far
2011-05-19 21:58:16,023 - INFO - Processed 40900000 reads so far
2011-05-19 21:58:25,012 - INFO - Processed 41000000 reads so far
2011-05-19 21:58:28,156 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:62990286-83010286
2011-05-19 21:58:35,768 - INFO - Processed 41100000 reads so far
2011-05-19 21:58:47,251 - INFO - Processed 41200000 reads so far
2011-05-19 21:58:58,592 - INFO - Processed 41300000 reads so far
2011-05-19 21:59:09,705 - INFO - Processed 41400000 reads so far
2011-05-19 21:59:20,302 - INFO - Processed 41500000 reads so far
2011-05-19 21:59:31,190 - INFO - Processed 41600000 reads so far
2011-05-19 21:59:40,258 - INFO - Processed 41700000 reads so far
2011-05-19 21:59:49,154 - INFO - Processed 41800000 reads so far
2011-05-19 21:59:57,927 - INFO - Processed 41900000 reads so far
2011-05-19 22:00:08,096 - INFO - Processed 42000000 reads so far
2011-05-19 22:00:16,431 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:82990304-103010304
2011-05-19 22:00:19,535 - INFO - Processed 42100000 reads so far
2011-05-19 22:00:29,275 - INFO - Processed 42200000 reads so far
2011-05-19 22:00:39,122 - INFO - Processed 42300000 reads so far
2011-05-19 22:00:49,640 - INFO - Processed 42400000 reads so far
2011-05-19 22:00:59,933 - INFO - Processed 42500000 reads so far
2011-05-19 22:01:08,966 - INFO - Processed 42600000 reads so far
2011-05-19 22:01:17,514 - INFO - Processed 42700000 reads so far
2011-05-19 22:01:29,030 - INFO - Processed 42800000 reads so far
2011-05-19 22:01:35,430 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16_random:0-20010088
2011-05-19 22:01:35,451 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:2989983-23009983
2011-05-19 22:01:37,049 - INFO - Processed 42900000 reads so far
2011-05-19 22:01:45,913 - INFO - Processed 43000000 reads so far
2011-05-19 22:01:58,014 - INFO - Processed 43100000 reads so far
2011-05-19 22:02:08,776 - INFO - Processed 43200000 reads so far
2011-05-19 22:02:19,810 - INFO - Processed 43300000 reads so far
2011-05-19 22:02:30,836 - INFO - Processed 43400000 reads so far
2011-05-19 22:02:40,723 - INFO - Processed 43500000 reads so far
2011-05-19 22:02:53,107 - INFO - Processed 43600000 reads so far
2011-05-19 22:03:02,355 - INFO - Processed 43700000 reads so far
2011-05-19 22:03:12,957 - INFO - Processed 43800000 reads so far
2011-05-19 22:03:23,224 - INFO - Processed 43900000 reads so far
2011-05-19 22:03:35,604 - INFO - Processed 44000000 reads so far
2011-05-19 22:03:39,618 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:22989987-43009987
2011-05-19 22:03:47,147 - INFO - Processed 44100000 reads so far
2011-05-19 22:03:58,422 - INFO - Processed 44200000 reads so far
2011-05-19 22:04:10,246 - INFO - Processed 44300000 reads so far
2011-05-19 22:04:21,754 - INFO - Processed 44400000 reads so far
2011-05-19 22:04:35,321 - INFO - Processed 44500000 reads so far
2011-05-19 22:04:44,600 - INFO - Processed 44600000 reads so far
2011-05-19 22:04:53,318 - INFO - Processed 44700000 reads so far
2011-05-19 22:05:03,068 - INFO - Processed 44800000 reads so far
2011-05-19 22:05:11,759 - INFO - Processed 44900000 reads so far
2011-05-19 22:05:21,254 - INFO - Processed 45000000 reads so far
2011-05-19 22:05:29,535 - INFO - Processed 45100000 reads so far
2011-05-19 22:05:38,021 - INFO - Processed 45200000 reads so far
2011-05-19 22:05:38,185 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:42990020-63010020
2011-05-19 22:05:47,273 - INFO - Processed 45300000 reads so far
2011-05-19 22:05:55,696 - INFO - Processed 45400000 reads so far
2011-05-19 22:06:05,021 - INFO - Processed 45500000 reads so far
2011-05-19 22:06:15,889 - INFO - Processed 45600000 reads so far
2011-05-19 22:06:27,046 - INFO - Processed 45700000 reads so far
2011-05-19 22:06:36,743 - INFO - Processed 45800000 reads so far
2011-05-19 22:06:47,573 - INFO - Processed 45900000 reads so far
2011-05-19 22:06:57,965 - INFO - Processed 46000000 reads so far
2011-05-19 22:07:07,265 - INFO - Processed 46100000 reads so far
2011-05-19 22:07:16,437 - INFO - Processed 46200000 reads so far
2011-05-19 22:07:21,351 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:62990039-83010039
2011-05-19 22:07:25,925 - INFO - Processed 46300000 reads so far
2011-05-19 22:07:33,376 - INFO - Processed 46400000 reads so far
2011-05-19 22:07:42,974 - INFO - Processed 46500000 reads so far
2011-05-19 22:07:53,891 - INFO - Processed 46600000 reads so far
2011-05-19 22:08:01,882 - INFO - Processed 46700000 reads so far
2011-05-19 22:08:10,323 - INFO - Processed 46800000 reads so far
2011-05-19 22:08:18,449 - INFO - Processed 46900000 reads so far
2011-05-19 22:08:29,963 - INFO - Processed 47000000 reads so far
2011-05-19 22:08:39,100 - INFO - Processed 47100000 reads so far
2011-05-19 22:08:47,946 - INFO - Processed 47200000 reads so far
2011-05-19 22:08:56,765 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:82990157-103010157
2011-05-19 22:08:57,166 - INFO - Processed 47300000 reads so far
2011-05-19 22:09:08,311 - INFO - Processed 47400000 reads so far
2011-05-19 22:09:39,203 - INFO - Processed 47500000 reads so far
2011-05-19 22:09:50,563 - INFO - Processed 47600000 reads so far
2011-05-19 22:10:00,871 - INFO - Processed 47700000 reads so far
2011-05-19 22:10:10,358 - INFO - Processed 47800000 reads so far
2011-05-19 22:10:20,718 - INFO - Processed 47900000 reads so far
2011-05-19 22:10:25,362 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17_random:0-20010055
2011-05-19 22:10:26,740 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:2989999-23009999
2011-05-19 22:10:30,021 - INFO - Processed 48000000 reads so far
2011-05-19 22:10:40,843 - INFO - Processed 48100000 reads so far
2011-05-19 22:10:49,978 - INFO - Processed 48200000 reads so far
2011-05-19 22:10:59,659 - INFO - Processed 48300000 reads so far
2011-05-19 22:11:09,792 - INFO - Processed 48400000 reads so far
2011-05-19 22:11:20,300 - INFO - Processed 48500000 reads so far
2011-05-19 22:11:30,022 - INFO - Processed 48600000 reads so far
2011-05-19 22:11:40,959 - INFO - Processed 48700000 reads so far
2011-05-19 22:11:49,936 - INFO - Processed 48800000 reads so far
2011-05-19 22:11:59,951 - INFO - Processed 48900000 reads so far
2011-05-19 22:12:09,777 - INFO - Processed 49000000 reads so far
2011-05-19 22:12:17,523 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:22990000-43010000
2011-05-19 22:12:20,156 - INFO - Processed 49100000 reads so far
2011-05-19 22:12:32,071 - INFO - Processed 49200000 reads so far
2011-05-19 22:12:41,659 - INFO - Processed 49300000 reads so far
2011-05-19 22:12:50,545 - INFO - Processed 49400000 reads so far
2011-05-19 22:13:01,129 - INFO - Processed 49500000 reads so far
2011-05-19 22:13:15,252 - INFO - Processed 49600000 reads so far
2011-05-19 22:13:26,488 - INFO - Processed 49700000 reads so far
2011-05-19 22:13:37,569 - INFO - Processed 49800000 reads so far
2011-05-19 22:13:47,479 - INFO - Processed 49900000 reads so far
2011-05-19 22:13:58,282 - INFO - Processed 50000000 reads so far
2011-05-19 22:14:07,582 - INFO - Processed 50100000 reads so far
2011-05-19 22:14:13,133 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:42990011-63010011
2011-05-19 22:14:17,456 - INFO - Processed 50200000 reads so far
2011-05-19 22:14:27,113 - INFO - Processed 50300000 reads so far
2011-05-19 22:14:37,038 - INFO - Processed 50400000 reads so far
2011-05-19 22:14:46,215 - INFO - Processed 50500000 reads so far
2011-05-19 22:14:55,370 - INFO - Processed 50600000 reads so far
2011-05-19 22:15:05,223 - INFO - Processed 50700000 reads so far
2011-05-19 22:15:16,860 - INFO - Processed 50800000 reads so far
2011-05-19 22:15:26,749 - INFO - Processed 50900000 reads so far
2011-05-19 22:15:37,344 - INFO - Processed 51000000 reads so far
2011-05-19 22:15:49,192 - INFO - Processed 51100000 reads so far
2011-05-19 22:15:57,989 - INFO - Processed 51200000 reads so far
2011-05-19 22:15:59,617 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:62990020-83010020
2011-05-19 22:16:07,887 - INFO - Processed 51300000 reads so far
2011-05-19 22:16:17,341 - INFO - Processed 51400000 reads so far
2011-05-19 22:16:29,367 - INFO - Processed 51500000 reads so far
2011-05-19 22:16:39,954 - INFO - Processed 51600000 reads so far
2011-05-19 22:16:51,386 - INFO - Processed 51700000 reads so far
2011-05-19 22:17:01,522 - INFO - Processed 51800000 reads so far
2011-05-19 22:17:11,389 - INFO - Processed 51900000 reads so far
2011-05-19 22:17:20,461 - INFO - Processed 52000000 reads so far
2011-05-19 22:17:31,786 - INFO - Processed 52100000 reads so far
2011-05-19 22:17:40,266 - INFO - Processed 52200000 reads so far
2011-05-19 22:17:47,122 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:82990023-103010023
2011-05-19 22:17:49,741 - INFO - Processed 52300000 reads so far
2011-05-19 22:18:01,707 - INFO - Processed 52400000 reads so far
2011-05-19 22:18:11,680 - INFO - Processed 52500000 reads so far
2011-05-19 22:18:23,050 - INFO - Processed 52600000 reads so far
2011-05-19 22:18:33,082 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:2990092-23010092
2011-05-19 22:18:33,352 - INFO - Processed 52700000 reads so far
2011-05-19 22:18:45,922 - INFO - Processed 52800000 reads so far
2011-05-19 22:18:58,168 - INFO - Processed 52900000 reads so far
2011-05-19 22:19:09,895 - INFO - Processed 53000000 reads so far
2011-05-19 22:19:21,293 - INFO - Processed 53100000 reads so far
2011-05-19 22:19:31,481 - INFO - Processed 53200000 reads so far
2011-05-19 22:19:41,797 - INFO - Processed 53300000 reads so far
2011-05-19 22:19:53,242 - INFO - Processed 53400000 reads so far
2011-05-19 22:20:03,815 - INFO - Processed 53500000 reads so far
2011-05-19 22:20:14,429 - INFO - Processed 53600000 reads so far
2011-05-19 22:20:24,936 - INFO - Processed 53700000 reads so far
2011-05-19 22:20:30,914 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:22990096-43010096
2011-05-19 22:20:35,221 - INFO - Processed 53800000 reads so far
2011-05-19 22:20:46,981 - INFO - Processed 53900000 reads so far
2011-05-19 22:20:56,642 - INFO - Processed 54000000 reads so far
2011-05-19 22:21:09,541 - INFO - Processed 54100000 reads so far
2011-05-19 22:21:18,779 - INFO - Processed 54200000 reads so far
2011-05-19 22:21:30,441 - INFO - Processed 54300000 reads so far
2011-05-19 22:21:42,109 - INFO - Processed 54400000 reads so far
2011-05-19 22:21:52,395 - INFO - Processed 54500000 reads so far
2011-05-19 22:22:03,147 - INFO - Processed 54600000 reads so far
2011-05-19 22:22:13,484 - INFO - Processed 54700000 reads so far
2011-05-19 22:22:23,339 - INFO - Processed 54800000 reads so far
2011-05-19 22:22:24,065 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:42990119-63010119
2011-05-19 22:22:33,815 - INFO - Processed 54900000 reads so far
2011-05-19 22:22:45,512 - INFO - Processed 55000000 reads so far
2011-05-19 22:22:55,847 - INFO - Processed 55100000 reads so far
2011-05-19 22:23:04,665 - INFO - Processed 55200000 reads so far
2011-05-19 22:23:15,834 - INFO - Processed 55300000 reads so far
2011-05-19 22:23:26,612 - INFO - Processed 55400000 reads so far
2011-05-19 22:23:36,510 - INFO - Processed 55500000 reads so far
2011-05-19 22:23:47,516 - INFO - Processed 55600000 reads so far
2011-05-19 22:24:05,305 - INFO - Processed 55700000 reads so far
2011-05-19 22:24:15,042 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:2989970-23009970
2011-05-19 22:24:15,276 - INFO - Processed 55800000 reads so far
2011-05-19 22:24:25,323 - INFO - Processed 55900000 reads so far
2011-05-19 22:24:35,289 - INFO - Processed 56000000 reads so far
2011-05-19 22:24:45,539 - INFO - Processed 56100000 reads so far
2011-05-19 22:24:56,220 - INFO - Processed 56200000 reads so far
2011-05-19 22:25:06,173 - INFO - Processed 56300000 reads so far
2011-05-19 22:25:16,106 - INFO - Processed 56400000 reads so far
2011-05-19 22:25:24,892 - INFO - Processed 56500000 reads so far
2011-05-19 22:25:36,571 - INFO - Processed 56600000 reads so far
2011-05-19 22:25:45,694 - INFO - Processed 56700000 reads so far
2011-05-19 22:25:57,011 - INFO - Processed 56800000 reads so far
2011-05-19 22:26:02,899 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:22990093-43010093
2011-05-19 22:26:06,788 - INFO - Processed 56900000 reads so far
2011-05-19 22:26:16,387 - INFO - Processed 57000000 reads so far
2011-05-19 22:26:27,220 - INFO - Processed 57100000 reads so far
2011-05-19 22:26:37,896 - INFO - Processed 57200000 reads so far
2011-05-19 22:26:48,003 - INFO - Processed 57300000 reads so far
2011-05-19 22:26:58,664 - INFO - Processed 57400000 reads so far
2011-05-19 22:27:08,680 - INFO - Processed 57500000 reads so far
2011-05-19 22:27:19,974 - INFO - Processed 57600000 reads so far
2011-05-19 22:27:31,295 - INFO - Processed 57700000 reads so far
2011-05-19 22:27:41,520 - INFO - Processed 57800000 reads so far
2011-05-19 22:27:52,025 - INFO - Processed 57900000 reads so far
2011-05-19 22:27:55,698 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:42990099-63010099
2011-05-19 22:28:02,189 - INFO - Processed 58000000 reads so far
2011-05-19 22:28:13,014 - INFO - Processed 58100000 reads so far
2011-05-19 22:28:23,202 - INFO - Processed 58200000 reads so far
2011-05-19 22:28:34,153 - INFO - Processed 58300000 reads so far
2011-05-19 22:28:43,975 - INFO - Processed 58400000 reads so far
2011-05-19 22:28:54,513 - INFO - Processed 58500000 reads so far
2011-05-19 22:29:07,514 - INFO - Processed 58600000 reads so far
2011-05-19 22:29:17,938 - INFO - Processed 58700000 reads so far
2011-05-19 22:29:28,403 - INFO - Processed 58800000 reads so far
2011-05-19 22:29:42,179 - INFO - Processed 58900000 reads so far
2011-05-19 22:29:51,823 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:62990108-83010108
2011-05-19 22:29:53,608 - INFO - Processed 59000000 reads so far
2011-05-19 22:30:04,967 - INFO - Processed 59100000 reads so far
2011-05-19 22:30:18,072 - INFO - Processed 59200000 reads so far
2011-05-19 22:30:30,915 - INFO - Processed 59300000 reads so far
2011-05-19 22:30:43,556 - INFO - Processed 59400000 reads so far
2011-05-19 22:30:55,520 - INFO - Processed 59500000 reads so far
2011-05-19 22:31:08,269 - INFO - Processed 59600000 reads so far
2011-05-19 22:31:21,628 - INFO - Processed 59700000 reads so far
2011-05-19 22:31:33,112 - INFO - Processed 59800000 reads so far
2011-05-19 22:31:44,244 - INFO - Processed 59900000 reads so far
2011-05-19 22:31:56,503 - INFO - Processed 60000000 reads so far
2011-05-19 22:32:00,713 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:82990129-103010129
2011-05-19 22:32:07,432 - INFO - Processed 60100000 reads so far
2011-05-19 22:32:16,430 - INFO - Processed 60200000 reads so far
2011-05-19 22:32:27,166 - INFO - Processed 60300000 reads so far
2011-05-19 22:32:39,106 - INFO - Processed 60400000 reads so far
2011-05-19 22:32:49,823 - INFO - Processed 60500000 reads so far
2011-05-19 22:32:59,240 - INFO - Processed 60600000 reads so far
2011-05-19 22:33:09,656 - INFO - Processed 60700000 reads so far
2011-05-19 22:33:20,929 - INFO - Processed 60800000 reads so far
2011-05-19 22:33:30,482 - INFO - Processed 60900000 reads so far
2011-05-19 22:33:39,491 - INFO - Processed 61000000 reads so far
2011-05-19 22:33:52,430 - INFO - Processed 61100000 reads so far
2011-05-19 22:33:54,819 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:102990160-123010160
2011-05-19 22:34:02,634 - INFO - Processed 61200000 reads so far
2011-05-19 22:34:13,149 - INFO - Processed 61300000 reads so far
2011-05-19 22:34:23,607 - INFO - Processed 61400000 reads so far
2011-05-19 22:34:34,843 - INFO - Processed 61500000 reads so far
2011-05-19 22:34:46,043 - INFO - Processed 61600000 reads so far
2011-05-19 22:34:57,137 - INFO - Processed 61700000 reads so far
2011-05-19 22:35:07,534 - INFO - Processed 61800000 reads so far
2011-05-19 22:35:17,734 - INFO - Processed 61900000 reads so far
2011-05-19 22:35:30,010 - INFO - Processed 62000000 reads so far
2011-05-19 22:35:40,142 - INFO - Processed 62100000 reads so far
2011-05-19 22:35:50,249 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:122990226-143010226
2011-05-19 22:35:50,509 - INFO - Processed 62200000 reads so far
2011-05-19 22:35:59,433 - INFO - Processed 62300000 reads so far
2011-05-19 22:36:11,957 - INFO - Processed 62400000 reads so far
2011-05-19 22:36:24,408 - INFO - Processed 62500000 reads so far
2011-05-19 22:36:36,426 - INFO - Processed 62600000 reads so far
2011-05-19 22:36:49,034 - INFO - Processed 62700000 reads so far
2011-05-19 22:37:02,358 - INFO - Processed 62800000 reads so far
2011-05-19 22:37:13,828 - INFO - Processed 62900000 reads so far
2011-05-19 22:37:26,184 - INFO - Processed 63000000 reads so far
2011-05-19 22:37:37,633 - INFO - Processed 63100000 reads so far
2011-05-19 22:37:49,059 - INFO - Processed 63200000 reads so far
2011-05-19 22:37:56,804 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:142990229-163010229
2011-05-19 22:38:00,884 - INFO - Processed 63300000 reads so far
2011-05-19 22:38:15,350 - INFO - Processed 63400000 reads so far
2011-05-19 22:38:26,727 - INFO - Processed 63500000 reads so far
2011-05-19 22:38:37,954 - INFO - Processed 63600000 reads so far
2011-05-19 22:38:51,263 - INFO - Processed 63700000 reads so far
2011-05-19 22:39:03,972 - INFO - Processed 63800000 reads so far
2011-05-19 22:39:13,832 - INFO - Processed 63900000 reads so far
2011-05-19 22:39:24,661 - INFO - Processed 64000000 reads so far
2011-05-19 22:39:37,191 - INFO - Processed 64100000 reads so far
2011-05-19 22:39:45,698 - INFO - Processed 64200000 reads so far
2011-05-19 22:39:54,675 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:162990230-183010230
2011-05-19 22:39:55,391 - INFO - Processed 64300000 reads so far
2011-05-19 22:40:06,077 - INFO - Processed 64400000 reads so far
2011-05-19 22:40:17,362 - INFO - Processed 64500000 reads so far
2011-05-19 22:40:25,839 - INFO - Processed 64600000 reads so far
2011-05-19 22:40:34,509 - INFO - Processed 64700000 reads so far
2011-05-19 22:40:43,865 - INFO - Processed 64800000 reads so far
2011-05-19 22:40:54,351 - INFO - Processed 64900000 reads so far
2011-05-19 22:41:04,854 - INFO - Processed 65000000 reads so far
2011-05-19 22:41:14,527 - INFO - Processed 65100000 reads so far
2011-05-19 22:41:25,181 - INFO - Processed 65200000 reads so far
2011-05-19 22:41:34,245 - INFO - Processed 65300000 reads so far
2011-05-19 22:41:42,384 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:182990254-203010254
2011-05-19 22:41:45,395 - INFO - Processed 65400000 reads so far
2011-05-19 22:41:55,690 - INFO - Processed 65500000 reads so far
2011-05-19 22:42:07,863 - INFO - Processed 65600000 reads so far
2011-05-19 22:42:19,900 - INFO - Processed 65700000 reads so far
2011-05-19 22:42:30,801 - INFO - Processed 65800000 reads so far
2011-05-19 22:42:43,403 - INFO - Processed 65900000 reads so far
2011-05-19 22:42:55,001 - INFO - Processed 66000000 reads so far
2011-05-19 22:43:04,990 - INFO - Processed 66100000 reads so far
2011-05-19 22:43:07,923 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1_random:0-20010000
2011-05-19 22:43:15,051 - INFO - Processed 66200000 reads so far
2011-05-19 22:43:21,141 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:2990003-23010003
2011-05-19 22:43:26,912 - INFO - Processed 66300000 reads so far
2011-05-19 22:43:35,588 - INFO - Processed 66400000 reads so far
2011-05-19 22:43:45,776 - INFO - Processed 66500000 reads so far
2011-05-19 22:43:55,768 - INFO - Processed 66600000 reads so far
2011-05-19 22:44:06,395 - INFO - Processed 66700000 reads so far
2011-05-19 22:44:15,303 - INFO - Processed 66800000 reads so far
2011-05-19 22:44:24,077 - INFO - Processed 66900000 reads so far
2011-05-19 22:44:35,051 - INFO - Processed 67000000 reads so far
2011-05-19 22:44:43,416 - INFO - Processed 67100000 reads so far
2011-05-19 22:44:54,438 - INFO - Processed 67200000 reads so far
2011-05-19 22:45:13,273 - INFO - Processed 67300000 reads so far
2011-05-19 22:45:15,635 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:22990027-43010027
2011-05-19 22:45:22,485 - INFO - Processed 67400000 reads so far
2011-05-19 22:45:32,886 - INFO - Processed 67500000 reads so far
2011-05-19 22:45:46,034 - INFO - Processed 67600000 reads so far
2011-05-19 22:45:54,577 - INFO - Processed 67700000 reads so far
2011-05-19 22:46:04,519 - INFO - Processed 67800000 reads so far
2011-05-19 22:46:16,752 - INFO - Processed 67900000 reads so far
2011-05-19 22:46:29,865 - INFO - Processed 68000000 reads so far
2011-05-19 22:46:40,562 - INFO - Processed 68100000 reads so far
2011-05-19 22:46:52,073 - INFO - Processed 68200000 reads so far
2011-05-19 22:46:59,499 - INFO - Processed 68300000 reads so far
2011-05-19 22:47:11,003 - INFO - Processed 68400000 reads so far
2011-05-19 22:47:12,778 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:42990035-63010035
2011-05-19 22:47:22,284 - INFO - Processed 68500000 reads so far
2011-05-19 22:47:34,189 - INFO - Processed 68600000 reads so far
2011-05-19 22:47:45,308 - INFO - Processed 68700000 reads so far
2011-05-19 22:47:56,334 - INFO - Processed 68800000 reads so far
2011-05-19 22:48:07,387 - INFO - Processed 68900000 reads so far
2011-05-19 22:48:18,860 - INFO - Processed 69000000 reads so far
2011-05-19 22:48:27,499 - INFO - Processed 69100000 reads so far
2011-05-19 22:48:37,040 - INFO - Processed 69200000 reads so far
2011-05-19 22:48:47,910 - INFO - Processed 69300000 reads so far
2011-05-19 22:48:57,187 - INFO - Processed 69400000 reads so far
2011-05-19 22:49:03,210 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:62990039-83010039
2011-05-19 22:49:06,814 - INFO - Processed 69500000 reads so far
2011-05-19 22:49:15,336 - INFO - Processed 69600000 reads so far
2011-05-19 22:49:23,506 - INFO - Processed 69700000 reads so far
2011-05-19 22:49:35,908 - INFO - Processed 69800000 reads so far
2011-05-19 22:49:45,597 - INFO - Processed 69900000 reads so far
2011-05-19 22:49:55,942 - INFO - Processed 70000000 reads so far
2011-05-19 22:50:03,779 - INFO - Processed 70100000 reads so far
2011-05-19 22:50:12,130 - INFO - Processed 70200000 reads so far
2011-05-19 22:50:19,983 - INFO - Processed 70300000 reads so far
2011-05-19 22:50:30,578 - INFO - Processed 70400000 reads so far
2011-05-19 22:50:38,571 - INFO - Processed 70500000 reads so far
2011-05-19 22:50:39,390 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:82990061-103010061
2011-05-19 22:50:47,769 - INFO - Processed 70600000 reads so far
2011-05-19 22:50:59,484 - INFO - Processed 70700000 reads so far
2011-05-19 22:51:10,896 - INFO - Processed 70800000 reads so far
2011-05-19 22:51:22,261 - INFO - Processed 70900000 reads so far
2011-05-19 22:51:32,730 - INFO - Processed 71000000 reads so far
2011-05-19 22:51:44,681 - INFO - Processed 71100000 reads so far
2011-05-19 22:51:53,743 - INFO - Processed 71200000 reads so far
2011-05-19 22:52:03,303 - INFO - Processed 71300000 reads so far
2011-05-19 22:52:11,486 - INFO - Processed 71400000 reads so far
2011-05-19 22:52:18,680 - INFO - Processed 71500000 reads so far
2011-05-19 22:52:25,432 - INFO - Processed 71600000 reads so far
2011-05-19 22:52:31,547 - INFO - Processed 71700000 reads so far
2011-05-19 22:52:38,479 - INFO - Processed 71800000 reads so far
2011-05-19 22:52:44,164 - INFO - Processed 71900000 reads so far
2011-05-19 22:52:52,999 - INFO - Processed 72000000 reads so far
2011-05-19 22:53:01,254 - INFO - Processed 72100000 reads so far
2011-05-19 22:53:10,598 - INFO - Processed 72200000 reads so far
2011-05-19 22:53:18,537 - INFO - Processed 72300000 reads so far
2011-05-19 22:53:26,531 - INFO - Processed 72400000 reads so far
2011-05-19 22:53:33,019 - INFO - Processed 72500000 reads so far
2011-05-19 22:53:39,485 - INFO - Processed 72600000 reads so far
2011-05-19 22:53:46,049 - INFO - Processed 72700000 reads so far
2011-05-19 22:53:52,750 - INFO - Processed 72800000 reads so far
2011-05-19 22:54:00,794 - INFO - Processed 72900000 reads so far
2011-05-19 22:54:07,105 - INFO - Processed 73000000 reads so far
2011-05-19 22:54:13,548 - INFO - Processed 73100000 reads so far
2011-05-19 22:54:20,262 - INFO - Processed 73200000 reads so far
2011-05-19 22:54:27,375 - INFO - Processed 73300000 reads so far
2011-05-19 22:54:35,497 - INFO - Processed 73400000 reads so far
2011-05-19 22:54:43,214 - INFO - Processed 73500000 reads so far
2011-05-19 22:54:50,420 - INFO - Processed 73600000 reads so far
2011-05-19 22:54:56,581 - INFO - Processed 73700000 reads so far
2011-05-19 22:55:04,568 - INFO - Processed 73800000 reads so far
2011-05-19 22:55:12,187 - INFO - Processed 73900000 reads so far
2011-05-19 22:55:21,306 - INFO - Processed 74000000 reads so far
2011-05-19 22:55:30,956 - INFO - Processed 74100000 reads so far
2011-05-19 22:55:38,851 - INFO - Processed 74200000 reads so far
2011-05-19 22:55:47,615 - INFO - Processed 74300000 reads so far
2011-05-19 22:55:54,583 - INFO - Processed 74400000 reads so far
2011-05-19 22:56:02,284 - INFO - Processed 74500000 reads so far
2011-05-19 22:56:10,759 - INFO - Processed 74600000 reads so far
2011-05-19 22:56:16,903 - INFO - Processed 74700000 reads so far
2011-05-19 22:56:22,708 - INFO - Processed 74800000 reads so far
2011-05-19 22:56:30,755 - INFO - Processed 74900000 reads so far
2011-05-19 22:56:39,820 - INFO - Processed 75000000 reads so far
2011-05-19 22:56:46,491 - INFO - Processed 75100000 reads so far
2011-05-19 22:56:52,431 - INFO - Processed 75200000 reads so far
2011-05-19 22:56:58,983 - INFO - Processed 75300000 reads so far
2011-05-19 22:57:08,609 - INFO - Processed 75400000 reads so far
2011-05-19 22:57:16,764 - INFO - Processed 75500000 reads so far
2011-05-19 22:57:26,298 - INFO - Processed 75600000 reads so far
2011-05-19 22:57:35,216 - INFO - Processed 75700000 reads so far
2011-05-19 22:57:42,225 - INFO - Processed 75800000 reads so far
2011-05-19 22:57:49,997 - INFO - Processed 75900000 reads so far
2011-05-19 22:57:56,710 - INFO - Processed 76000000 reads so far
2011-05-19 22:58:05,309 - INFO - Processed 76100000 reads so far
2011-05-19 22:58:12,061 - INFO - Processed 76200000 reads so far
2011-05-19 22:58:19,769 - INFO - Processed 76300000 reads so far
2011-05-19 22:58:26,647 - INFO - Processed 76400000 reads so far
2011-05-19 22:58:34,249 - INFO - Processed 76500000 reads so far
2011-05-19 22:58:42,322 - INFO - Processed 76600000 reads so far
2011-05-19 22:58:50,287 - INFO - Processed 76700000 reads so far
2011-05-19 22:58:57,555 - INFO - Processed 76800000 reads so far
2011-05-19 22:59:05,288 - INFO - Processed 76900000 reads so far
2011-05-19 22:59:14,149 - INFO - Processed 77000000 reads so far
2011-05-19 22:59:22,946 - INFO - Processed 77100000 reads so far
2011-05-19 22:59:29,734 - INFO - Processed 77200000 reads so far
2011-05-19 22:59:36,662 - INFO - Processed 77300000 reads so far
2011-05-19 22:59:46,005 - INFO - Processed 77400000 reads so far
2011-05-19 22:59:55,140 - INFO - Processed 77500000 reads so far
2011-05-19 23:00:02,324 - INFO - Processed 77600000 reads so far
2011-05-19 23:00:09,680 - INFO - Processed 77700000 reads so far
2011-05-19 23:00:17,028 - INFO - Processed 77800000 reads so far
2011-05-19 23:00:24,121 - INFO - Processed 77900000 reads so far
2011-05-19 23:00:31,210 - INFO - Processed 78000000 reads so far
2011-05-19 23:00:38,799 - INFO - Processed 78100000 reads so far
2011-05-19 23:00:45,828 - INFO - Processed 78200000 reads so far
2011-05-19 23:00:54,698 - INFO - Processed 78300000 reads so far
2011-05-19 23:01:02,482 - INFO - Processed 78400000 reads so far
2011-05-19 23:01:09,596 - INFO - Processed 78500000 reads so far
2011-05-19 23:01:18,562 - INFO - Processed 78600000 reads so far
2011-05-19 23:01:33,369 - INFO - Processed 78700000 reads so far
2011-05-19 23:01:41,099 - INFO - Processed 78800000 reads so far
2011-05-19 23:01:51,619 - INFO - Processed 78900000 reads so far
2011-05-19 23:01:59,951 - INFO - Processed 79000000 reads so far
2011-05-19 23:02:07,827 - INFO - Processed 79100000 reads so far
2011-05-19 23:02:14,783 - INFO - Processed 79200000 reads so far
2011-05-19 23:02:22,779 - INFO - Processed 79300000 reads so far
2011-05-19 23:02:30,288 - INFO - Processed 79400000 reads so far
2011-05-19 23:02:38,147 - INFO - Processed 79500000 reads so far
2011-05-19 23:02:46,586 - INFO - Processed 79600000 reads so far
2011-05-19 23:02:57,036 - INFO - Processed 79700000 reads so far
2011-05-19 23:03:05,953 - INFO - Processed 79800000 reads so far
2011-05-19 23:03:12,729 - INFO - Processed 79900000 reads so far
2011-05-19 23:03:21,174 - INFO - Processed 80000000 reads so far
2011-05-19 23:03:31,134 - INFO - Processed 80100000 reads so far
2011-05-19 23:03:42,431 - INFO - Processed 80200000 reads so far
2011-05-19 23:03:50,209 - INFO - Processed 80300000 reads so far
2011-05-19 23:03:59,151 - INFO - Processed 80400000 reads so far
2011-05-19 23:04:10,345 - INFO - Processed 80500000 reads so far
2011-05-19 23:04:19,259 - INFO - Processed 80600000 reads so far
2011-05-19 23:04:26,759 - INFO - Processed 80700000 reads so far
2011-05-19 23:04:36,068 - INFO - Processed 80800000 reads so far
2011-05-19 23:04:42,934 - INFO - Processed 80900000 reads so far
2011-05-19 23:04:51,878 - INFO - Processed 81000000 reads so far
2011-05-19 23:04:59,991 - INFO - Processed 81100000 reads so far
2011-05-19 23:05:07,426 - INFO - Processed 81200000 reads so far
2011-05-19 23:05:14,449 - INFO - Processed 81300000 reads so far
2011-05-19 23:05:22,841 - INFO - Processed 81400000 reads so far
2011-05-19 23:05:30,310 - INFO - Processed 81500000 reads so far
2011-05-19 23:05:38,610 - INFO - Processed 81600000 reads so far
2011-05-19 23:05:46,524 - INFO - Processed 81700000 reads so far
2011-05-19 23:05:54,225 - INFO - Processed 81800000 reads so far
2011-05-19 23:06:03,979 - INFO - Processed 81900000 reads so far
2011-05-19 23:06:15,241 - INFO - Processed 82000000 reads so far
2011-05-19 23:06:26,473 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:102990067-123010067
2011-05-19 23:06:28,682 - INFO - Processed 82100000 reads so far
2011-05-19 23:06:37,998 - INFO - Processed 82200000 reads so far
2011-05-19 23:06:47,822 - INFO - Processed 82300000 reads so far
2011-05-19 23:06:56,216 - INFO - Processed 82400000 reads so far
2011-05-19 23:07:06,052 - INFO - Processed 82500000 reads so far
2011-05-19 23:07:15,949 - INFO - Processed 82600000 reads so far
2011-05-19 23:07:24,157 - INFO - Processed 82700000 reads so far
2011-05-19 23:07:35,119 - INFO - Processed 82800000 reads so far
2011-05-19 23:07:44,364 - INFO - Processed 82900000 reads so far
2011-05-19 23:07:53,061 - INFO - Processed 83000000 reads so far
2011-05-19 23:08:02,349 - INFO - Processed 83100000 reads so far
2011-05-19 23:08:07,697 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:122990076-143010076
2011-05-19 23:08:15,144 - INFO - Processed 83200000 reads so far
2011-05-19 23:08:24,871 - INFO - Processed 83300000 reads so far
2011-05-19 23:08:35,444 - INFO - Processed 83400000 reads so far
2011-05-19 23:08:45,338 - INFO - Processed 83500000 reads so far
2011-05-19 23:08:54,501 - INFO - Processed 83600000 reads so far
2011-05-19 23:09:04,791 - INFO - Processed 83700000 reads so far
2011-05-19 23:09:15,888 - INFO - Processed 83800000 reads so far
2011-05-19 23:09:25,188 - INFO - Processed 83900000 reads so far
2011-05-19 23:09:33,899 - INFO - Processed 84000000 reads so far
2011-05-19 23:09:43,219 - INFO - Processed 84100000 reads so far
2011-05-19 23:09:54,770 - INFO - Processed 84200000 reads so far
2011-05-19 23:09:55,204 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:142990138-163010138
2011-05-19 23:10:04,059 - INFO - Processed 84300000 reads so far
2011-05-19 23:10:15,751 - INFO - Processed 84400000 reads so far
2011-05-19 23:10:24,480 - INFO - Processed 84500000 reads so far
2011-05-19 23:10:34,686 - INFO - Processed 84600000 reads so far
2011-05-19 23:10:45,186 - INFO - Processed 84700000 reads so far
2011-05-19 23:10:56,943 - INFO - Processed 84800000 reads so far
2011-05-19 23:11:07,719 - INFO - Processed 84900000 reads so far
2011-05-19 23:11:20,756 - INFO - Processed 85000000 reads so far
2011-05-19 23:11:34,074 - INFO - Processed 85100000 reads so far
2011-05-19 23:11:46,126 - INFO - Processed 85200000 reads so far
2011-05-19 23:11:53,430 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:162990140-183010140
2011-05-19 23:11:55,933 - INFO - Processed 85300000 reads so far
2011-05-19 23:12:05,251 - INFO - Processed 85400000 reads so far
2011-05-19 23:12:16,597 - INFO - Processed 85500000 reads so far
2011-05-19 23:12:25,308 - INFO - Processed 85600000 reads so far
2011-05-19 23:12:34,692 - INFO - Processed 85700000 reads so far
2011-05-19 23:12:46,656 - INFO - Processed 85800000 reads so far
2011-05-19 23:12:57,126 - INFO - Processed 85900000 reads so far
2011-05-19 23:13:08,405 - INFO - Processed 86000000 reads so far
2011-05-19 23:13:19,214 - INFO - Processed 86100000 reads so far
2011-05-19 23:13:27,676 - INFO - Processed 86200000 reads so far
2011-05-19 23:13:37,664 - INFO - Processed 86300000 reads so far
2011-05-19 23:13:44,342 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:2989994-23009994
2011-05-19 23:13:45,880 - INFO - Processed 86400000 reads so far
2011-05-19 23:13:57,570 - INFO - Processed 86500000 reads so far
2011-05-19 23:14:09,966 - INFO - Processed 86600000 reads so far
2011-05-19 23:14:21,313 - INFO - Processed 86700000 reads so far
2011-05-19 23:14:32,909 - INFO - Processed 86800000 reads so far
2011-05-19 23:14:44,905 - INFO - Processed 86900000 reads so far
2011-05-19 23:14:57,922 - INFO - Processed 87000000 reads so far
2011-05-19 23:15:10,086 - INFO - Processed 87100000 reads so far
2011-05-19 23:15:18,666 - INFO - Processed 87200000 reads so far
2011-05-19 23:15:28,552 - INFO - Processed 87300000 reads so far
2011-05-19 23:15:38,417 - INFO - Processed 87400000 reads so far
2011-05-19 23:15:46,590 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:22990044-43010044
2011-05-19 23:15:51,826 - INFO - Processed 87500000 reads so far
2011-05-19 23:16:03,304 - INFO - Processed 87600000 reads so far
2011-05-19 23:16:13,439 - INFO - Processed 87700000 reads so far
2011-05-19 23:16:30,148 - INFO - Processed 87800000 reads so far
2011-05-19 23:16:41,740 - INFO - Processed 87900000 reads so far
2011-05-19 23:16:54,834 - INFO - Processed 88000000 reads so far
2011-05-19 23:17:09,655 - INFO - Processed 88100000 reads so far
2011-05-19 23:17:21,708 - INFO - Processed 88200000 reads so far
2011-05-19 23:17:36,106 - INFO - Processed 88300000 reads so far
2011-05-19 23:17:46,997 - INFO - Processed 88400000 reads so far
2011-05-19 23:17:58,019 - INFO - Processed 88500000 reads so far
2011-05-19 23:18:00,357 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:42990098-63010098
2011-05-19 23:18:10,209 - INFO - Processed 88600000 reads so far
2011-05-19 23:18:20,142 - INFO - Processed 88700000 reads so far
2011-05-19 23:18:29,978 - INFO - Processed 88800000 reads so far
2011-05-19 23:18:47,490 - INFO - Processed 88900000 reads so far
2011-05-19 23:19:03,231 - INFO - Processed 89000000 reads so far
2011-05-19 23:19:13,752 - INFO - Processed 89100000 reads so far
2011-05-19 23:19:22,757 - INFO - Processed 89200000 reads so far
2011-05-19 23:19:31,282 - INFO - Processed 89300000 reads so far
2011-05-19 23:19:40,318 - INFO - Processed 89400000 reads so far
2011-05-19 23:19:49,467 - INFO - Processed 89500000 reads so far
2011-05-19 23:19:58,339 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:62990173-83010173
2011-05-19 23:20:01,268 - INFO - Processed 89600000 reads so far
2011-05-19 23:20:08,726 - INFO - Processed 89700000 reads so far
2011-05-19 23:20:21,171 - INFO - Processed 89800000 reads so far
2011-05-19 23:20:31,832 - INFO - Processed 89900000 reads so far
2011-05-19 23:20:42,997 - INFO - Processed 90000000 reads so far
2011-05-19 23:20:54,139 - INFO - Processed 90100000 reads so far
2011-05-19 23:21:04,913 - INFO - Processed 90200000 reads so far
2011-05-19 23:21:16,587 - INFO - Processed 90300000 reads so far
2011-05-19 23:21:26,357 - INFO - Processed 90400000 reads so far
2011-05-19 23:21:35,031 - INFO - Processed 90500000 reads so far
2011-05-19 23:21:44,062 - INFO - Processed 90600000 reads so far
2011-05-19 23:21:46,391 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:82990190-103010190
2011-05-19 23:21:55,643 - INFO - Processed 90700000 reads so far
2011-05-19 23:22:07,026 - INFO - Processed 90800000 reads so far
2011-05-19 23:22:20,042 - INFO - Processed 90900000 reads so far
2011-05-19 23:22:31,904 - INFO - Processed 91000000 reads so far
2011-05-19 23:22:43,136 - INFO - Processed 91100000 reads so far
2011-05-19 23:22:54,837 - INFO - Processed 91200000 reads so far
2011-05-19 23:23:07,436 - INFO - Processed 91300000 reads so far
2011-05-19 23:23:18,582 - INFO - Processed 91400000 reads so far
2011-05-19 23:23:30,428 - INFO - Processed 91500000 reads so far
2011-05-19 23:23:41,698 - INFO - Processed 91600000 reads so far
2011-05-19 23:23:50,189 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:102990192-123010192
2011-05-19 23:23:53,248 - INFO - Processed 91700000 reads so far
2011-05-19 23:24:04,700 - INFO - Processed 91800000 reads so far
2011-05-19 23:24:14,940 - INFO - Processed 91900000 reads so far
2011-05-19 23:24:24,163 - INFO - Processed 92000000 reads so far
2011-05-19 23:24:34,009 - INFO - Processed 92100000 reads so far
2011-05-19 23:24:43,454 - INFO - Processed 92200000 reads so far
2011-05-19 23:24:55,020 - INFO - Processed 92300000 reads so far
2011-05-19 23:25:05,958 - INFO - Processed 92400000 reads so far
2011-05-19 23:25:17,518 - INFO - Processed 92500000 reads so far
2011-05-19 23:25:36,498 - INFO - Processed 92600000 reads so far
2011-05-19 23:25:46,957 - INFO - Processed 92700000 reads so far
2011-05-19 23:25:50,572 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:122990206-143010206
2011-05-19 23:25:58,543 - INFO - Processed 92800000 reads so far
2011-05-19 23:26:10,113 - INFO - Processed 92900000 reads so far
2011-05-19 23:26:21,002 - INFO - Processed 93000000 reads so far
2011-05-19 23:26:32,231 - INFO - Processed 93100000 reads so far
2011-05-19 23:26:43,260 - INFO - Processed 93200000 reads so far
2011-05-19 23:26:54,249 - INFO - Processed 93300000 reads so far
2011-05-19 23:27:05,301 - INFO - Processed 93400000 reads so far
2011-05-19 23:27:15,082 - INFO - Processed 93500000 reads so far
2011-05-19 23:27:25,172 - INFO - Processed 93600000 reads so far
2011-05-19 23:27:34,512 - INFO - Processed 93700000 reads so far
2011-05-19 23:27:43,423 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:142990217-163010217
2011-05-19 23:27:44,433 - INFO - Processed 93800000 reads so far
2011-05-19 23:27:54,991 - INFO - Processed 93900000 reads so far
2011-05-19 23:28:03,727 - INFO - Processed 94000000 reads so far
2011-05-19 23:28:12,000 - INFO - Processed 94100000 reads so far
2011-05-19 23:28:22,198 - INFO - Processed 94200000 reads so far
2011-05-19 23:28:31,235 - INFO - Processed 94300000 reads so far
2011-05-19 23:28:41,185 - INFO - Processed 94400000 reads so far
2011-05-19 23:28:49,231 - INFO - Processed 94500000 reads so far
2011-05-19 23:29:00,369 - INFO - Processed 94600000 reads so far
2011-05-19 23:29:10,015 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3_random:0-20010158
2011-05-19 23:29:10,153 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:2989995-23009995
2011-05-19 23:29:11,000 - INFO - Processed 94700000 reads so far
2011-05-19 23:29:22,063 - INFO - Processed 94800000 reads so far
2011-05-19 23:29:33,722 - INFO - Processed 94900000 reads so far
2011-05-19 23:29:44,903 - INFO - Processed 95000000 reads so far
2011-05-19 23:29:54,633 - INFO - Processed 95100000 reads so far
2011-05-19 23:30:06,568 - INFO - Processed 95200000 reads so far
2011-05-19 23:30:18,093 - INFO - Processed 95300000 reads so far
2011-05-19 23:30:29,224 - INFO - Processed 95400000 reads so far
2011-05-19 23:30:41,934 - INFO - Processed 95500000 reads so far
2011-05-19 23:30:51,856 - INFO - Processed 95600000 reads so far
2011-05-19 23:31:04,057 - INFO - Processed 95700000 reads so far
2011-05-19 23:31:14,597 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:22990014-43010014
2011-05-19 23:31:16,056 - INFO - Processed 95800000 reads so far
2011-05-19 23:31:26,193 - INFO - Processed 95900000 reads so far
2011-05-19 23:31:37,049 - INFO - Processed 96000000 reads so far
2011-05-19 23:31:51,031 - INFO - Processed 96100000 reads so far
2011-05-19 23:32:01,014 - INFO - Processed 96200000 reads so far
2011-05-19 23:32:12,116 - INFO - Processed 96300000 reads so far
2011-05-19 23:32:21,125 - INFO - Processed 96400000 reads so far
2011-05-19 23:32:31,261 - INFO - Processed 96500000 reads so far
2011-05-19 23:32:41,488 - INFO - Processed 96600000 reads so far
2011-05-19 23:32:50,396 - INFO - Processed 96700000 reads so far
2011-05-19 23:33:02,643 - INFO - Processed 96800000 reads so far
2011-05-19 23:33:03,253 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:42990017-63010017
2011-05-19 23:33:12,255 - INFO - Processed 96900000 reads so far
2011-05-19 23:33:26,869 - INFO - Processed 97000000 reads so far
2011-05-19 23:33:38,614 - INFO - Processed 97100000 reads so far
2011-05-19 23:33:48,851 - INFO - Processed 97200000 reads so far
2011-05-19 23:33:58,437 - INFO - Processed 97300000 reads so far
2011-05-19 23:34:10,186 - INFO - Processed 97400000 reads so far
2011-05-19 23:34:22,732 - INFO - Processed 97500000 reads so far
2011-05-19 23:34:34,106 - INFO - Processed 97600000 reads so far
2011-05-19 23:34:47,786 - INFO - Processed 97700000 reads so far
2011-05-19 23:34:58,502 - INFO - Processed 97800000 reads so far
2011-05-19 23:35:09,655 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:62990041-83010041
2011-05-19 23:35:09,904 - INFO - Processed 97900000 reads so far
2011-05-19 23:35:21,973 - INFO - Processed 98000000 reads so far
2011-05-19 23:35:33,727 - INFO - Processed 98100000 reads so far
2011-05-19 23:35:43,530 - INFO - Processed 98200000 reads so far
2011-05-19 23:35:53,017 - INFO - Processed 98300000 reads so far
2011-05-19 23:36:01,940 - INFO - Processed 98400000 reads so far
2011-05-19 23:36:10,986 - INFO - Processed 98500000 reads so far
2011-05-19 23:36:19,114 - INFO - Processed 98600000 reads so far
2011-05-19 23:36:29,108 - INFO - Processed 98700000 reads so far
2011-05-19 23:36:37,368 - INFO - Processed 98800000 reads so far
2011-05-19 23:36:48,062 - INFO - Processed 98900000 reads so far
2011-05-19 23:36:57,933 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:82990060-103010060
2011-05-19 23:36:59,285 - INFO - Processed 99000000 reads so far
2011-05-19 23:37:09,054 - INFO - Processed 99100000 reads so far
2011-05-19 23:37:16,768 - INFO - Processed 99200000 reads so far
2011-05-19 23:37:26,537 - INFO - Processed 99300000 reads so far
2011-05-19 23:37:38,946 - INFO - Processed 99400000 reads so far
2011-05-19 23:37:50,122 - INFO - Processed 99500000 reads so far
2011-05-19 23:38:01,131 - INFO - Processed 99600000 reads so far
2011-05-19 23:38:17,112 - INFO - Processed 99700000 reads so far
2011-05-19 23:38:28,509 - INFO - Processed 99800000 reads so far
2011-05-19 23:38:40,765 - INFO - Processed 99900000 reads so far
2011-05-19 23:39:01,177 - INFO - Processed 100000000 reads so far
2011-05-19 23:39:21,062 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:102990063-123010063
2011-05-19 23:39:36,741 - INFO - Processed 100100000 reads so far
2011-05-19 23:39:47,389 - INFO - Processed 100200000 reads so far
2011-05-19 23:39:56,763 - INFO - Processed 100300000 reads so far
2011-05-19 23:40:07,995 - INFO - Processed 100400000 reads so far
2011-05-19 23:40:17,823 - INFO - Processed 100500000 reads so far
2011-05-19 23:40:26,857 - INFO - Processed 100600000 reads so far
2011-05-19 23:40:35,038 - INFO - Processed 100700000 reads so far
2011-05-19 23:40:46,989 - INFO - Processed 100800000 reads so far
2011-05-19 23:40:58,111 - INFO - Processed 100900000 reads so far
2011-05-19 23:41:09,758 - INFO - Processed 101000000 reads so far
2011-05-19 23:41:13,656 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:122990115-143010115
2011-05-19 23:41:22,569 - INFO - Processed 101100000 reads so far
2011-05-19 23:41:33,365 - INFO - Processed 101200000 reads so far
2011-05-19 23:41:44,274 - INFO - Processed 101300000 reads so far
2011-05-19 23:41:58,159 - INFO - Processed 101400000 reads so far
2011-05-19 23:42:08,910 - INFO - Processed 101500000 reads so far
2011-05-19 23:42:20,474 - INFO - Processed 101600000 reads so far
2011-05-19 23:42:32,029 - INFO - Processed 101700000 reads so far
2011-05-19 23:42:44,272 - INFO - Processed 101800000 reads so far
2011-05-19 23:42:55,431 - INFO - Processed 101900000 reads so far
2011-05-19 23:43:07,245 - INFO - Processed 102000000 reads so far
2011-05-19 23:43:16,540 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:142990152-163010152
2011-05-19 23:43:18,057 - INFO - Processed 102100000 reads so far
2011-05-19 23:43:28,605 - INFO - Processed 102200000 reads so far
2011-05-19 23:43:41,881 - INFO - Processed 102300000 reads so far
2011-05-19 23:43:51,515 - INFO - Processed 102400000 reads so far
2011-05-19 23:44:00,327 - INFO - Processed 102500000 reads so far
2011-05-19 23:44:09,314 - INFO - Processed 102600000 reads so far
2011-05-19 23:44:23,212 - INFO - Processed 102700000 reads so far
2011-05-19 23:44:33,413 - INFO - Processed 102800000 reads so far
2011-05-19 23:44:44,366 - INFO - Processed 102900000 reads so far
2011-05-19 23:44:52,192 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4_random:0-20010037
2011-05-19 23:44:53,287 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:2990023-23010023
2011-05-19 23:44:56,763 - INFO - Processed 103000000 reads so far
2011-05-19 23:45:06,488 - INFO - Processed 103100000 reads so far
2011-05-19 23:45:16,215 - INFO - Processed 103200000 reads so far
2011-05-19 23:45:27,069 - INFO - Processed 103300000 reads so far
2011-05-19 23:45:39,281 - INFO - Processed 103400000 reads so far
2011-05-19 23:45:51,034 - INFO - Processed 103500000 reads so far
2011-05-19 23:46:04,266 - INFO - Processed 103600000 reads so far
2011-05-19 23:46:14,486 - INFO - Processed 103700000 reads so far
2011-05-19 23:46:25,849 - INFO - Processed 103800000 reads so far
2011-05-19 23:46:42,463 - INFO - Processed 103900000 reads so far
2011-05-19 23:46:53,710 - INFO - Processed 104000000 reads so far
2011-05-19 23:47:05,363 - INFO - Processed 104100000 reads so far
2011-05-19 23:47:05,846 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:22990047-43010047
2011-05-19 23:47:19,826 - INFO - Processed 104200000 reads so far
2011-05-19 23:47:31,165 - INFO - Processed 104300000 reads so far
2011-05-19 23:47:43,702 - INFO - Processed 104400000 reads so far
2011-05-19 23:47:56,138 - INFO - Processed 104500000 reads so far
2011-05-19 23:48:08,051 - INFO - Processed 104600000 reads so far
2011-05-19 23:48:32,275 - INFO - Processed 104700000 reads so far
2011-05-19 23:48:55,609 - INFO - Processed 104800000 reads so far
2011-05-19 23:49:09,040 - INFO - Processed 104900000 reads so far
2011-05-19 23:49:20,954 - INFO - Processed 105000000 reads so far
2011-05-19 23:49:35,748 - INFO - Processed 105100000 reads so far
2011-05-19 23:49:43,979 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:42990053-63010053
2011-05-19 23:49:47,150 - INFO - Processed 105200000 reads so far
2011-05-19 23:50:00,700 - INFO - Processed 105300000 reads so far
2011-05-19 23:50:13,019 - INFO - Processed 105400000 reads so far
2011-05-19 23:50:24,695 - INFO - Processed 105500000 reads so far
2011-05-19 23:50:36,153 - INFO - Processed 105600000 reads so far
2011-05-19 23:50:47,638 - INFO - Processed 105700000 reads so far
2011-05-19 23:50:58,266 - INFO - Processed 105800000 reads so far
2011-05-19 23:51:08,674 - INFO - Processed 105900000 reads so far
2011-05-19 23:51:21,171 - INFO - Processed 106000000 reads so far
2011-05-19 23:51:32,186 - INFO - Processed 106100000 reads so far
2011-05-19 23:51:45,496 - INFO - Processed 106200000 reads so far
2011-05-19 23:51:47,725 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:62990165-83010165
2011-05-19 23:51:57,235 - INFO - Processed 106300000 reads so far
2011-05-19 23:52:11,035 - INFO - Processed 106400000 reads so far
2011-05-19 23:52:22,861 - INFO - Processed 106500000 reads so far
2011-05-19 23:52:32,510 - INFO - Processed 106600000 reads so far
2011-05-19 23:52:43,244 - INFO - Processed 106700000 reads so far
2011-05-19 23:52:54,282 - INFO - Processed 106800000 reads so far
2011-05-19 23:53:05,127 - INFO - Processed 106900000 reads so far
2011-05-19 23:53:15,053 - INFO - Processed 107000000 reads so far
2011-05-19 23:53:26,729 - INFO - Processed 107100000 reads so far
2011-05-19 23:53:37,813 - INFO - Processed 107200000 reads so far
2011-05-19 23:53:44,740 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:82990192-103010192
2011-05-19 23:53:49,428 - INFO - Processed 107300000 reads so far
2011-05-19 23:54:02,964 - INFO - Processed 107400000 reads so far
2011-05-19 23:54:14,352 - INFO - Processed 107500000 reads so far
2011-05-19 23:54:26,062 - INFO - Processed 107600000 reads so far
2011-05-19 23:54:37,023 - INFO - Processed 107700000 reads so far
2011-05-19 23:54:49,939 - INFO - Processed 107800000 reads so far
2011-05-19 23:55:02,074 - INFO - Processed 107900000 reads so far
2011-05-19 23:55:13,769 - INFO - Processed 108000000 reads so far
2011-05-19 23:55:26,158 - INFO - Processed 108100000 reads so far
2011-05-19 23:55:58,633 - INFO - Processed 108200000 reads so far
2011-05-19 23:56:06,421 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:102990214-123010214
2011-05-19 23:56:10,748 - INFO - Processed 108300000 reads so far
2011-05-19 23:56:22,274 - INFO - Processed 108400000 reads so far
2011-05-19 23:56:34,656 - INFO - Processed 108500000 reads so far
2011-05-19 23:56:45,662 - INFO - Processed 108600000 reads so far
2011-05-19 23:56:56,133 - INFO - Processed 108700000 reads so far
2011-05-19 23:57:08,715 - INFO - Processed 108800000 reads so far
2011-05-19 23:57:20,799 - INFO - Processed 108900000 reads so far
2011-05-19 23:57:35,657 - INFO - Processed 109000000 reads so far
2011-05-19 23:57:46,773 - INFO - Processed 109100000 reads so far
2011-05-19 23:57:58,132 - INFO - Processed 109200000 reads so far
2011-05-19 23:58:11,534 - INFO - Processed 109300000 reads so far
2011-05-19 23:58:16,718 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:122990220-143010220
2011-05-19 23:58:23,304 - INFO - Processed 109400000 reads so far
2011-05-19 23:58:36,907 - INFO - Processed 109500000 reads so far
2011-05-19 23:58:46,978 - INFO - Processed 109600000 reads so far
2011-05-19 23:58:58,632 - INFO - Processed 109700000 reads so far
2011-05-19 23:59:09,437 - INFO - Processed 109800000 reads so far
2011-05-19 23:59:18,997 - INFO - Processed 109900000 reads so far
2011-05-19 23:59:28,886 - INFO - Processed 110000000 reads so far
2011-05-19 23:59:41,548 - INFO - Processed 110100000 reads so far
2011-05-19 23:59:53,863 - INFO - Processed 110200000 reads so far
2011-05-20 00:00:06,172 - INFO - Processed 110300000 reads so far
2011-05-20 00:00:15,947 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:142990224-163010224
2011-05-20 00:00:16,394 - INFO - Processed 110400000 reads so far
2011-05-20 00:00:28,906 - INFO - Processed 110500000 reads so far
2011-05-20 00:00:40,148 - INFO - Processed 110600000 reads so far
2011-05-20 00:00:51,566 - INFO - Processed 110700000 reads so far
2011-05-20 00:01:00,190 - INFO - Processed 110800000 reads so far
2011-05-20 00:01:09,321 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5_random:0-20010109
2011-05-20 00:01:09,377 - INFO - Processed 110900000 reads so far
2011-05-20 00:01:09,828 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:2989990-23009990
2011-05-20 00:01:20,507 - INFO - Processed 111000000 reads so far
2011-05-20 00:01:33,691 - INFO - Processed 111100000 reads so far
2011-05-20 00:01:42,830 - INFO - Processed 111200000 reads so far
2011-05-20 00:01:54,145 - INFO - Processed 111300000 reads so far
2011-05-20 00:02:02,811 - INFO - Processed 111400000 reads so far
2011-05-20 00:02:12,116 - INFO - Processed 111500000 reads so far
2011-05-20 00:02:22,918 - INFO - Processed 111600000 reads so far
2011-05-20 00:02:34,125 - INFO - Processed 111700000 reads so far
2011-05-20 00:02:44,459 - INFO - Processed 111800000 reads so far
2011-05-20 00:02:54,407 - INFO - Processed 111900000 reads so far
2011-05-20 00:02:59,673 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:22990001-43010001
2011-05-20 00:03:03,897 - INFO - Processed 112000000 reads so far
2011-05-20 00:03:11,694 - INFO - Processed 112100000 reads so far
2011-05-20 00:03:19,537 - INFO - Processed 112200000 reads so far
2011-05-20 00:03:30,451 - INFO - Processed 112300000 reads so far
2011-05-20 00:03:56,764 - INFO - Processed 112400000 reads so far
2011-05-20 00:04:22,204 - INFO - Processed 112500000 reads so far
2011-05-20 00:04:32,722 - INFO - Processed 112600000 reads so far
2011-05-20 00:04:44,353 - INFO - Processed 112700000 reads so far
2011-05-20 00:04:55,383 - INFO - Processed 112800000 reads so far
2011-05-20 00:05:05,897 - INFO - Processed 112900000 reads so far
2011-05-20 00:05:17,934 - INFO - Processed 113000000 reads so far
2011-05-20 00:05:20,761 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:42990052-63010052
2011-05-20 00:05:31,403 - INFO - Processed 113100000 reads so far
2011-05-20 00:05:42,565 - INFO - Processed 113200000 reads so far
2011-05-20 00:05:54,409 - INFO - Processed 113300000 reads so far
2011-05-20 00:06:10,096 - INFO - Processed 113400000 reads so far
2011-05-20 00:06:20,797 - INFO - Processed 113500000 reads so far
2011-05-20 00:06:31,444 - INFO - Processed 113600000 reads so far
2011-05-20 00:06:42,719 - INFO - Processed 113700000 reads so far
2011-05-20 00:06:55,493 - INFO - Processed 113800000 reads so far
2011-05-20 00:07:04,741 - INFO - Processed 113900000 reads so far
2011-05-20 00:07:15,207 - INFO - Processed 114000000 reads so far
2011-05-20 00:07:27,482 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:62990120-83010120
2011-05-20 00:07:27,812 - INFO - Processed 114100000 reads so far
2011-05-20 00:07:38,532 - INFO - Processed 114200000 reads so far
2011-05-20 00:07:50,516 - INFO - Processed 114300000 reads so far
2011-05-20 00:08:05,568 - INFO - Processed 114400000 reads so far
2011-05-20 00:08:18,205 - INFO - Processed 114500000 reads so far
2011-05-20 00:08:33,785 - INFO - Processed 114600000 reads so far
2011-05-20 00:08:44,559 - INFO - Processed 114700000 reads so far
2011-05-20 00:08:56,992 - INFO - Processed 114800000 reads so far
2011-05-20 00:09:09,554 - INFO - Processed 114900000 reads so far
2011-05-20 00:09:21,552 - INFO - Processed 115000000 reads so far
2011-05-20 00:09:32,436 - INFO - Processed 115100000 reads so far
2011-05-20 00:09:35,930 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:82990125-103010125
2011-05-20 00:09:45,676 - INFO - Processed 115200000 reads so far
2011-05-20 00:09:57,271 - INFO - Processed 115300000 reads so far
2011-05-20 00:10:09,649 - INFO - Processed 115400000 reads so far
2011-05-20 00:10:30,219 - INFO - Processed 115500000 reads so far
2011-05-20 00:10:58,257 - INFO - Processed 115600000 reads so far
2011-05-20 00:11:08,995 - INFO - Processed 115700000 reads so far
2011-05-20 00:11:21,746 - INFO - Processed 115800000 reads so far
2011-05-20 00:11:30,038 - INFO - Processed 115900000 reads so far
2011-05-20 00:11:39,261 - INFO - Processed 116000000 reads so far
2011-05-20 00:11:50,341 - INFO - Processed 116100000 reads so far
2011-05-20 00:12:01,275 - INFO - Processed 116200000 reads so far
2011-05-20 00:12:08,288 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:102990137-123010137
2011-05-20 00:12:27,547 - INFO - Processed 116300000 reads so far
2011-05-20 00:12:37,697 - INFO - Processed 116400000 reads so far
2011-05-20 00:13:00,945 - INFO - Processed 116500000 reads so far
2011-05-20 00:13:09,825 - INFO - Processed 116600000 reads so far
2011-05-20 00:13:18,359 - INFO - Processed 116700000 reads so far
2011-05-20 00:13:26,781 - INFO - Processed 116800000 reads so far
2011-05-20 00:13:36,954 - INFO - Processed 116900000 reads so far
2011-05-20 00:13:45,626 - INFO - Processed 117000000 reads so far
2011-05-20 00:13:54,058 - INFO - Processed 117100000 reads so far
2011-05-20 00:14:02,349 - INFO - Processed 117200000 reads so far
2011-05-20 00:14:10,029 - INFO - Processed 117300000 reads so far
2011-05-20 00:14:23,517 - INFO - Processed 117400000 reads so far
2011-05-20 00:14:32,958 - INFO - Processed 117500000 reads so far
2011-05-20 00:14:42,866 - INFO - Processed 117600000 reads so far
2011-05-20 00:15:00,636 - INFO - Processed 117700000 reads so far
2011-05-20 00:15:16,493 - INFO - Processed 117800000 reads so far
2011-05-20 00:15:27,738 - INFO - Processed 117900000 reads so far
2011-05-20 00:15:37,088 - INFO - Processed 118000000 reads so far
2011-05-20 00:15:49,193 - INFO - Processed 118100000 reads so far
2011-05-20 00:16:00,066 - INFO - Processed 118200000 reads so far
2011-05-20 00:16:12,878 - INFO - Processed 118300000 reads so far
2011-05-20 00:16:16,024 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:122990141-143010141
2011-05-20 00:16:25,010 - INFO - Processed 118400000 reads so far
2011-05-20 00:16:37,750 - INFO - Processed 118500000 reads so far
2011-05-20 00:16:47,093 - INFO - Processed 118600000 reads so far
2011-05-20 00:16:57,316 - INFO - Processed 118700000 reads so far
2011-05-20 00:17:05,688 - INFO - Processed 118800000 reads so far
2011-05-20 00:17:14,548 - INFO - Processed 118900000 reads so far
2011-05-20 00:17:24,705 - INFO - Processed 119000000 reads so far
2011-05-20 00:17:37,231 - INFO - Processed 119100000 reads so far
2011-05-20 00:17:48,032 - INFO - Processed 119200000 reads so far
2011-05-20 00:17:56,913 - INFO - Processed 119300000 reads so far
2011-05-20 00:18:09,964 - INFO - Processed 119400000 reads so far
2011-05-20 00:18:10,977 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:142990202-163010202
2011-05-20 00:18:21,942 - INFO - Processed 119500000 reads so far
2011-05-20 00:18:31,633 - INFO - Processed 119600000 reads so far
2011-05-20 00:18:43,342 - INFO - Processed 119700000 reads so far
2011-05-20 00:18:50,401 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:2990123-23010123
2011-05-20 00:18:55,516 - INFO - Processed 119800000 reads so far
2011-05-20 00:19:11,105 - INFO - Processed 119900000 reads so far
2011-05-20 00:19:24,285 - INFO - Processed 120000000 reads so far
2011-05-20 00:19:34,886 - INFO - Processed 120100000 reads so far
2011-05-20 00:19:47,641 - INFO - Processed 120200000 reads so far
2011-05-20 00:19:57,882 - INFO - Processed 120300000 reads so far
2011-05-20 00:20:07,515 - INFO - Processed 120400000 reads so far
2011-05-20 00:20:18,216 - INFO - Processed 120500000 reads so far
2011-05-20 00:20:27,536 - INFO - Processed 120600000 reads so far
2011-05-20 00:20:39,518 - INFO - Processed 120700000 reads so far
2011-05-20 00:20:42,813 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:22990338-43010338
2011-05-20 00:20:53,957 - INFO - Processed 120800000 reads so far
2011-05-20 00:21:06,042 - INFO - Processed 120900000 reads so far
2011-05-20 00:21:16,989 - INFO - Processed 121000000 reads so far
2011-05-20 00:21:27,721 - INFO - Processed 121100000 reads so far
2011-05-20 00:21:38,993 - INFO - Processed 121200000 reads so far
2011-05-20 00:21:47,722 - INFO - Processed 121300000 reads so far
2011-05-20 00:21:59,375 - INFO - Processed 121400000 reads so far
2011-05-20 00:22:09,705 - INFO - Processed 121500000 reads so far
2011-05-20 00:22:16,728 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:46352106-66372106
2011-05-20 00:22:25,179 - INFO - Processed 121600000 reads so far
2011-05-20 00:22:35,480 - INFO - Processed 121700000 reads so far
2011-05-20 00:22:48,902 - INFO - Processed 121800000 reads so far
2011-05-20 00:22:59,336 - INFO - Processed 121900000 reads so far
2011-05-20 00:23:10,781 - INFO - Processed 122000000 reads so far
2011-05-20 00:23:27,024 - INFO - Processed 122100000 reads so far
2011-05-20 00:23:38,377 - INFO - Processed 122200000 reads so far
2011-05-20 00:23:50,140 - INFO - Processed 122300000 reads so far
2011-05-20 00:23:59,524 - INFO - Processed 122400000 reads so far
2011-05-20 00:24:09,385 - INFO - Processed 122500000 reads so far
2011-05-20 00:24:18,660 - INFO - Processed 122600000 reads so far
2011-05-20 00:24:20,439 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:66352113-86372113
2011-05-20 00:24:29,051 - INFO - Processed 122700000 reads so far
2011-05-20 00:24:39,835 - INFO - Processed 122800000 reads so far
2011-05-20 00:24:51,357 - INFO - Processed 122900000 reads so far
2011-05-20 00:25:00,580 - INFO - Processed 123000000 reads so far
2011-05-20 00:25:09,219 - INFO - Processed 123100000 reads so far
2011-05-20 00:25:18,358 - INFO - Processed 123200000 reads so far
2011-05-20 00:25:29,022 - INFO - Processed 123300000 reads so far
2011-05-20 00:25:38,602 - INFO - Processed 123400000 reads so far
2011-05-20 00:25:51,091 - INFO - Processed 123500000 reads so far
2011-05-20 00:26:03,563 - INFO - Processed 123600000 reads so far
2011-05-20 00:26:15,997 - INFO - Processed 123700000 reads so far
2011-05-20 00:26:16,502 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:86352160-106372160
2011-05-20 00:26:28,850 - INFO - Processed 123800000 reads so far
2011-05-20 00:26:39,881 - INFO - Processed 123900000 reads so far
2011-05-20 00:26:51,504 - INFO - Processed 124000000 reads so far
2011-05-20 00:27:04,046 - INFO - Processed 124100000 reads so far
2011-05-20 00:27:15,929 - INFO - Processed 124200000 reads so far
2011-05-20 00:27:29,585 - INFO - Processed 124300000 reads so far
2011-05-20 00:27:42,182 - INFO - Processed 124400000 reads so far
2011-05-20 00:28:06,786 - INFO - Processed 124500000 reads so far
2011-05-20 00:28:29,086 - INFO - Processed 124600000 reads so far
2011-05-20 00:28:40,914 - INFO - Processed 124700000 reads so far
2011-05-20 00:28:49,882 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:106352161-126372161
2011-05-20 00:28:53,745 - INFO - Processed 124800000 reads so far
2011-05-20 00:29:06,625 - INFO - Processed 124900000 reads so far
2011-05-20 00:29:17,987 - INFO - Processed 125000000 reads so far
2011-05-20 00:29:29,373 - INFO - Processed 125100000 reads so far
2011-05-20 00:29:44,289 - INFO - Processed 125200000 reads so far
2011-05-20 00:29:57,384 - INFO - Processed 125300000 reads so far
2011-05-20 00:30:08,960 - INFO - Processed 125400000 reads so far
2011-05-20 00:30:22,648 - INFO - Processed 125500000 reads so far
2011-05-20 00:30:34,144 - INFO - Processed 125600000 reads so far
2011-05-20 00:30:42,005 - INFO - Processed 125700000 reads so far
2011-05-20 00:30:50,925 - INFO - Processed 125800000 reads so far
2011-05-20 00:30:54,407 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:126352168-146372168
2011-05-20 00:31:01,279 - INFO - Processed 125900000 reads so far
2011-05-20 00:31:09,107 - INFO - Processed 126000000 reads so far
2011-05-20 00:31:19,301 - INFO - Processed 126100000 reads so far
2011-05-20 00:31:33,761 - INFO - Processed 126200000 reads so far
2011-05-20 00:31:45,153 - INFO - Processed 126300000 reads so far
2011-05-20 00:31:56,813 - INFO - Processed 126400000 reads so far
2011-05-20 00:32:08,194 - INFO - Processed 126500000 reads so far
2011-05-20 00:32:20,988 - INFO - Processed 126600000 reads so far
2011-05-20 00:32:30,069 - INFO - Processed 126700000 reads so far
2011-05-20 00:32:40,675 - INFO - Processed 126800000 reads so far
2011-05-20 00:32:49,887 - INFO - Processed 126900000 reads so far
2011-05-20 00:32:51,731 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:146352213-166372213
2011-05-20 00:33:00,572 - INFO - Processed 127000000 reads so far
2011-05-20 00:33:10,355 - INFO - Processed 127100000 reads so far
2011-05-20 00:33:20,391 - INFO - Processed 127200000 reads so far
2011-05-20 00:33:27,971 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7_random:0-20010213
2011-05-20 00:33:29,314 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:2990049-23010049
2011-05-20 00:33:30,817 - INFO - Processed 127300000 reads so far
2011-05-20 00:33:41,097 - INFO - Processed 127400000 reads so far
2011-05-20 00:33:50,815 - INFO - Processed 127500000 reads so far
2011-05-20 00:34:02,296 - INFO - Processed 127600000 reads so far
2011-05-20 00:34:12,273 - INFO - Processed 127700000 reads so far
2011-05-20 00:34:23,145 - INFO - Processed 127800000 reads so far
2011-05-20 00:34:38,035 - INFO - Processed 127900000 reads so far
2011-05-20 00:34:49,757 - INFO - Processed 128000000 reads so far
2011-05-20 00:35:02,030 - INFO - Processed 128100000 reads so far
2011-05-20 00:35:13,389 - INFO - Processed 128200000 reads so far
2011-05-20 00:35:23,017 - INFO - Processed 128300000 reads so far
2011-05-20 00:35:31,348 - INFO - Processed 128400000 reads so far
2011-05-20 00:35:40,449 - INFO - Processed 128500000 reads so far
2011-05-20 00:35:40,498 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:22990091-43010091
2011-05-20 00:35:50,482 - INFO - Processed 128600000 reads so far
2011-05-20 00:35:59,211 - INFO - Processed 128700000 reads so far
2011-05-20 00:36:09,133 - INFO - Processed 128800000 reads so far
2011-05-20 00:36:18,195 - INFO - Processed 128900000 reads so far
2011-05-20 00:36:30,440 - INFO - Processed 129000000 reads so far
2011-05-20 00:36:43,011 - INFO - Processed 129100000 reads so far
2011-05-20 00:36:54,907 - INFO - Processed 129200000 reads so far
2011-05-20 00:37:06,310 - INFO - Processed 129300000 reads so far
2011-05-20 00:37:18,420 - INFO - Processed 129400000 reads so far
2011-05-20 00:37:32,661 - INFO - Processed 129500000 reads so far
2011-05-20 00:37:37,365 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:42990095-63010095
2011-05-20 00:37:45,068 - INFO - Processed 129600000 reads so far
2011-05-20 00:37:54,887 - INFO - Processed 129700000 reads so far
2011-05-20 00:38:05,742 - INFO - Processed 129800000 reads so far
2011-05-20 00:38:15,794 - INFO - Processed 129900000 reads so far
2011-05-20 00:38:24,515 - INFO - Processed 130000000 reads so far
2011-05-20 00:38:35,281 - INFO - Processed 130100000 reads so far
2011-05-20 00:38:44,146 - INFO - Processed 130200000 reads so far
2011-05-20 00:38:54,831 - INFO - Processed 130300000 reads so far
2011-05-20 00:39:04,902 - INFO - Processed 130400000 reads so far
2011-05-20 00:39:15,162 - INFO - Processed 130500000 reads so far
2011-05-20 00:39:15,269 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:62990109-83010109
2011-05-20 00:39:25,463 - INFO - Processed 130600000 reads so far
2011-05-20 00:39:34,018 - INFO - Processed 130700000 reads so far
2011-05-20 00:39:45,624 - INFO - Processed 130800000 reads so far
2011-05-20 00:39:58,566 - INFO - Processed 130900000 reads so far
2011-05-20 00:40:09,026 - INFO - Processed 131000000 reads so far
2011-05-20 00:40:20,769 - INFO - Processed 131100000 reads so far
2011-05-20 00:40:30,382 - INFO - Processed 131200000 reads so far
2011-05-20 00:40:39,625 - INFO - Processed 131300000 reads so far
2011-05-20 00:40:49,108 - INFO - Processed 131400000 reads so far
2011-05-20 00:41:00,528 - INFO - Processed 131500000 reads so far
2011-05-20 00:41:10,233 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:82990153-103010153
2011-05-20 00:41:12,302 - INFO - Processed 131600000 reads so far
2011-05-20 00:41:20,723 - INFO - Processed 131700000 reads so far
2011-05-20 00:41:29,506 - INFO - Processed 131800000 reads so far
2011-05-20 00:41:41,501 - INFO - Processed 131900000 reads so far
2011-05-20 00:41:50,411 - INFO - Processed 132000000 reads so far
2011-05-20 00:41:59,733 - INFO - Processed 132100000 reads so far
2011-05-20 00:42:08,392 - INFO - Processed 132200000 reads so far
2011-05-20 00:42:18,394 - INFO - Processed 132300000 reads so far
2011-05-20 00:42:30,036 - INFO - Processed 132400000 reads so far
2011-05-20 00:42:38,801 - INFO - Processed 132500000 reads so far
2011-05-20 00:42:50,104 - INFO - Processed 132600000 reads so far
2011-05-20 00:42:53,995 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:102990191-123010191
2011-05-20 00:43:01,641 - INFO - Processed 132700000 reads so far
2011-05-20 00:43:12,785 - INFO - Processed 132800000 reads so far
2011-05-20 00:43:25,558 - INFO - Processed 132900000 reads so far
2011-05-20 00:43:36,633 - INFO - Processed 133000000 reads so far
2011-05-20 00:43:44,514 - INFO - Processed 133100000 reads so far
2011-05-20 00:43:52,350 - INFO - Processed 133200000 reads so far
2011-05-20 00:44:04,753 - INFO - Processed 133300000 reads so far
2011-05-20 00:44:14,809 - INFO - Processed 133400000 reads so far
2011-05-20 00:44:23,437 - INFO - Processed 133500000 reads so far
2011-05-20 00:44:36,222 - INFO - Processed 133600000 reads so far
2011-05-20 00:44:44,053 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:122990229-143010229
2011-05-20 00:44:44,978 - INFO - Processed 133700000 reads so far
2011-05-20 00:44:52,795 - INFO - Processed 133800000 reads so far
2011-05-20 00:45:02,068 - INFO - Processed 133900000 reads so far
2011-05-20 00:45:13,545 - INFO - Processed 134000000 reads so far
2011-05-20 00:45:21,351 - INFO - Processed 134100000 reads so far
2011-05-20 00:45:29,265 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8_random:0-20010012
2011-05-20 00:45:30,988 - INFO - Processed 134200000 reads so far
2011-05-20 00:45:39,314 - INFO - Processed 134300000 reads so far
2011-05-20 00:45:44,823 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:2989958-23009958
2011-05-20 00:45:48,078 - INFO - Processed 134400000 reads so far
2011-05-20 00:45:55,902 - INFO - Processed 134500000 reads so far
2011-05-20 00:46:02,910 - INFO - Processed 134600000 reads so far
2011-05-20 00:46:11,130 - INFO - Processed 134700000 reads so far
2011-05-20 00:46:19,893 - INFO - Processed 134800000 reads so far
2011-05-20 00:46:27,269 - INFO - Processed 134900000 reads so far
2011-05-20 00:46:35,732 - INFO - Processed 135000000 reads so far
2011-05-20 00:46:43,214 - INFO - Processed 135100000 reads so far
2011-05-20 00:46:51,165 - INFO - Processed 135200000 reads so far
2011-05-20 00:46:58,325 - INFO - Processed 135300000 reads so far
2011-05-20 00:47:05,705 - INFO - Processed 135400000 reads so far
2011-05-20 00:47:13,142 - INFO - Processed 135500000 reads so far
2011-05-20 00:47:21,621 - INFO - Processed 135600000 reads so far
2011-05-20 00:47:29,622 - INFO - Processed 135700000 reads so far
2011-05-20 00:47:38,636 - INFO - Processed 135800000 reads so far
2011-05-20 00:47:45,868 - INFO - Processed 135900000 reads so far
2011-05-20 00:47:53,909 - INFO - Processed 136000000 reads so far
2011-05-20 00:48:03,399 - INFO - Processed 136100000 reads so far
2011-05-20 00:48:12,761 - INFO - Processed 136200000 reads so far
2011-05-20 00:48:21,337 - INFO - Processed 136300000 reads so far
2011-05-20 00:48:31,040 - INFO - Processed 136400000 reads so far
2011-05-20 00:48:38,680 - INFO - Processed 136500000 reads so far
2011-05-20 00:48:47,925 - INFO - Processed 136600000 reads so far
2011-05-20 00:48:55,649 - INFO - Processed 136700000 reads so far
2011-05-20 00:49:05,081 - INFO - Processed 136800000 reads so far
2011-05-20 00:49:15,547 - INFO - Processed 136900000 reads so far
2011-05-20 00:49:25,865 - INFO - Processed 137000000 reads so far
2011-05-20 00:49:33,162 - INFO - Processed 137100000 reads so far
2011-05-20 00:49:42,449 - INFO - Processed 137200000 reads so far
2011-05-20 00:49:50,470 - INFO - Processed 137300000 reads so far
2011-05-20 00:49:59,457 - INFO - Processed 137400000 reads so far
2011-05-20 00:50:09,030 - INFO - Processed 137500000 reads so far
2011-05-20 00:50:24,970 - INFO - Processed 137600000 reads so far
2011-05-20 00:50:37,773 - INFO - Processed 137700000 reads so far
2011-05-20 00:50:47,471 - INFO - Processed 137800000 reads so far
2011-05-20 00:50:56,284 - INFO - Processed 137900000 reads so far
2011-05-20 00:51:05,436 - INFO - Processed 138000000 reads so far
2011-05-20 00:51:16,063 - INFO - Processed 138100000 reads so far
2011-05-20 00:51:26,027 - INFO - Processed 138200000 reads so far
2011-05-20 00:51:36,658 - INFO - Processed 138300000 reads so far
2011-05-20 00:51:46,310 - INFO - Processed 138400000 reads so far
2011-05-20 00:51:57,337 - INFO - Processed 138500000 reads so far
2011-05-20 00:52:07,771 - INFO - Processed 138600000 reads so far
2011-05-20 00:52:16,972 - INFO - Processed 138700000 reads so far
2011-05-20 00:52:29,046 - INFO - Processed 138800000 reads so far
2011-05-20 00:52:38,318 - INFO - Processed 138900000 reads so far
2011-05-20 00:52:46,680 - INFO - Processed 139000000 reads so far
2011-05-20 00:52:54,394 - INFO - Processed 139100000 reads so far
2011-05-20 00:53:02,770 - INFO - Processed 139200000 reads so far
2011-05-20 00:53:10,869 - INFO - Processed 139300000 reads so far
2011-05-20 00:53:18,654 - INFO - Processed 139400000 reads so far
2011-05-20 00:53:26,284 - INFO - Processed 139500000 reads so far
2011-05-20 00:53:34,262 - INFO - Processed 139600000 reads so far
2011-05-20 00:53:43,206 - INFO - Processed 139700000 reads so far
2011-05-20 00:53:51,238 - INFO - Processed 139800000 reads so far
2011-05-20 00:53:58,817 - INFO - Processed 139900000 reads so far
2011-05-20 00:54:05,521 - INFO - Processed 140000000 reads so far
2011-05-20 00:54:15,040 - INFO - Processed 140100000 reads so far
2011-05-20 00:54:22,280 - INFO - Processed 140200000 reads so far
2011-05-20 00:54:29,135 - INFO - Processed 140300000 reads so far
2011-05-20 00:54:35,436 - INFO - Processed 140400000 reads so far
2011-05-20 00:54:44,126 - INFO - Processed 140500000 reads so far
2011-05-20 00:54:50,790 - INFO - Processed 140600000 reads so far
2011-05-20 00:54:58,426 - INFO - Processed 140700000 reads so far
2011-05-20 00:55:05,244 - INFO - Processed 140800000 reads so far
2011-05-20 00:55:11,497 - INFO - Processed 140900000 reads so far
2011-05-20 00:55:22,313 - INFO - Processed 141000000 reads so far
2011-05-20 00:55:29,362 - INFO - Processed 141100000 reads so far
2011-05-20 00:55:38,736 - INFO - Processed 141200000 reads so far
2011-05-20 00:55:46,631 - INFO - Processed 141300000 reads so far
2011-05-20 00:55:55,304 - INFO - Processed 141400000 reads so far
2011-05-20 00:56:03,827 - INFO - Processed 141500000 reads so far
2011-05-20 00:56:13,770 - INFO - Processed 141600000 reads so far
2011-05-20 00:56:20,354 - INFO - Processed 141700000 reads so far
2011-05-20 00:56:28,449 - INFO - Processed 141800000 reads so far
2011-05-20 00:56:36,566 - INFO - Processed 141900000 reads so far
2011-05-20 00:56:44,724 - INFO - Processed 142000000 reads so far
2011-05-20 00:56:52,753 - INFO - Processed 142100000 reads so far
2011-05-20 00:57:03,117 - INFO - Processed 142200000 reads so far
2011-05-20 00:57:11,140 - INFO - Processed 142300000 reads so far
2011-05-20 00:57:20,485 - INFO - Processed 142400000 reads so far
2011-05-20 00:57:31,194 - INFO - Processed 142500000 reads so far
2011-05-20 00:57:41,219 - INFO - Processed 142600000 reads so far
2011-05-20 00:57:50,309 - INFO - Processed 142700000 reads so far
2011-05-20 00:58:00,456 - INFO - Processed 142800000 reads so far
2011-05-20 00:58:13,929 - INFO - Processed 142900000 reads so far
2011-05-20 00:58:25,376 - INFO - Processed 143000000 reads so far
2011-05-20 00:58:35,866 - INFO - Processed 143100000 reads so far
2011-05-20 00:58:47,283 - INFO - Processed 143200000 reads so far
2011-05-20 00:58:55,660 - INFO - Processed 143300000 reads so far
2011-05-20 00:59:09,558 - INFO - Processed 143400000 reads so far
2011-05-20 00:59:10,003 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:22990007-43010007
2011-05-20 00:59:17,992 - INFO - Processed 143500000 reads so far
2011-05-20 00:59:29,148 - INFO - Processed 143600000 reads so far
2011-05-20 00:59:38,340 - INFO - Processed 143700000 reads so far
2011-05-20 00:59:49,851 - INFO - Processed 143800000 reads so far
2011-05-20 01:00:03,017 - INFO - Processed 143900000 reads so far
2011-05-20 01:00:17,749 - INFO - Processed 144000000 reads so far
2011-05-20 01:00:29,335 - INFO - Processed 144100000 reads so far
2011-05-20 01:00:39,527 - INFO - Processed 144200000 reads so far
2011-05-20 01:00:54,086 - INFO - Processed 144300000 reads so far
2011-05-20 01:01:05,360 - INFO - Processed 144400000 reads so far
2011-05-20 01:01:16,692 - INFO - Processed 144500000 reads so far
2011-05-20 01:01:32,419 - INFO - Processed 144600000 reads so far
2011-05-20 01:01:35,640 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:42990026-63010026
2011-05-20 01:01:42,926 - INFO - Processed 144700000 reads so far
2011-05-20 01:01:52,279 - INFO - Processed 144800000 reads so far
2011-05-20 01:02:01,274 - INFO - Processed 144900000 reads so far
2011-05-20 01:02:13,679 - INFO - Processed 145000000 reads so far
2011-05-20 01:02:24,922 - INFO - Processed 145100000 reads so far
2011-05-20 01:02:34,832 - INFO - Processed 145200000 reads so far
2011-05-20 01:02:51,412 - INFO - Processed 145300000 reads so far
2011-05-20 01:02:59,963 - INFO - Processed 145400000 reads so far
2011-05-20 01:03:11,009 - INFO - Processed 145500000 reads so far
2011-05-20 01:03:23,055 - INFO - Processed 145600000 reads so far
2011-05-20 01:03:32,112 - INFO - Processed 145700000 reads so far
2011-05-20 01:03:32,273 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:62990030-83010030
2011-05-20 01:03:40,765 - INFO - Processed 145800000 reads so far
2011-05-20 01:03:50,222 - INFO - Processed 145900000 reads so far
2011-05-20 01:03:59,758 - INFO - Processed 146000000 reads so far
2011-05-20 01:04:07,612 - INFO - Processed 146100000 reads so far
2011-05-20 01:04:15,779 - INFO - Processed 146200000 reads so far
2011-05-20 01:04:23,640 - INFO - Processed 146300000 reads so far
2011-05-20 01:04:34,016 - INFO - Processed 146400000 reads so far
2011-05-20 01:04:45,859 - INFO - Processed 146500000 reads so far
2011-05-20 01:04:55,892 - INFO - Processed 146600000 reads so far
2011-05-20 01:05:05,838 - INFO - Processed 146700000 reads so far
2011-05-20 01:05:11,869 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:82990048-103010048
2011-05-20 01:05:18,434 - INFO - Processed 146800000 reads so far
2011-05-20 01:05:29,225 - INFO - Processed 146900000 reads so far
2011-05-20 01:05:39,633 - INFO - Processed 147000000 reads so far
2011-05-20 01:05:49,631 - INFO - Processed 147100000 reads so far
2011-05-20 01:06:02,243 - INFO - Processed 147200000 reads so far
2011-05-20 01:06:13,421 - INFO - Processed 147300000 reads so far
2011-05-20 01:06:26,141 - INFO - Processed 147400000 reads so far
2011-05-20 01:06:38,890 - INFO - Processed 147500000 reads so far
2011-05-20 01:06:51,747 - INFO - Processed 147600000 reads so far
2011-05-20 01:07:04,048 - INFO - Processed 147700000 reads so far
2011-05-20 01:07:16,641 - INFO - Processed 147800000 reads so far
2011-05-20 01:07:19,150 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:102990053-123010053
2011-05-20 01:07:28,153 - INFO - Processed 147900000 reads so far
2011-05-20 01:07:39,932 - INFO - Processed 148000000 reads so far
2011-05-20 01:07:52,499 - INFO - Processed 148100000 reads so far
2011-05-20 01:08:04,374 - INFO - Processed 148200000 reads so far
2011-05-20 01:08:15,937 - INFO - Processed 148300000 reads so far
2011-05-20 01:08:28,132 - INFO - Processed 148400000 reads so far
2011-05-20 01:08:40,761 - INFO - Processed 148500000 reads so far
2011-05-20 01:08:51,998 - INFO - Processed 148600000 reads so far
2011-05-20 01:09:03,776 - INFO - Processed 148700000 reads so far
2011-05-20 01:09:11,803 - INFO - Processed 148800000 reads so far
2011-05-20 01:09:23,162 - INFO - Processed 148900000 reads so far
2011-05-20 01:09:23,265 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:122990056-143010056
2011-05-20 01:09:31,386 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9_random:0-20010037
2011-05-20 01:09:35,911 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrM:0-20010000
2011-05-20 01:09:36,356 - INFO - Processed 149000000 reads so far
2011-05-20 01:09:42,329 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrUn_random:0-20010000
2011-05-20 01:09:43,152 - INFO - Processed 149100000 reads so far
2011-05-20 01:10:24,631 - INFO - Processed 149200000 reads so far
2011-05-20 01:11:11,029 - INFO - Processed 149300000 reads so far
2011-05-20 01:12:24,954 - INFO - Processed 149400000 reads so far
2011-05-20 01:13:05,446 - INFO - Processed 149500000 reads so far
2011-05-20 01:13:14,413 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:2990055-23010055
2011-05-20 01:13:18,363 - INFO - Processed 149600000 reads so far
2011-05-20 01:13:30,976 - INFO - Processed 149700000 reads so far
2011-05-20 01:13:38,301 - INFO - Processed 149800000 reads so far
2011-05-20 01:13:51,297 - INFO - Processed 149900000 reads so far
2011-05-20 01:14:02,335 - INFO - Processed 150000000 reads so far
2011-05-20 01:14:12,787 - INFO - Processed 150100000 reads so far
2011-05-20 01:14:22,903 - INFO - Processed 150200000 reads so far
2011-05-20 01:14:32,237 - INFO - Processed 150300000 reads so far
2011-05-20 01:14:40,471 - INFO - Processed 150400000 reads so far
2011-05-20 01:14:48,719 - INFO - Processed 150500000 reads so far
2011-05-20 01:14:55,978 - INFO - Processed 150600000 reads so far
2011-05-20 01:15:04,728 - INFO - Processed 150700000 reads so far
2011-05-20 01:15:12,536 - INFO - Processed 150800000 reads so far
2011-05-20 01:15:13,800 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:22990083-43010083
2011-05-20 01:15:23,676 - INFO - Processed 150900000 reads so far
2011-05-20 01:15:34,695 - INFO - Processed 151000000 reads so far
2011-05-20 01:15:43,738 - INFO - Processed 151100000 reads so far
2011-05-20 01:15:51,987 - INFO - Processed 151200000 reads so far
2011-05-20 01:16:00,180 - INFO - Processed 151300000 reads so far
2011-05-20 01:16:08,642 - INFO - Processed 151400000 reads so far
2011-05-20 01:16:16,472 - INFO - Processed 151500000 reads so far
2011-05-20 01:16:26,498 - INFO - Processed 151600000 reads so far
2011-05-20 01:16:39,909 - INFO - Processed 151700000 reads so far
2011-05-20 01:16:48,540 - INFO - Processed 151800000 reads so far
2011-05-20 01:16:56,405 - INFO - Processed 151900000 reads so far
2011-05-20 01:17:05,342 - INFO - Processed 152000000 reads so far
2011-05-20 01:17:12,254 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:42990103-63010103
2011-05-20 01:17:15,796 - INFO - Processed 152100000 reads so far
2011-05-20 01:17:24,914 - INFO - Processed 152200000 reads so far
2011-05-20 01:17:33,408 - INFO - Processed 152300000 reads so far
2011-05-20 01:17:45,343 - INFO - Processed 152400000 reads so far
2011-05-20 01:17:54,565 - INFO - Processed 152500000 reads so far
2011-05-20 01:18:04,478 - INFO - Processed 152600000 reads so far
2011-05-20 01:18:12,564 - INFO - Processed 152700000 reads so far
2011-05-20 01:18:21,821 - INFO - Processed 152800000 reads so far
2011-05-20 01:18:31,620 - INFO - Processed 152900000 reads so far
2011-05-20 01:18:41,149 - INFO - Processed 153000000 reads so far
2011-05-20 01:18:51,330 - INFO - Processed 153100000 reads so far
2011-05-20 01:18:56,595 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:62990111-83010111
2011-05-20 01:19:01,853 - INFO - Processed 153200000 reads so far
2011-05-20 01:19:10,546 - INFO - Processed 153300000 reads so far
2011-05-20 01:19:17,733 - INFO - Processed 153400000 reads so far
2011-05-20 01:19:28,011 - INFO - Processed 153500000 reads so far
2011-05-20 01:19:37,534 - INFO - Processed 153600000 reads so far
2011-05-20 01:19:46,517 - INFO - Processed 153700000 reads so far
2011-05-20 01:20:00,204 - INFO - Processed 153800000 reads so far
2011-05-20 01:20:10,533 - INFO - Processed 153900000 reads so far
2011-05-20 01:20:19,299 - INFO - Processed 154000000 reads so far
2011-05-20 01:20:30,375 - INFO - Processed 154100000 reads so far
2011-05-20 01:20:40,524 - INFO - Processed 154200000 reads so far
2011-05-20 01:20:44,823 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:82990138-103010138
2011-05-20 01:20:52,139 - INFO - Processed 154300000 reads so far
2011-05-20 01:21:01,494 - INFO - Processed 154400000 reads so far
2011-05-20 01:21:11,438 - INFO - Processed 154500000 reads so far
2011-05-20 01:21:21,187 - INFO - Processed 154600000 reads so far
2011-05-20 01:21:34,315 - INFO - Processed 154700000 reads so far
2011-05-20 01:21:43,487 - INFO - Processed 154800000 reads so far
2011-05-20 01:21:52,491 - INFO - Processed 154900000 reads so far
2011-05-20 01:22:01,972 - INFO - Processed 155000000 reads so far
2011-05-20 01:22:13,408 - INFO - Processed 155100000 reads so far
2011-05-20 01:22:23,654 - INFO - Processed 155200000 reads so far
2011-05-20 01:22:32,979 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:102990139-123010139
2011-05-20 01:22:33,937 - INFO - Processed 155300000 reads so far
2011-05-20 01:22:46,163 - INFO - Processed 155400000 reads so far
2011-05-20 01:22:54,417 - INFO - Processed 155500000 reads so far
2011-05-20 01:23:03,445 - INFO - Processed 155600000 reads so far
2011-05-20 01:23:11,154 - INFO - Processed 155700000 reads so far
2011-05-20 01:23:23,649 - INFO - Processed 155800000 reads so far
2011-05-20 01:23:33,222 - INFO - Processed 155900000 reads so far
2011-05-20 01:23:43,111 - INFO - Processed 156000000 reads so far
2011-05-20 01:23:53,753 - INFO - Processed 156100000 reads so far
2011-05-20 01:24:04,398 - INFO - Processed 156200000 reads so far
2011-05-20 01:24:12,904 - INFO - Processed 156300000 reads so far
2011-05-20 01:24:13,994 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:122990140-143010140
2011-05-20 01:24:22,686 - INFO - Processed 156400000 reads so far
2011-05-20 01:24:36,296 - INFO - Processed 156500000 reads so far
2011-05-20 01:24:46,706 - INFO - Processed 156600000 reads so far
2011-05-20 01:24:55,616 - INFO - Processed 156700000 reads so far
2011-05-20 01:25:05,177 - INFO - Processed 156800000 reads so far
2011-05-20 01:25:15,435 - INFO - Processed 156900000 reads so far
2011-05-20 01:25:25,478 - INFO - Processed 157000000 reads so far
2011-05-20 01:25:35,904 - INFO - Processed 157100000 reads so far
2011-05-20 01:25:43,867 - INFO - Processed 157200000 reads so far
2011-05-20 01:25:51,765 - INFO - Processed 157300000 reads so far
2011-05-20 01:26:00,293 - INFO - Processed 157400000 reads so far
2011-05-20 01:26:04,985 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:142990142-163010142
2011-05-20 01:26:08,786 - INFO - Processed 157500000 reads so far
2011-05-20 01:26:16,981 - INFO - Processed 157600000 reads so far
2011-05-20 01:26:28,451 - INFO - Processed 157700000 reads so far
2011-05-20 01:26:40,120 - INFO - Processed 157800000 reads so far
2011-05-20 01:26:51,218 - INFO - Processed 157900000 reads so far
2011-05-20 01:27:00,789 - INFO - Processed 158000000 reads so far
2011-05-20 01:27:13,070 - INFO - Processed 158100000 reads so far
2011-05-20 01:27:26,365 - INFO - Processed 158200000 reads so far
2011-05-20 01:27:36,856 - INFO - Processed 158300000 reads so far
2011-05-20 01:27:46,266 - INFO - Processed 158400000 reads so far
2011-05-20 01:27:57,798 - INFO - Processed 158500000 reads so far
2011-05-20 01:27:58,174 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:162990148-183010148
2011-05-20 01:28:08,844 - INFO - Processed 158600000 reads so far
2011-05-20 01:28:20,228 - INFO - Processed 158700000 reads so far
2011-05-20 01:28:27,281 - INFO - Processed 158800000 reads so far
2011-05-20 01:28:27,908 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX_random:0-20010000
2011-05-20 01:28:38,527 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY:0-20014274
2011-05-20 01:28:39,399 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:0-20016984
2011-05-20 01:28:40,369 - INFO - Processed 158900000 reads so far
2011-05-20 01:28:41,609 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:20034823-40054823
2011-05-20 01:28:42,826 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:40042069-60062069
2011-05-20 01:28:46,868 - INFO - Processed 159000000 reads so far
2011-05-20 01:28:52,684 - INFO - Processed 159100000 reads so far
2011-05-20 01:28:56,317 - INFO - Processed 159200000 reads so far
2011-05-20 01:28:59,490 - INFO - Processed 159300000 reads so far
2011-05-20 01:29:03,128 - INFO - Processed 159400000 reads so far
2011-05-20 01:29:07,979 - INFO - Processed 159500000 reads so far
2011-05-20 01:29:11,280 - INFO - Processed 159600000 reads so far
2011-05-20 01:29:15,499 - INFO - Processed 159700000 reads so far
2011-05-20 01:29:19,687 - INFO - Processed 159800000 reads so far
2011-05-20 01:29:23,861 - INFO - Processed 159900000 reads so far
2011-05-20 01:29:28,359 - INFO - Processed 160000000 reads so far
2011-05-20 01:29:32,760 - INFO - Processed 160100000 reads so far
2011-05-20 01:29:37,176 - INFO - Processed 160200000 reads so far
2011-05-20 01:29:42,164 - INFO - Processed 160300000 reads so far
2011-05-20 01:29:46,207 - INFO - Processed 160400000 reads so far
2011-05-20 01:29:49,590 - INFO - Processed 160500000 reads so far
2011-05-20 01:29:53,765 - INFO - Processed 160600000 reads so far
2011-05-20 01:29:58,947 - INFO - Processed 160700000 reads so far
2011-05-20 01:30:03,853 - INFO - Processed 160800000 reads so far
2011-05-20 01:30:08,025 - INFO - Processed 160900000 reads so far
2011-05-20 01:30:12,137 - INFO - Processed 161000000 reads so far
2011-05-20 01:30:16,119 - INFO - Finished loading data. Outputting QC metrics
2011-05-20 01:30:39,704 - INFO - Finished outputting QC metrics
2011-05-20 01:30:39,803 - INFO - Finished generating QC metrics