2011-05-19 15:51:38,944 - INFO - Generating QC metrics for BAM File ['WTCHG_12344.bam']
2011-05-19 15:51:38,945 - INFO - Output will go to WTCHG_12344.qc.txt.tmp
2011-05-19 15:51:38,945 - INFO - Reading GC Map from file /data/Genomes/gcMap/Mouse37.gcMap.gz
2011-05-19 15:54:55,860 - INFO - Finished reading GC Map
2011-05-19 15:54:55,860 - INFO - Reading CDS from exon definition file /data/Genomes/annotation/Mouse37.refGene.txt.gz
2011-05-19 15:54:58,824 - INFO - Read 382138 exons (33804740 nucleotides) for 32 chromosomes
2011-05-19 15:54:58,825 - INFO - Computing coverage cut-off
2011-05-19 15:54:58,825 - INFO - Retrieving BAM file coverage info from samtools pileup
2011-05-19 15:55:03,544 - INFO - Processed 1000000 pile-up sites
2011-05-19 15:55:08,187 - INFO - Processed 2000000 pile-up sites
2011-05-19 15:55:12,790 - INFO - Processed 3000000 pile-up sites
2011-05-19 15:55:16,753 - INFO - Processed 4000000 pile-up sites
2011-05-19 15:55:20,381 - INFO - Processed 5000000 pile-up sites
2011-05-19 15:55:25,119 - INFO - Processed 6000000 pile-up sites
2011-05-19 15:55:30,128 - INFO - Processed 7000000 pile-up sites
2011-05-19 15:55:34,518 - INFO - Processed 8000000 pile-up sites
2011-05-19 15:55:39,619 - INFO - Processed 9000000 pile-up sites
2011-05-19 15:55:44,425 - INFO - Processed 10000000 pile-up sites
2011-05-19 15:55:49,175 - INFO - Processed 11000000 pile-up sites
2011-05-19 15:55:54,022 - INFO - Processed 12000000 pile-up sites
2011-05-19 15:55:58,960 - INFO - Processed 13000000 pile-up sites
2011-05-19 15:56:03,309 - INFO - Processed 14000000 pile-up sites
2011-05-19 15:56:09,370 - INFO - Processed 15000000 pile-up sites
2011-05-19 15:56:15,235 - INFO - Processed 16000000 pile-up sites
2011-05-19 15:56:21,978 - INFO - Processed 17000000 pile-up sites
2011-05-19 15:56:26,724 - INFO - Processed 18000000 pile-up sites
2011-05-19 15:56:31,619 - INFO - Processed 19000000 pile-up sites
2011-05-19 15:56:36,618 - INFO - Processed 20000000 pile-up sites
2011-05-19 15:56:41,412 - INFO - Processed 21000000 pile-up sites
2011-05-19 15:56:48,563 - INFO - Processed 22000000 pile-up sites
2011-05-19 15:56:53,014 - INFO - Processed 23000000 pile-up sites
2011-05-19 15:56:57,368 - INFO - Processed 24000000 pile-up sites
2011-05-19 15:57:01,719 - INFO - Processed 25000000 pile-up sites
2011-05-19 15:57:06,070 - INFO - Processed 26000000 pile-up sites
2011-05-19 15:57:11,371 - INFO - Processed 27000000 pile-up sites
2011-05-19 15:57:16,299 - INFO - Processed 28000000 pile-up sites
2011-05-19 15:57:20,940 - INFO - Processed 29000000 pile-up sites
2011-05-19 15:57:25,889 - INFO - Processed 30000000 pile-up sites
2011-05-19 15:57:30,646 - INFO - Processed 31000000 pile-up sites
2011-05-19 15:57:35,524 - INFO - Processed 32000000 pile-up sites
2011-05-19 15:57:40,261 - INFO - Processed 33000000 pile-up sites
2011-05-19 15:57:44,984 - INFO - Processed 34000000 pile-up sites
2011-05-19 15:57:49,705 - INFO - Processed 35000000 pile-up sites
2011-05-19 15:57:52,789 - INFO - Finished processing pile-up on 35651090 sites (200000001 nucleotides)
2011-05-19 15:57:52,789 - INFO - Coverage cut-off value is 20
2011-05-19 15:57:52,790 - INFO - Loading data into QC data manager
2011-05-19 15:57:52,974 - WARNING - Found RG tag 'SM' (value: 329) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:52,974 - WARNING - Found RG tag 'ID' (value: WTCHG_12344) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:52,974 - WARNING - Found RG tag 'SM' (value: 329) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:52,974 - WARNING - Found RG tag 'ID' (value: WTCHG_12344) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:52,974 - WARNING - Found RG tag 'SM' (value: 329) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:52,975 - WARNING - Found RG tag 'ID' (value: WTCHG_12344) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:52,975 - WARNING - Found RG tag 'SM' (value: 329) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:52,975 - WARNING - Found RG tag 'ID' (value: WTCHG_12344) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:53,026 - WARNING - Found RG tag 'SM' (value: 329) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:53,026 - WARNING - Found RG tag 'ID' (value: WTCHG_12344) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:53,027 - WARNING - Found RG tag 'SM' (value: 329) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:53,027 - WARNING - Found RG tag 'ID' (value: WTCHG_12344) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:53,027 - WARNING - Found RG tag 'SM' (value: 329) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:53,027 - WARNING - Found RG tag 'ID' (value: WTCHG_12344) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:53,027 - WARNING - Found RG tag 'SM' (value: 329) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:53,027 - WARNING - Found RG tag 'ID' (value: WTCHG_12344) duplicated in CO field (value: 4634/10) -- ignoring CO value
2011-05-19 15:57:53,035 - INFO - Reading data from BAM file WTCHG_12344.bam. All reads in file will be read
2011-05-19 15:57:53,077 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:2990067-23010067
2011-05-19 15:58:04,591 - INFO - Processed 100000 reads so far
2011-05-19 15:58:15,707 - INFO - Processed 200000 reads so far
2011-05-19 15:58:26,714 - INFO - Processed 300000 reads so far
2011-05-19 15:58:37,674 - INFO - Processed 400000 reads so far
2011-05-19 15:58:48,637 - INFO - Processed 500000 reads so far
2011-05-19 15:58:59,655 - INFO - Processed 600000 reads so far
2011-05-19 15:59:10,976 - INFO - Processed 700000 reads so far
2011-05-19 15:59:22,123 - INFO - Processed 800000 reads so far
2011-05-19 15:59:33,255 - INFO - Processed 900000 reads so far
2011-05-19 15:59:44,375 - INFO - Processed 1000000 reads so far
2011-05-19 15:59:54,464 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:22990157-43010157
2011-05-19 15:59:55,395 - INFO - Processed 1100000 reads so far
2011-05-19 16:00:06,452 - INFO - Processed 1200000 reads so far
2011-05-19 16:00:17,534 - INFO - Processed 1300000 reads so far
2011-05-19 16:00:28,596 - INFO - Processed 1400000 reads so far
2011-05-19 16:00:38,848 - INFO - Processed 1500000 reads so far
2011-05-19 16:00:49,517 - INFO - Processed 1600000 reads so far
2011-05-19 16:01:01,744 - INFO - Processed 1700000 reads so far
2011-05-19 16:01:12,915 - INFO - Processed 1800000 reads so far
2011-05-19 16:01:24,584 - INFO - Processed 1900000 reads so far
2011-05-19 16:01:38,185 - INFO - Processed 2000000 reads so far
2011-05-19 16:01:49,773 - INFO - Processed 2100000 reads so far
2011-05-19 16:01:57,980 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:42990164-63010164
2011-05-19 16:02:00,900 - INFO - Processed 2200000 reads so far
2011-05-19 16:02:10,725 - INFO - Processed 2300000 reads so far
2011-05-19 16:02:21,482 - INFO - Processed 2400000 reads so far
2011-05-19 16:02:33,695 - INFO - Processed 2500000 reads so far
2011-05-19 16:02:45,689 - INFO - Processed 2600000 reads so far
2011-05-19 16:02:57,259 - INFO - Processed 2700000 reads so far
2011-05-19 16:03:09,249 - INFO - Processed 2800000 reads so far
2011-05-19 16:03:20,808 - INFO - Processed 2900000 reads so far
2011-05-19 16:03:33,079 - INFO - Processed 3000000 reads so far
2011-05-19 16:03:44,546 - INFO - Processed 3100000 reads so far
2011-05-19 16:03:57,196 - INFO - Processed 3200000 reads so far
2011-05-19 16:04:00,474 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:62990195-83010195
2011-05-19 16:04:10,793 - INFO - Processed 3300000 reads so far
2011-05-19 16:04:22,697 - INFO - Processed 3400000 reads so far
2011-05-19 16:04:34,652 - INFO - Processed 3500000 reads so far
2011-05-19 16:04:45,916 - INFO - Processed 3600000 reads so far
2011-05-19 16:04:56,188 - INFO - Processed 3700000 reads so far
2011-05-19 16:05:07,469 - INFO - Processed 3800000 reads so far
2011-05-19 16:05:20,128 - INFO - Processed 3900000 reads so far
2011-05-19 16:05:31,923 - INFO - Processed 4000000 reads so far
2011-05-19 16:05:44,544 - INFO - Processed 4100000 reads so far
2011-05-19 16:05:56,337 - INFO - Processed 4200000 reads so far
2011-05-19 16:06:05,101 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:82990234-103010234
2011-05-19 16:06:08,663 - INFO - Processed 4300000 reads so far
2011-05-19 16:06:23,999 - INFO - Processed 4400000 reads so far
2011-05-19 16:06:34,157 - INFO - Processed 4500000 reads so far
2011-05-19 16:06:46,853 - INFO - Processed 4600000 reads so far
2011-05-19 16:06:57,622 - INFO - Processed 4700000 reads so far
2011-05-19 16:07:08,427 - INFO - Processed 4800000 reads so far
2011-05-19 16:07:18,997 - INFO - Processed 4900000 reads so far
2011-05-19 16:07:30,441 - INFO - Processed 5000000 reads so far
2011-05-19 16:07:41,692 - INFO - Processed 5100000 reads so far
2011-05-19 16:07:52,501 - INFO - Processed 5200000 reads so far
2011-05-19 16:08:04,791 - INFO - Processed 5300000 reads so far
2011-05-19 16:08:13,516 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:102990239-123010239
2011-05-19 16:08:17,283 - INFO - Processed 5400000 reads so far
2011-05-19 16:08:31,587 - INFO - Processed 5500000 reads so far
2011-05-19 16:09:02,817 - INFO - Processed 5600000 reads so far
2011-05-19 16:09:15,175 - INFO - Processed 5700000 reads so far
2011-05-19 16:09:25,637 - INFO - Processed 5800000 reads so far
2011-05-19 16:09:37,616 - INFO - Processed 5900000 reads so far
2011-05-19 16:09:47,569 - INFO - Processed 6000000 reads so far
2011-05-19 16:09:58,852 - INFO - Processed 6100000 reads so far
2011-05-19 16:10:09,883 - INFO - Processed 6200000 reads so far
2011-05-19 16:10:20,390 - INFO - Processed 6300000 reads so far
2011-05-19 16:10:31,950 - INFO - Processed 6400000 reads so far
2011-05-19 16:10:35,347 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:122990252-143010252
2011-05-19 16:10:43,409 - INFO - Processed 6500000 reads so far
2011-05-19 16:10:53,927 - INFO - Processed 6600000 reads so far
2011-05-19 16:11:04,143 - INFO - Processed 6700000 reads so far
2011-05-19 16:11:13,906 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:2990003-23010003
2011-05-19 16:11:14,161 - INFO - Processed 6800000 reads so far
2011-05-19 16:11:24,875 - INFO - Processed 6900000 reads so far
2011-05-19 16:11:34,795 - INFO - Processed 7000000 reads so far
2011-05-19 16:11:46,416 - INFO - Processed 7100000 reads so far
2011-05-19 16:11:57,507 - INFO - Processed 7200000 reads so far
2011-05-19 16:12:09,271 - INFO - Processed 7300000 reads so far
2011-05-19 16:12:20,406 - INFO - Processed 7400000 reads so far
2011-05-19 16:12:32,616 - INFO - Processed 7500000 reads so far
2011-05-19 16:12:44,923 - INFO - Processed 7600000 reads so far
2011-05-19 16:12:58,267 - INFO - Processed 7700000 reads so far
2011-05-19 16:13:11,199 - INFO - Processed 7800000 reads so far
2011-05-19 16:13:19,570 - INFO - Processed 7900000 reads so far
2011-05-19 16:13:29,491 - INFO - Processed 8000000 reads so far
2011-05-19 16:13:32,493 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:22990027-43010027
2011-05-19 16:13:39,223 - INFO - Processed 8100000 reads so far
2011-05-19 16:13:48,276 - INFO - Processed 8200000 reads so far
2011-05-19 16:13:59,532 - INFO - Processed 8300000 reads so far
2011-05-19 16:14:10,733 - INFO - Processed 8400000 reads so far
2011-05-19 16:14:21,362 - INFO - Processed 8500000 reads so far
2011-05-19 16:14:31,434 - INFO - Processed 8600000 reads so far
2011-05-19 16:14:42,951 - INFO - Processed 8700000 reads so far
2011-05-19 16:14:53,876 - INFO - Processed 8800000 reads so far
2011-05-19 16:15:04,625 - INFO - Processed 8900000 reads so far
2011-05-19 16:15:16,575 - INFO - Processed 9000000 reads so far
2011-05-19 16:15:27,580 - INFO - Processed 9100000 reads so far
2011-05-19 16:15:28,371 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:42990031-63010031
2011-05-19 16:15:38,681 - INFO - Processed 9200000 reads so far
2011-05-19 16:15:51,590 - INFO - Processed 9300000 reads so far
2011-05-19 16:16:01,997 - INFO - Processed 9400000 reads so far
2011-05-19 16:16:13,322 - INFO - Processed 9500000 reads so far
2011-05-19 16:16:24,345 - INFO - Processed 9600000 reads so far
2011-05-19 16:16:36,683 - INFO - Processed 9700000 reads so far
2011-05-19 16:17:16,878 - INFO - Processed 9800000 reads so far
2011-05-19 16:17:28,656 - INFO - Processed 9900000 reads so far
2011-05-19 16:17:39,982 - INFO - Processed 10000000 reads so far
2011-05-19 16:17:52,967 - INFO - Processed 10100000 reads so far
2011-05-19 16:18:04,307 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:62990063-83010063
2011-05-19 16:18:04,545 - INFO - Processed 10200000 reads so far
2011-05-19 16:18:15,752 - INFO - Processed 10300000 reads so far
2011-05-19 16:18:26,357 - INFO - Processed 10400000 reads so far
2011-05-19 16:18:38,053 - INFO - Processed 10500000 reads so far
2011-05-19 16:18:53,984 - INFO - Processed 10600000 reads so far
2011-05-19 16:19:05,147 - INFO - Processed 10700000 reads so far
2011-05-19 16:19:16,453 - INFO - Processed 10800000 reads so far
2011-05-19 16:19:29,390 - INFO - Processed 10900000 reads so far
2011-05-19 16:19:42,930 - INFO - Processed 11000000 reads so far
2011-05-19 16:19:53,892 - INFO - Processed 11100000 reads so far
2011-05-19 16:20:05,249 - INFO - Processed 11200000 reads so far
2011-05-19 16:20:13,191 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:82990071-103010071
2011-05-19 16:20:16,553 - INFO - Processed 11300000 reads so far
2011-05-19 16:20:27,660 - INFO - Processed 11400000 reads so far
2011-05-19 16:20:39,548 - INFO - Processed 11500000 reads so far
2011-05-19 16:20:52,444 - INFO - Processed 11600000 reads so far
2011-05-19 16:21:03,536 - INFO - Processed 11700000 reads so far
2011-05-19 16:21:15,825 - INFO - Processed 11800000 reads so far
2011-05-19 16:21:26,358 - INFO - Processed 11900000 reads so far
2011-05-19 16:21:39,154 - INFO - Processed 12000000 reads so far
2011-05-19 16:21:51,249 - INFO - Processed 12100000 reads so far
2011-05-19 16:22:00,090 - INFO - Processed 12200000 reads so far
2011-05-19 16:22:14,545 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:102990098-123010098
2011-05-19 16:22:14,649 - INFO - Processed 12300000 reads so far
2011-05-19 16:22:27,191 - INFO - Processed 12400000 reads so far
2011-05-19 16:22:40,781 - INFO - Processed 12500000 reads so far
2011-05-19 16:22:52,099 - INFO - Processed 12600000 reads so far
2011-05-19 16:23:03,639 - INFO - Processed 12700000 reads so far
2011-05-19 16:23:14,930 - INFO - Processed 12800000 reads so far
2011-05-19 16:23:26,374 - INFO - Processed 12900000 reads so far
2011-05-19 16:23:40,050 - INFO - Processed 13000000 reads so far
2011-05-19 16:23:51,804 - INFO - Processed 13100000 reads so far
2011-05-19 16:24:03,525 - INFO - Processed 13200000 reads so far
2011-05-19 16:24:14,647 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:2990033-23010033
2011-05-19 16:24:16,502 - INFO - Processed 13300000 reads so far
2011-05-19 16:24:27,183 - INFO - Processed 13400000 reads so far
2011-05-19 16:24:37,776 - INFO - Processed 13500000 reads so far
2011-05-19 16:24:49,843 - INFO - Processed 13600000 reads so far
2011-05-19 16:25:01,847 - INFO - Processed 13700000 reads so far
2011-05-19 16:25:14,586 - INFO - Processed 13800000 reads so far
2011-05-19 16:25:26,307 - INFO - Processed 13900000 reads so far
2011-05-19 16:25:38,014 - INFO - Processed 14000000 reads so far
2011-05-19 16:25:49,746 - INFO - Processed 14100000 reads so far
2011-05-19 16:26:02,323 - INFO - Processed 14200000 reads so far
2011-05-19 16:26:14,475 - INFO - Processed 14300000 reads so far
2011-05-19 16:26:25,916 - INFO - Processed 14400000 reads so far
2011-05-19 16:26:37,589 - INFO - Processed 14500000 reads so far
2011-05-19 16:26:38,459 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:22990196-43010196
2011-05-19 16:26:49,959 - INFO - Processed 14600000 reads so far
2011-05-19 16:27:02,138 - INFO - Processed 14700000 reads so far
2011-05-19 16:27:13,463 - INFO - Processed 14800000 reads so far
2011-05-19 16:27:25,872 - INFO - Processed 14900000 reads so far
2011-05-19 16:27:38,418 - INFO - Processed 15000000 reads so far
2011-05-19 16:27:51,144 - INFO - Processed 15100000 reads so far
2011-05-19 16:28:04,564 - INFO - Processed 15200000 reads so far
2011-05-19 16:28:18,156 - INFO - Processed 15300000 reads so far
2011-05-19 16:28:34,983 - INFO - Processed 15400000 reads so far
2011-05-19 16:28:46,724 - INFO - Processed 15500000 reads so far
2011-05-19 16:28:51,979 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:42990197-63010197
2011-05-19 16:29:01,029 - INFO - Processed 15600000 reads so far
2011-05-19 16:29:11,714 - INFO - Processed 15700000 reads so far
2011-05-19 16:29:28,444 - INFO - Processed 15800000 reads so far
2011-05-19 16:29:43,713 - INFO - Processed 15900000 reads so far
2011-05-19 16:29:55,252 - INFO - Processed 16000000 reads so far
2011-05-19 16:30:08,878 - INFO - Processed 16100000 reads so far
2011-05-19 16:30:20,911 - INFO - Processed 16200000 reads so far
2011-05-19 16:30:34,617 - INFO - Processed 16300000 reads so far
2011-05-19 16:30:46,056 - INFO - Processed 16400000 reads so far
2011-05-19 16:30:59,173 - INFO - Processed 16500000 reads so far
2011-05-19 16:31:09,583 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:62990266-83010266
2011-05-19 16:31:11,896 - INFO - Processed 16600000 reads so far
2011-05-19 16:31:32,351 - INFO - Processed 16700000 reads so far
2011-05-19 16:31:46,140 - INFO - Processed 16800000 reads so far
2011-05-19 16:31:59,937 - INFO - Processed 16900000 reads so far
2011-05-19 16:32:14,886 - INFO - Processed 17000000 reads so far
2011-05-19 16:32:30,270 - INFO - Processed 17100000 reads so far
2011-05-19 16:32:44,826 - INFO - Processed 17200000 reads so far
2011-05-19 16:32:53,897 - INFO - Processed 17300000 reads so far
2011-05-19 16:33:05,692 - INFO - Processed 17400000 reads so far
2011-05-19 16:33:16,872 - INFO - Processed 17500000 reads so far
2011-05-19 16:33:29,733 - INFO - Processed 17600000 reads so far
2011-05-19 16:33:36,415 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:82990285-103010285
2011-05-19 16:33:41,060 - INFO - Processed 17700000 reads so far
2011-05-19 16:33:52,378 - INFO - Processed 17800000 reads so far
2011-05-19 16:34:11,000 - INFO - Processed 17900000 reads so far
2011-05-19 16:34:22,296 - INFO - Processed 18000000 reads so far
2011-05-19 16:34:34,183 - INFO - Processed 18100000 reads so far
2011-05-19 16:34:45,604 - INFO - Processed 18200000 reads so far
2011-05-19 16:34:58,848 - INFO - Processed 18300000 reads so far
2011-05-19 16:35:11,302 - INFO - Processed 18400000 reads so far
2011-05-19 16:35:22,726 - INFO - Processed 18500000 reads so far
2011-05-19 16:35:34,567 - INFO - Processed 18600000 reads so far
2011-05-19 16:35:47,627 - INFO - Processed 18700000 reads so far
2011-05-19 16:35:50,988 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:102990348-123010348
2011-05-19 16:35:59,150 - INFO - Processed 18800000 reads so far
2011-05-19 16:36:11,210 - INFO - Processed 18900000 reads so far
2011-05-19 16:36:23,893 - INFO - Processed 19000000 reads so far
2011-05-19 16:36:34,875 - INFO - Processed 19100000 reads so far
2011-05-19 16:36:46,171 - INFO - Processed 19200000 reads so far
2011-05-19 16:36:57,592 - INFO - Processed 19300000 reads so far
2011-05-19 16:37:08,480 - INFO - Processed 19400000 reads so far
2011-05-19 16:37:20,793 - INFO - Processed 19500000 reads so far
2011-05-19 16:37:32,085 - INFO - Processed 19600000 reads so far
2011-05-19 16:37:44,010 - INFO - Processed 19700000 reads so far
2011-05-19 16:37:53,722 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:2990019-23010019
2011-05-19 16:37:56,168 - INFO - Processed 19800000 reads so far
2011-05-19 16:38:10,084 - INFO - Processed 19900000 reads so far
2011-05-19 16:38:24,052 - INFO - Processed 20000000 reads so far
2011-05-19 16:38:35,242 - INFO - Processed 20100000 reads so far
2011-05-19 16:40:18,046 - INFO - Processed 20200000 reads so far
2011-05-19 16:40:29,135 - INFO - Processed 20300000 reads so far
2011-05-19 16:40:41,041 - INFO - Processed 20400000 reads so far
2011-05-19 16:40:53,547 - INFO - Processed 20500000 reads so far
2011-05-19 16:41:03,929 - INFO - Processed 20600000 reads so far
2011-05-19 16:41:16,368 - INFO - Processed 20700000 reads so far
2011-05-19 16:41:26,640 - INFO - Processed 20800000 reads so far
2011-05-19 16:41:30,337 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:22990022-43010022
2011-05-19 16:41:34,801 - INFO - Processed 20900000 reads so far
2011-05-19 16:41:46,913 - INFO - Processed 21000000 reads so far
2011-05-19 16:41:59,374 - INFO - Processed 21100000 reads so far
2011-05-19 16:42:11,068 - INFO - Processed 21200000 reads so far
2011-05-19 16:42:21,138 - INFO - Processed 21300000 reads so far
2011-05-19 16:42:31,791 - INFO - Processed 21400000 reads so far
2011-05-19 16:42:42,358 - INFO - Processed 21500000 reads so far
2011-05-19 16:42:51,210 - INFO - Processed 21600000 reads so far
2011-05-19 16:43:04,904 - INFO - Processed 21700000 reads so far
2011-05-19 16:43:21,458 - INFO - Processed 21800000 reads so far
2011-05-19 16:43:36,374 - INFO - Processed 21900000 reads so far
2011-05-19 16:43:43,237 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:42990034-63010034
2011-05-19 16:43:48,564 - INFO - Processed 22000000 reads so far
2011-05-19 16:44:00,073 - INFO - Processed 22100000 reads so far
2011-05-19 16:44:14,679 - INFO - Processed 22200000 reads so far
2011-05-19 16:44:27,678 - INFO - Processed 22300000 reads so far
2011-05-19 16:44:39,633 - INFO - Processed 22400000 reads so far
2011-05-19 16:44:56,311 - INFO - Processed 22500000 reads so far
2011-05-19 16:45:10,227 - INFO - Processed 22600000 reads so far
2011-05-19 16:45:25,249 - INFO - Processed 22700000 reads so far
2011-05-19 16:45:35,956 - INFO - Processed 22800000 reads so far
2011-05-19 16:45:49,474 - INFO - Processed 22900000 reads so far
2011-05-19 16:46:00,746 - INFO - Processed 23000000 reads so far
2011-05-19 16:46:10,118 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:62990053-83010053
2011-05-19 16:46:13,975 - INFO - Processed 23100000 reads so far
2011-05-19 16:46:29,125 - INFO - Processed 23200000 reads so far
2011-05-19 16:46:42,649 - INFO - Processed 23300000 reads so far
2011-05-19 16:46:54,372 - INFO - Processed 23400000 reads so far
2011-05-19 16:47:05,681 - INFO - Processed 23500000 reads so far
2011-05-19 16:47:17,082 - INFO - Processed 23600000 reads so far
2011-05-19 16:47:28,510 - INFO - Processed 23700000 reads so far
2011-05-19 16:47:41,315 - INFO - Processed 23800000 reads so far
2011-05-19 16:47:55,080 - INFO - Processed 23900000 reads so far
2011-05-19 16:48:10,948 - INFO - Processed 24000000 reads so far
2011-05-19 16:48:27,030 - INFO - Processed 24100000 reads so far
2011-05-19 16:48:32,716 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:82990061-103010061
2011-05-19 16:48:38,930 - INFO - Processed 24200000 reads so far
2011-05-19 16:48:50,707 - INFO - Processed 24300000 reads so far
2011-05-19 16:49:02,184 - INFO - Processed 24400000 reads so far
2011-05-19 16:49:18,332 - INFO - Processed 24500000 reads so far
2011-05-19 16:49:30,193 - INFO - Processed 24600000 reads so far
2011-05-19 16:49:41,552 - INFO - Processed 24700000 reads so far
2011-05-19 16:49:52,965 - INFO - Processed 24800000 reads so far
2011-05-19 16:50:03,892 - INFO - Processed 24900000 reads so far
2011-05-19 16:50:16,645 - INFO - Processed 25000000 reads so far
2011-05-19 16:50:28,896 - INFO - Processed 25100000 reads so far
2011-05-19 16:50:40,529 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:102990062-123010062
2011-05-19 16:50:42,102 - INFO - Processed 25200000 reads so far
2011-05-19 16:50:54,161 - INFO - Processed 25300000 reads so far
2011-05-19 16:51:05,203 - INFO - Processed 25400000 reads so far
2011-05-19 16:51:16,526 - INFO - Processed 25500000 reads so far
2011-05-19 16:51:26,111 - INFO - Processed 25600000 reads so far
2011-05-19 16:51:37,267 - INFO - Processed 25700000 reads so far
2011-05-19 16:51:49,629 - INFO - Processed 25800000 reads so far
2011-05-19 16:52:02,946 - INFO - Processed 25900000 reads so far
2011-05-19 16:52:14,365 - INFO - Processed 26000000 reads so far
2011-05-19 16:52:26,852 - INFO - Processed 26100000 reads so far
2011-05-19 16:52:33,895 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13_random:0-20010000
2011-05-19 16:52:34,961 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:2990029-23010029
2011-05-19 16:52:42,454 - INFO - Processed 26200000 reads so far
2011-05-19 16:52:57,056 - INFO - Processed 26300000 reads so far
2011-05-19 16:53:08,364 - INFO - Processed 26400000 reads so far
2011-05-19 16:53:20,211 - INFO - Processed 26500000 reads so far
2011-05-19 16:53:36,044 - INFO - Processed 26600000 reads so far
2011-05-19 16:53:48,913 - INFO - Processed 26700000 reads so far
2011-05-19 16:54:03,345 - INFO - Processed 26800000 reads so far
2011-05-19 16:54:18,266 - INFO - Processed 26900000 reads so far
2011-05-19 16:54:29,568 - INFO - Processed 27000000 reads so far
2011-05-19 16:54:41,830 - INFO - Processed 27100000 reads so far
2011-05-19 16:54:58,088 - INFO - Processed 27200000 reads so far
2011-05-19 16:55:00,678 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:22990037-43010037
2011-05-19 16:55:09,464 - INFO - Processed 27300000 reads so far
2011-05-19 16:55:20,434 - INFO - Processed 27400000 reads so far
2011-05-19 16:55:31,870 - INFO - Processed 27500000 reads so far
2011-05-19 16:55:43,440 - INFO - Processed 27600000 reads so far
2011-05-19 16:55:55,789 - INFO - Processed 27700000 reads so far
2011-05-19 16:56:08,108 - INFO - Processed 27800000 reads so far
2011-05-19 16:56:23,236 - INFO - Processed 27900000 reads so far
2011-05-19 16:56:36,788 - INFO - Processed 28000000 reads so far
2011-05-19 16:56:50,671 - INFO - Processed 28100000 reads so far
2011-05-19 16:57:03,143 - INFO - Processed 28200000 reads so far
2011-05-19 16:57:14,701 - INFO - Processed 28300000 reads so far
2011-05-19 16:57:15,275 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:42990098-63010098
2011-05-19 16:57:27,053 - INFO - Processed 28400000 reads so far
2011-05-19 16:57:38,475 - INFO - Processed 28500000 reads so far
2011-05-19 16:57:52,261 - INFO - Processed 28600000 reads so far
2011-05-19 16:58:05,017 - INFO - Processed 28700000 reads so far
2011-05-19 16:58:17,044 - INFO - Processed 28800000 reads so far
2011-05-19 16:58:28,656 - INFO - Processed 28900000 reads so far
2011-05-19 16:58:40,342 - INFO - Processed 29000000 reads so far
2011-05-19 16:58:54,102 - INFO - Processed 29100000 reads so far
2011-05-19 16:59:05,906 - INFO - Processed 29200000 reads so far
2011-05-19 16:59:17,138 - INFO - Processed 29300000 reads so far
2011-05-19 16:59:29,406 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:62990099-83010099
2011-05-19 16:59:30,094 - INFO - Processed 29400000 reads so far
2011-05-19 16:59:42,705 - INFO - Processed 29500000 reads so far
2011-05-19 16:59:54,148 - INFO - Processed 29600000 reads so far
2011-05-19 17:00:07,109 - INFO - Processed 29700000 reads so far
2011-05-19 17:00:15,931 - INFO - Processed 29800000 reads so far
2011-05-19 17:00:25,459 - INFO - Processed 29900000 reads so far
2011-05-19 17:00:36,060 - INFO - Processed 30000000 reads so far
2011-05-19 17:00:48,550 - INFO - Processed 30100000 reads so far
2011-05-19 17:01:02,642 - INFO - Processed 30200000 reads so far
2011-05-19 17:01:15,844 - INFO - Processed 30300000 reads so far
2011-05-19 17:01:32,013 - INFO - Processed 30400000 reads so far
2011-05-19 17:01:42,359 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:82990156-103010156
2011-05-19 17:01:43,408 - INFO - Processed 30500000 reads so far
2011-05-19 17:01:56,983 - INFO - Processed 30600000 reads so far
2011-05-19 17:02:09,497 - INFO - Processed 30700000 reads so far
2011-05-19 17:02:20,875 - INFO - Processed 30800000 reads so far
2011-05-19 17:02:32,271 - INFO - Processed 30900000 reads so far
2011-05-19 17:02:43,772 - INFO - Processed 31000000 reads so far
2011-05-19 17:02:55,020 - INFO - Processed 31100000 reads so far
2011-05-19 17:03:04,852 - INFO - Processed 31200000 reads so far
2011-05-19 17:03:16,278 - INFO - Processed 31300000 reads so far
2011-05-19 17:03:34,145 - INFO - Processed 31400000 reads so far
2011-05-19 17:03:50,746 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:102990173-123010173
2011-05-19 17:03:51,421 - INFO - Processed 31500000 reads so far
2011-05-19 17:04:05,098 - INFO - Processed 31600000 reads so far
2011-05-19 17:04:15,781 - INFO - Processed 31700000 reads so far
2011-05-19 17:04:27,631 - INFO - Processed 31800000 reads so far
2011-05-19 17:04:39,609 - INFO - Processed 31900000 reads so far
2011-05-19 17:04:55,461 - INFO - Processed 32000000 reads so far
2011-05-19 17:05:08,488 - INFO - Processed 32100000 reads so far
2011-05-19 17:05:19,711 - INFO - Processed 32200000 reads so far
2011-05-19 17:05:30,454 - INFO - Processed 32300000 reads so far
2011-05-19 17:05:42,748 - INFO - Processed 32400000 reads so far
2011-05-19 17:05:54,993 - INFO - Processed 32500000 reads so far
2011-05-19 17:05:59,536 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:122990190-143010190
2011-05-19 17:06:09,448 - INFO - Processed 32600000 reads so far
2011-05-19 17:06:16,964 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:2990009-23010009
2011-05-19 17:06:24,016 - INFO - Processed 32700000 reads so far
2011-05-19 17:06:35,197 - INFO - Processed 32800000 reads so far
2011-05-19 17:06:47,016 - INFO - Processed 32900000 reads so far
2011-05-19 17:06:58,796 - INFO - Processed 33000000 reads so far
2011-05-19 17:07:13,206 - INFO - Processed 33100000 reads so far
2011-05-19 17:07:25,598 - INFO - Processed 33200000 reads so far
2011-05-19 17:07:39,637 - INFO - Processed 33300000 reads so far
2011-05-19 17:07:54,200 - INFO - Processed 33400000 reads so far
2011-05-19 17:08:02,483 - INFO - Processed 33500000 reads so far
2011-05-19 17:08:11,700 - INFO - Processed 33600000 reads so far
2011-05-19 17:08:24,490 - INFO - Processed 33700000 reads so far
2011-05-19 17:08:24,790 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:22990023-43010023
2011-05-19 17:08:36,352 - INFO - Processed 33800000 reads so far
2011-05-19 17:08:48,129 - INFO - Processed 33900000 reads so far
2011-05-19 17:09:00,854 - INFO - Processed 34000000 reads so far
2011-05-19 17:09:13,780 - INFO - Processed 34100000 reads so far
2011-05-19 17:09:24,254 - INFO - Processed 34200000 reads so far
2011-05-19 17:09:36,051 - INFO - Processed 34300000 reads so far
2011-05-19 17:09:48,970 - INFO - Processed 34400000 reads so far
2011-05-19 17:10:02,544 - INFO - Processed 34500000 reads so far
2011-05-19 17:10:15,310 - INFO - Processed 34600000 reads so far
2011-05-19 17:10:26,513 - INFO - Processed 34700000 reads so far
2011-05-19 17:10:36,237 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:42990031-63010031
2011-05-19 17:10:37,772 - INFO - Processed 34800000 reads so far
2011-05-19 17:10:49,637 - INFO - Processed 34900000 reads so far
2011-05-19 17:10:59,282 - INFO - Processed 35000000 reads so far
2011-05-19 17:11:11,379 - INFO - Processed 35100000 reads so far
2011-05-19 17:11:23,119 - INFO - Processed 35200000 reads so far
2011-05-19 17:11:35,624 - INFO - Processed 35300000 reads so far
2011-05-19 17:11:47,343 - INFO - Processed 35400000 reads so far
2011-05-19 17:12:00,308 - INFO - Processed 35500000 reads so far
2011-05-19 17:12:11,966 - INFO - Processed 35600000 reads so far
2011-05-19 17:12:24,236 - INFO - Processed 35700000 reads so far
2011-05-19 17:12:38,182 - INFO - Processed 35800000 reads so far
2011-05-19 17:12:44,780 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:62990097-83010097
2011-05-19 17:12:49,446 - INFO - Processed 35900000 reads so far
2011-05-19 17:13:03,019 - INFO - Processed 36000000 reads so far
2011-05-19 17:13:14,814 - INFO - Processed 36100000 reads so far
2011-05-19 17:13:27,895 - INFO - Processed 36200000 reads so far
2011-05-19 17:13:43,836 - INFO - Processed 36300000 reads so far
2011-05-19 17:13:56,493 - INFO - Processed 36400000 reads so far
2011-05-19 17:14:10,893 - INFO - Processed 36500000 reads so far
2011-05-19 17:14:26,744 - INFO - Processed 36600000 reads so far
2011-05-19 17:14:38,168 - INFO - Processed 36700000 reads so far
2011-05-19 17:14:49,697 - INFO - Processed 36800000 reads so far
2011-05-19 17:15:02,572 - INFO - Processed 36900000 reads so far
2011-05-19 17:15:06,852 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:82990132-103010132
2011-05-19 17:15:12,545 - INFO - Processed 37000000 reads so far
2011-05-19 17:15:23,821 - INFO - Processed 37100000 reads so far
2011-05-19 17:15:34,971 - INFO - Processed 37200000 reads so far
2011-05-19 17:15:44,296 - INFO - Processed 37300000 reads so far
2011-05-19 17:15:53,121 - INFO - Processed 37400000 reads so far
2011-05-19 17:16:03,486 - INFO - Processed 37500000 reads so far
2011-05-19 17:16:14,768 - INFO - Processed 37600000 reads so far
2011-05-19 17:16:30,460 - INFO - Processed 37700000 reads so far
2011-05-19 17:16:45,212 - INFO - Processed 37800000 reads so far
2011-05-19 17:16:57,479 - INFO - Processed 37900000 reads so far
2011-05-19 17:17:09,937 - INFO - Processed 38000000 reads so far
2011-05-19 17:17:10,431 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:102990154-123010154
2011-05-19 17:17:13,395 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:2990025-23010025
2011-05-19 17:17:20,977 - INFO - Processed 38100000 reads so far
2011-05-19 17:17:32,719 - INFO - Processed 38200000 reads so far
2011-05-19 17:17:45,487 - INFO - Processed 38300000 reads so far
2011-05-19 17:17:58,137 - INFO - Processed 38400000 reads so far
2011-05-19 17:18:15,804 - INFO - Processed 38500000 reads so far
2011-05-19 17:18:27,347 - INFO - Processed 38600000 reads so far
2011-05-19 17:18:40,243 - INFO - Processed 38700000 reads so far
2011-05-19 17:18:54,348 - INFO - Processed 38800000 reads so far
2011-05-19 17:19:06,470 - INFO - Processed 38900000 reads so far
2011-05-19 17:19:21,168 - INFO - Processed 39000000 reads so far
2011-05-19 17:19:33,409 - INFO - Processed 39100000 reads so far
2011-05-19 17:19:42,100 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:22990032-43010032
2011-05-19 17:19:45,271 - INFO - Processed 39200000 reads so far
2011-05-19 17:19:57,600 - INFO - Processed 39300000 reads so far
2011-05-19 17:20:08,286 - INFO - Processed 39400000 reads so far
2011-05-19 17:20:16,536 - INFO - Processed 39500000 reads so far
2011-05-19 17:20:29,814 - INFO - Processed 39600000 reads so far
2011-05-19 17:20:41,839 - INFO - Processed 39700000 reads so far
2011-05-19 17:20:53,121 - INFO - Processed 39800000 reads so far
2011-05-19 17:21:06,408 - INFO - Processed 39900000 reads so far
2011-05-19 17:21:17,458 - INFO - Processed 40000000 reads so far
2011-05-19 17:21:27,047 - INFO - Processed 40100000 reads so far
2011-05-19 17:21:40,693 - INFO - Processed 40200000 reads so far
2011-05-19 17:21:46,894 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:42990059-63010059
2011-05-19 17:21:52,636 - INFO - Processed 40300000 reads so far
2011-05-19 17:22:06,025 - INFO - Processed 40400000 reads so far
2011-05-19 17:22:19,870 - INFO - Processed 40500000 reads so far
2011-05-19 17:22:31,193 - INFO - Processed 40600000 reads so far
2011-05-19 17:22:43,674 - INFO - Processed 40700000 reads so far
2011-05-19 17:22:55,147 - INFO - Processed 40800000 reads so far
2011-05-19 17:23:12,077 - INFO - Processed 40900000 reads so far
2011-05-19 17:23:26,308 - INFO - Processed 41000000 reads so far
2011-05-19 17:23:37,761 - INFO - Processed 41100000 reads so far
2011-05-19 17:23:51,528 - INFO - Processed 41200000 reads so far
2011-05-19 17:24:05,485 - INFO - Processed 41300000 reads so far
2011-05-19 17:24:07,419 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:62990079-83010079
2011-05-19 17:24:16,513 - INFO - Processed 41400000 reads so far
2011-05-19 17:24:28,964 - INFO - Processed 41500000 reads so far
2011-05-19 17:24:43,396 - INFO - Processed 41600000 reads so far
2011-05-19 17:24:55,061 - INFO - Processed 41700000 reads so far
2011-05-19 17:25:09,610 - INFO - Processed 41800000 reads so far
2011-05-19 17:25:19,465 - INFO - Processed 41900000 reads so far
2011-05-19 17:25:33,501 - INFO - Processed 42000000 reads so far
2011-05-19 17:25:47,989 - INFO - Processed 42100000 reads so far
2011-05-19 17:26:01,441 - INFO - Processed 42200000 reads so far
2011-05-19 17:26:11,645 - INFO - Processed 42300000 reads so far
2011-05-19 17:26:16,371 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:82990092-103010092
2011-05-19 17:26:22,267 - INFO - Processed 42400000 reads so far
2011-05-19 17:26:33,751 - INFO - Processed 42500000 reads so far
2011-05-19 17:26:45,655 - INFO - Processed 42600000 reads so far
2011-05-19 17:26:56,554 - INFO - Processed 42700000 reads so far
2011-05-19 17:27:07,729 - INFO - Processed 42800000 reads so far
2011-05-19 17:27:16,912 - INFO - Processed 42900000 reads so far
2011-05-19 17:27:28,755 - INFO - Processed 43000000 reads so far
2011-05-19 17:27:37,359 - INFO - Processed 43100000 reads so far
2011-05-19 17:27:43,969 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16_random:0-20010119
2011-05-19 17:27:43,993 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:2989978-23009978
2011-05-19 17:27:45,955 - INFO - Processed 43200000 reads so far
2011-05-19 17:27:57,232 - INFO - Processed 43300000 reads so far
2011-05-19 17:28:10,168 - INFO - Processed 43400000 reads so far
2011-05-19 17:28:20,887 - INFO - Processed 43500000 reads so far
2011-05-19 17:28:33,585 - INFO - Processed 43600000 reads so far
2011-05-19 17:28:44,884 - INFO - Processed 43700000 reads so far
2011-05-19 17:28:55,705 - INFO - Processed 43800000 reads so far
2011-05-19 17:29:08,183 - INFO - Processed 43900000 reads so far
2011-05-19 17:29:22,613 - INFO - Processed 44000000 reads so far
2011-05-19 17:29:34,063 - INFO - Processed 44100000 reads so far
2011-05-19 17:29:45,714 - INFO - Processed 44200000 reads so far
2011-05-19 17:29:55,934 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:22990032-43010032
2011-05-19 17:30:01,573 - INFO - Processed 44300000 reads so far
2011-05-19 17:30:13,555 - INFO - Processed 44400000 reads so far
2011-05-19 17:30:29,104 - INFO - Processed 44500000 reads so far
2011-05-19 17:30:40,833 - INFO - Processed 44600000 reads so far
2011-05-19 17:30:53,044 - INFO - Processed 44700000 reads so far
2011-05-19 17:31:07,084 - INFO - Processed 44800000 reads so far
2011-05-19 17:31:18,090 - INFO - Processed 44900000 reads so far
2011-05-19 17:31:34,217 - INFO - Processed 45000000 reads so far
2011-05-19 17:31:45,676 - INFO - Processed 45100000 reads so far
2011-05-19 17:31:56,663 - INFO - Processed 45200000 reads so far
2011-05-19 17:32:09,594 - INFO - Processed 45300000 reads so far
2011-05-19 17:32:12,548 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:42990053-63010053
2011-05-19 17:32:21,266 - INFO - Processed 45400000 reads so far
2011-05-19 17:32:34,234 - INFO - Processed 45500000 reads so far
2011-05-19 17:32:51,560 - INFO - Processed 45600000 reads so far
2011-05-19 17:33:02,918 - INFO - Processed 45700000 reads so far
2011-05-19 17:33:15,339 - INFO - Processed 45800000 reads so far
2011-05-19 17:33:27,517 - INFO - Processed 45900000 reads so far
2011-05-19 17:33:39,828 - INFO - Processed 46000000 reads so far
2011-05-19 17:33:53,636 - INFO - Processed 46100000 reads so far
2011-05-19 17:34:05,844 - INFO - Processed 46200000 reads so far
2011-05-19 17:34:20,500 - INFO - Processed 46300000 reads so far
2011-05-19 17:34:29,497 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:62990074-83010074
2011-05-19 17:34:34,996 - INFO - Processed 46400000 reads so far
2011-05-19 17:34:47,137 - INFO - Processed 46500000 reads so far
2011-05-19 17:35:00,978 - INFO - Processed 46600000 reads so far
2011-05-19 17:35:12,789 - INFO - Processed 46700000 reads so far
2011-05-19 17:35:24,044 - INFO - Processed 46800000 reads so far
2011-05-19 17:35:38,253 - INFO - Processed 46900000 reads so far
2011-05-19 17:35:50,291 - INFO - Processed 47000000 reads so far
2011-05-19 17:36:03,182 - INFO - Processed 47100000 reads so far
2011-05-19 17:36:14,934 - INFO - Processed 47200000 reads so far
2011-05-19 17:36:26,095 - INFO - Processed 47300000 reads so far
2011-05-19 17:36:36,771 - INFO - Processed 47400000 reads so far
2011-05-19 17:36:41,624 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:82990134-103010134
2011-05-19 17:36:47,869 - INFO - Processed 47500000 reads so far
2011-05-19 17:37:00,846 - INFO - Processed 47600000 reads so far
2011-05-19 17:37:12,798 - INFO - Processed 47700000 reads so far
2011-05-19 17:37:26,357 - INFO - Processed 47800000 reads so far
2011-05-19 17:37:38,748 - INFO - Processed 47900000 reads so far
2011-05-19 17:37:49,430 - INFO - Processed 48000000 reads so far
2011-05-19 17:38:01,696 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17_random:0-20010153
2011-05-19 17:38:02,346 - INFO - Processed 48100000 reads so far
2011-05-19 17:38:03,513 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:2989999-23009999
2011-05-19 17:38:13,274 - INFO - Processed 48200000 reads so far
2011-05-19 17:38:28,272 - INFO - Processed 48300000 reads so far
2011-05-19 17:38:44,433 - INFO - Processed 48400000 reads so far
2011-05-19 17:38:57,445 - INFO - Processed 48500000 reads so far
2011-05-19 17:39:13,216 - INFO - Processed 48600000 reads so far
2011-05-19 17:39:24,475 - INFO - Processed 48700000 reads so far
2011-05-19 17:39:35,517 - INFO - Processed 48800000 reads so far
2011-05-19 17:39:48,608 - INFO - Processed 48900000 reads so far
2011-05-19 17:40:00,224 - INFO - Processed 49000000 reads so far
2011-05-19 17:40:11,654 - INFO - Processed 49100000 reads so far
2011-05-19 17:40:21,195 - INFO - Processed 49200000 reads so far
2011-05-19 17:40:27,626 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:22990006-43010006
2011-05-19 17:40:33,814 - INFO - Processed 49300000 reads so far
2011-05-19 17:40:42,811 - INFO - Processed 49400000 reads so far
2011-05-19 17:40:57,390 - INFO - Processed 49500000 reads so far
2011-05-19 17:41:08,394 - INFO - Processed 49600000 reads so far
2011-05-19 17:41:19,837 - INFO - Processed 49700000 reads so far
2011-05-19 17:41:35,306 - INFO - Processed 49800000 reads so far
2011-05-19 17:41:46,817 - INFO - Processed 49900000 reads so far
2011-05-19 17:41:59,846 - INFO - Processed 50000000 reads so far
2011-05-19 17:42:10,035 - INFO - Processed 50100000 reads so far
2011-05-19 17:42:20,721 - INFO - Processed 50200000 reads so far
2011-05-19 17:42:31,156 - INFO - Processed 50300000 reads so far
2011-05-19 17:42:34,672 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:42990035-63010035
2011-05-19 17:42:44,779 - INFO - Processed 50400000 reads so far
2011-05-19 17:42:56,515 - INFO - Processed 50500000 reads so far
2011-05-19 17:43:08,737 - INFO - Processed 50600000 reads so far
2011-05-19 17:43:25,131 - INFO - Processed 50700000 reads so far
2011-05-19 17:43:35,496 - INFO - Processed 50800000 reads so far
2011-05-19 17:43:46,437 - INFO - Processed 50900000 reads so far
2011-05-19 17:43:59,789 - INFO - Processed 51000000 reads so far
2011-05-19 17:44:09,999 - INFO - Processed 51100000 reads so far
2011-05-19 17:44:21,625 - INFO - Processed 51200000 reads so far
2011-05-19 17:44:32,607 - INFO - Processed 51300000 reads so far
2011-05-19 17:44:42,907 - INFO - Processed 51400000 reads so far
2011-05-19 17:44:44,320 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:62990039-83010039
2011-05-19 17:44:51,873 - INFO - Processed 51500000 reads so far
2011-05-19 17:45:03,650 - INFO - Processed 51600000 reads so far
2011-05-19 17:45:15,080 - INFO - Processed 51700000 reads so far
2011-05-19 17:45:26,912 - INFO - Processed 51800000 reads so far
2011-05-19 17:45:40,474 - INFO - Processed 51900000 reads so far
2011-05-19 17:45:51,679 - INFO - Processed 52000000 reads so far
2011-05-19 17:46:02,501 - INFO - Processed 52100000 reads so far
2011-05-19 17:46:13,775 - INFO - Processed 52200000 reads so far
2011-05-19 17:46:27,148 - INFO - Processed 52300000 reads so far
2011-05-19 17:46:38,383 - INFO - Processed 52400000 reads so far
2011-05-19 17:46:49,395 - INFO - Processed 52500000 reads so far
2011-05-19 17:46:49,558 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:82990045-103010045
2011-05-19 17:47:01,471 - INFO - Processed 52600000 reads so far
2011-05-19 17:47:12,577 - INFO - Processed 52700000 reads so far
2011-05-19 17:47:23,650 - INFO - Processed 52800000 reads so far
2011-05-19 17:47:36,444 - INFO - Processed 52900000 reads so far
2011-05-19 17:47:40,540 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:2990018-23010018
2011-05-19 17:47:50,604 - INFO - Processed 53000000 reads so far
2011-05-19 17:48:02,043 - INFO - Processed 53100000 reads so far
2011-05-19 17:48:14,887 - INFO - Processed 53200000 reads so far
2011-05-19 17:48:26,232 - INFO - Processed 53300000 reads so far
2011-05-19 17:48:37,463 - INFO - Processed 53400000 reads so far
2011-05-19 17:48:51,486 - INFO - Processed 53500000 reads so far
2011-05-19 17:49:03,497 - INFO - Processed 53600000 reads so far
2011-05-19 17:49:15,310 - INFO - Processed 53700000 reads so far
2011-05-19 17:49:25,924 - INFO - Processed 53800000 reads so far
2011-05-19 17:49:35,709 - INFO - Processed 53900000 reads so far
2011-05-19 17:49:42,995 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:22990049-43010049
2011-05-19 17:49:48,485 - INFO - Processed 54000000 reads so far
2011-05-19 17:50:01,816 - INFO - Processed 54100000 reads so far
2011-05-19 17:50:13,533 - INFO - Processed 54200000 reads so far
2011-05-19 17:50:26,652 - INFO - Processed 54300000 reads so far
2011-05-19 17:50:39,214 - INFO - Processed 54400000 reads so far
2011-05-19 17:50:52,268 - INFO - Processed 54500000 reads so far
2011-05-19 17:51:02,558 - INFO - Processed 54600000 reads so far
2011-05-19 17:51:16,552 - INFO - Processed 54700000 reads so far
2011-05-19 17:51:28,108 - INFO - Processed 54800000 reads so far
2011-05-19 17:51:39,902 - INFO - Processed 54900000 reads so far
2011-05-19 17:51:52,169 - INFO - Processed 55000000 reads so far
2011-05-19 17:51:58,262 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:42990069-63010069
2011-05-19 17:52:04,475 - INFO - Processed 55100000 reads so far
2011-05-19 17:52:14,779 - INFO - Processed 55200000 reads so far
2011-05-19 17:52:26,262 - INFO - Processed 55300000 reads so far
2011-05-19 17:52:38,805 - INFO - Processed 55400000 reads so far
2011-05-19 17:52:49,257 - INFO - Processed 55500000 reads so far
2011-05-19 17:53:02,195 - INFO - Processed 55600000 reads so far
2011-05-19 17:53:13,787 - INFO - Processed 55700000 reads so far
2011-05-19 17:53:24,785 - INFO - Processed 55800000 reads so far
2011-05-19 17:53:37,584 - INFO - Processed 55900000 reads so far
2011-05-19 17:53:48,047 - INFO - Processed 56000000 reads so far
2011-05-19 17:53:51,435 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:2989988-23009988
2011-05-19 17:53:57,431 - INFO - Processed 56100000 reads so far
2011-05-19 17:54:07,702 - INFO - Processed 56200000 reads so far
2011-05-19 17:54:21,410 - INFO - Processed 56300000 reads so far
2011-05-19 17:54:35,029 - INFO - Processed 56400000 reads so far
2011-05-19 17:54:45,865 - INFO - Processed 56500000 reads so far
2011-05-19 17:54:58,769 - INFO - Processed 56600000 reads so far
2011-05-19 17:55:09,366 - INFO - Processed 56700000 reads so far
2011-05-19 17:55:21,250 - INFO - Processed 56800000 reads so far
2011-05-19 17:55:32,502 - INFO - Processed 56900000 reads so far
2011-05-19 17:55:42,951 - INFO - Processed 57000000 reads so far
2011-05-19 17:55:52,453 - INFO - Processed 57100000 reads so far
2011-05-19 17:55:53,191 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:22989994-43009994
2011-05-19 17:55:59,246 - INFO - Processed 57200000 reads so far
2011-05-19 17:56:10,241 - INFO - Processed 57300000 reads so far
2011-05-19 17:56:25,185 - INFO - Processed 57400000 reads so far
2011-05-19 17:56:38,178 - INFO - Processed 57500000 reads so far
2011-05-19 17:56:49,030 - INFO - Processed 57600000 reads so far
2011-05-19 17:57:01,924 - INFO - Processed 57700000 reads so far
2011-05-19 17:57:14,271 - INFO - Processed 57800000 reads so far
2011-05-19 17:57:25,160 - INFO - Processed 57900000 reads so far
2011-05-19 17:57:37,315 - INFO - Processed 58000000 reads so far
2011-05-19 17:57:47,600 - INFO - Processed 58100000 reads so far
2011-05-19 17:57:57,920 - INFO - Processed 58200000 reads so far
2011-05-19 17:57:58,115 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:42990002-63010002
2011-05-19 17:58:09,753 - INFO - Processed 58300000 reads so far
2011-05-19 17:58:21,102 - INFO - Processed 58400000 reads so far
2011-05-19 17:58:31,791 - INFO - Processed 58500000 reads so far
2011-05-19 17:58:44,317 - INFO - Processed 58600000 reads so far
2011-05-19 17:58:54,989 - INFO - Processed 58700000 reads so far
2011-05-19 17:59:05,826 - INFO - Processed 58800000 reads so far
2011-05-19 17:59:17,298 - INFO - Processed 58900000 reads so far
2011-05-19 17:59:30,596 - INFO - Processed 59000000 reads so far
2011-05-19 17:59:41,785 - INFO - Processed 59100000 reads so far
2011-05-19 17:59:51,930 - INFO - Processed 59200000 reads so far
2011-05-19 17:59:57,593 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:62990005-83010005
2011-05-19 17:59:59,807 - INFO - Processed 59300000 reads so far
2011-05-19 18:00:10,311 - INFO - Processed 59400000 reads so far
2011-05-19 18:00:20,450 - INFO - Processed 59500000 reads so far
2011-05-19 18:00:27,589 - INFO - Processed 59600000 reads so far
2011-05-19 18:00:38,050 - INFO - Processed 59700000 reads so far
2011-05-19 18:00:49,370 - INFO - Processed 59800000 reads so far
2011-05-19 18:00:59,907 - INFO - Processed 59900000 reads so far
2011-05-19 18:01:09,281 - INFO - Processed 60000000 reads so far
2011-05-19 18:01:18,202 - INFO - Processed 60100000 reads so far
2011-05-19 18:01:27,998 - INFO - Processed 60200000 reads so far
2011-05-19 18:01:37,979 - INFO - Processed 60300000 reads so far
2011-05-19 18:01:43,995 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:82990015-103010015
2011-05-19 18:01:48,332 - INFO - Processed 60400000 reads so far
2011-05-19 18:01:58,560 - INFO - Processed 60500000 reads so far
2011-05-19 18:02:05,587 - INFO - Processed 60600000 reads so far
2011-05-19 18:02:17,561 - INFO - Processed 60700000 reads so far
2011-05-19 18:02:24,520 - INFO - Processed 60800000 reads so far
2011-05-19 18:02:31,657 - INFO - Processed 60900000 reads so far
2011-05-19 18:02:41,589 - INFO - Processed 61000000 reads so far
2011-05-19 18:02:51,171 - INFO - Processed 61100000 reads so far
2011-05-19 18:02:58,089 - INFO - Processed 61200000 reads so far
2011-05-19 18:03:08,161 - INFO - Processed 61300000 reads so far
2011-05-19 18:03:17,192 - INFO - Processed 61400000 reads so far
2011-05-19 18:03:24,690 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:102990059-123010059
2011-05-19 18:03:26,514 - INFO - Processed 61500000 reads so far
2011-05-19 18:03:33,199 - INFO - Processed 61600000 reads so far
2011-05-19 18:03:39,741 - INFO - Processed 61700000 reads so far
2011-05-19 18:03:46,734 - INFO - Processed 61800000 reads so far
2011-05-19 18:03:54,132 - INFO - Processed 61900000 reads so far
2011-05-19 18:04:03,872 - INFO - Processed 62000000 reads so far
2011-05-19 18:04:12,039 - INFO - Processed 62100000 reads so far
2011-05-19 18:04:21,136 - INFO - Processed 62200000 reads so far
2011-05-19 18:04:36,106 - INFO - Processed 62300000 reads so far
2011-05-19 18:04:48,623 - INFO - Processed 62400000 reads so far
2011-05-19 18:05:00,157 - INFO - Processed 62500000 reads so far
2011-05-19 18:05:07,152 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:122990141-143010141
2011-05-19 18:05:10,250 - INFO - Processed 62600000 reads so far
2011-05-19 18:05:17,760 - INFO - Processed 62700000 reads so far
2011-05-19 18:05:27,762 - INFO - Processed 62800000 reads so far
2011-05-19 18:05:41,985 - INFO - Processed 62900000 reads so far
2011-05-19 18:05:53,160 - INFO - Processed 63000000 reads so far
2011-05-19 18:06:05,726 - INFO - Processed 63100000 reads so far
2011-05-19 18:06:15,417 - INFO - Processed 63200000 reads so far
2011-05-19 18:06:27,548 - INFO - Processed 63300000 reads so far
2011-05-19 18:06:35,722 - INFO - Processed 63400000 reads so far
2011-05-19 18:06:49,125 - INFO - Processed 63500000 reads so far
2011-05-19 18:07:00,190 - INFO - Processed 63600000 reads so far
2011-05-19 18:07:04,375 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:142990156-163010156
2011-05-19 18:07:09,952 - INFO - Processed 63700000 reads so far
2011-05-19 18:07:19,652 - INFO - Processed 63800000 reads so far
2011-05-19 18:07:30,140 - INFO - Processed 63900000 reads so far
2011-05-19 18:07:40,126 - INFO - Processed 64000000 reads so far
2011-05-19 18:07:51,952 - INFO - Processed 64100000 reads so far
2011-05-19 18:08:02,175 - INFO - Processed 64200000 reads so far
2011-05-19 18:08:11,392 - INFO - Processed 64300000 reads so far
2011-05-19 18:08:21,114 - INFO - Processed 64400000 reads so far
2011-05-19 18:08:33,397 - INFO - Processed 64500000 reads so far
2011-05-19 18:08:46,125 - INFO - Processed 64600000 reads so far
2011-05-19 18:08:55,750 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:162990160-183010160
2011-05-19 18:08:58,493 - INFO - Processed 64700000 reads so far
2011-05-19 18:09:11,221 - INFO - Processed 64800000 reads so far
2011-05-19 18:09:23,472 - INFO - Processed 64900000 reads so far
2011-05-19 18:09:34,960 - INFO - Processed 65000000 reads so far
2011-05-19 18:09:49,041 - INFO - Processed 65100000 reads so far
2011-05-19 18:10:00,895 - INFO - Processed 65200000 reads so far
2011-05-19 18:10:14,680 - INFO - Processed 65300000 reads so far
2011-05-19 18:10:25,242 - INFO - Processed 65400000 reads so far
2011-05-19 18:10:34,099 - INFO - Processed 65500000 reads so far
2011-05-19 18:10:43,319 - INFO - Processed 65600000 reads so far
2011-05-19 18:10:57,638 - INFO - Processed 65700000 reads so far
2011-05-19 18:11:06,253 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:182990174-203010174
2011-05-19 18:11:07,189 - INFO - Processed 65800000 reads so far
2011-05-19 18:11:15,651 - INFO - Processed 65900000 reads so far
2011-05-19 18:11:25,247 - INFO - Processed 66000000 reads so far
2011-05-19 18:11:38,394 - INFO - Processed 66100000 reads so far
2011-05-19 18:11:49,600 - INFO - Processed 66200000 reads so far
2011-05-19 18:12:00,226 - INFO - Processed 66300000 reads so far
2011-05-19 18:12:11,435 - INFO - Processed 66400000 reads so far
2011-05-19 18:12:22,308 - INFO - Processed 66500000 reads so far
2011-05-19 18:12:27,541 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1_random:0-20010004
2011-05-19 18:12:33,410 - INFO - Processed 66600000 reads so far
2011-05-19 18:12:47,007 - INFO - Processed 66700000 reads so far
2011-05-19 18:12:47,594 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:2989997-23009997
2011-05-19 18:12:55,780 - INFO - Processed 66800000 reads so far
2011-05-19 18:13:07,818 - INFO - Processed 66900000 reads so far
2011-05-19 18:13:19,781 - INFO - Processed 67000000 reads so far
2011-05-19 18:13:31,308 - INFO - Processed 67100000 reads so far
2011-05-19 18:13:43,309 - INFO - Processed 67200000 reads so far
2011-05-19 18:13:55,543 - INFO - Processed 67300000 reads so far
2011-05-19 18:14:06,108 - INFO - Processed 67400000 reads so far
2011-05-19 18:14:18,380 - INFO - Processed 67500000 reads so far
2011-05-19 18:14:31,651 - INFO - Processed 67600000 reads so far
2011-05-19 18:14:42,118 - INFO - Processed 67700000 reads so far
2011-05-19 18:14:53,568 - INFO - Processed 67800000 reads so far
2011-05-19 18:14:54,554 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:22990020-43010020
2011-05-19 18:15:01,903 - INFO - Processed 67900000 reads so far
2011-05-19 18:15:13,858 - INFO - Processed 68000000 reads so far
2011-05-19 18:15:25,907 - INFO - Processed 68100000 reads so far
2011-05-19 18:15:37,655 - INFO - Processed 68200000 reads so far
2011-05-19 18:15:48,684 - INFO - Processed 68300000 reads so far
2011-05-19 18:16:00,585 - INFO - Processed 68400000 reads so far
2011-05-19 18:16:10,801 - INFO - Processed 68500000 reads so far
2011-05-19 18:16:19,561 - INFO - Processed 68600000 reads so far
2011-05-19 18:16:31,337 - INFO - Processed 68700000 reads so far
2011-05-19 18:16:40,848 - INFO - Processed 68800000 reads so far
2011-05-19 18:16:46,214 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:42990024-63010024
2011-05-19 18:16:49,819 - INFO - Processed 68900000 reads so far
2011-05-19 18:16:58,214 - INFO - Processed 69000000 reads so far
2011-05-19 18:17:06,257 - INFO - Processed 69100000 reads so far
2011-05-19 18:17:19,022 - INFO - Processed 69200000 reads so far
2011-05-19 18:17:29,558 - INFO - Processed 69300000 reads so far
2011-05-19 18:17:38,228 - INFO - Processed 69400000 reads so far
2011-05-19 18:17:48,135 - INFO - Processed 69500000 reads so far
2011-05-19 18:17:56,737 - INFO - Processed 69600000 reads so far
2011-05-19 18:18:04,921 - INFO - Processed 69700000 reads so far
2011-05-19 18:24:12,434 - INFO - Processed 69800000 reads so far
2011-05-19 18:24:25,233 - INFO - Processed 69900000 reads so far
2011-05-19 18:24:28,218 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:62990025-83010025
2011-05-19 18:24:36,315 - INFO - Processed 70000000 reads so far
2011-05-19 18:24:45,176 - INFO - Processed 70100000 reads so far
2011-05-19 18:24:56,637 - INFO - Processed 70200000 reads so far
2011-05-19 18:25:09,826 - INFO - Processed 70300000 reads so far
2011-05-19 18:25:18,840 - INFO - Processed 70400000 reads so far
2011-05-19 18:25:29,707 - INFO - Processed 70500000 reads so far
2011-05-19 18:25:39,833 - INFO - Processed 70600000 reads so far
2011-05-19 18:25:50,483 - INFO - Processed 70700000 reads so far
2011-05-19 18:25:59,672 - INFO - Processed 70800000 reads so far
2011-05-19 18:26:09,745 - INFO - Processed 70900000 reads so far
2011-05-19 18:26:19,130 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:82990027-103010027
2011-05-19 18:26:19,639 - INFO - Processed 71000000 reads so far
2011-05-19 18:26:30,126 - INFO - Processed 71100000 reads so far
2011-05-19 18:26:39,858 - INFO - Processed 71200000 reads so far
2011-05-19 18:26:49,292 - INFO - Processed 71300000 reads so far
2011-05-19 18:26:59,600 - INFO - Processed 71400000 reads so far
2011-05-19 18:27:12,640 - INFO - Processed 71500000 reads so far
2011-05-19 18:27:25,625 - INFO - Processed 71600000 reads so far
2011-05-19 18:27:34,728 - INFO - Processed 71700000 reads so far
2011-05-19 18:27:42,905 - INFO - Processed 71800000 reads so far
2011-05-19 18:27:50,637 - INFO - Processed 71900000 reads so far
2011-05-19 18:27:59,644 - INFO - Processed 72000000 reads so far
2011-05-19 18:28:06,917 - INFO - Processed 72100000 reads so far
2011-05-19 18:28:13,849 - INFO - Processed 72200000 reads so far
2011-05-19 18:28:21,323 - INFO - Processed 72300000 reads so far
2011-05-19 18:28:29,778 - INFO - Processed 72400000 reads so far
2011-05-19 18:28:37,138 - INFO - Processed 72500000 reads so far
2011-05-19 18:28:44,225 - INFO - Processed 72600000 reads so far
2011-05-19 18:28:52,766 - INFO - Processed 72700000 reads so far
2011-05-19 18:29:04,355 - INFO - Processed 72800000 reads so far
2011-05-19 18:29:12,693 - INFO - Processed 72900000 reads so far
2011-05-19 18:29:19,828 - INFO - Processed 73000000 reads so far
2011-05-19 18:29:30,224 - INFO - Processed 73100000 reads so far
2011-05-19 18:29:37,373 - INFO - Processed 73200000 reads so far
2011-05-19 18:29:44,564 - INFO - Processed 73300000 reads so far
2011-05-19 18:29:53,029 - INFO - Processed 73400000 reads so far
2011-05-19 18:30:00,927 - INFO - Processed 73500000 reads so far
2011-05-19 18:30:09,857 - INFO - Processed 73600000 reads so far
2011-05-19 18:30:20,292 - INFO - Processed 73700000 reads so far
2011-05-19 18:30:30,611 - INFO - Processed 73800000 reads so far
2011-05-19 18:30:39,086 - INFO - Processed 73900000 reads so far
2011-05-19 18:30:48,263 - INFO - Processed 74000000 reads so far
2011-05-19 18:30:57,410 - INFO - Processed 74100000 reads so far
2011-05-19 18:31:04,003 - INFO - Processed 74200000 reads so far
2011-05-19 18:31:12,221 - INFO - Processed 74300000 reads so far
2011-05-19 18:31:23,308 - INFO - Processed 74400000 reads so far
2011-05-19 18:31:34,784 - INFO - Processed 74500000 reads so far
2011-05-19 18:31:42,703 - INFO - Processed 74600000 reads so far
2011-05-19 18:31:52,604 - INFO - Processed 74700000 reads so far
2011-05-19 18:32:00,413 - INFO - Processed 74800000 reads so far
2011-05-19 18:32:11,753 - INFO - Processed 74900000 reads so far
2011-05-19 18:32:20,016 - INFO - Processed 75000000 reads so far
2011-05-19 18:32:28,242 - INFO - Processed 75100000 reads so far
2011-05-19 18:32:36,234 - INFO - Processed 75200000 reads so far
2011-05-19 18:32:43,591 - INFO - Processed 75300000 reads so far
2011-05-19 18:32:51,476 - INFO - Processed 75400000 reads so far
2011-05-19 18:33:00,423 - INFO - Processed 75500000 reads so far
2011-05-19 18:33:08,481 - INFO - Processed 75600000 reads so far
2011-05-19 18:33:16,023 - INFO - Processed 75700000 reads so far
2011-05-19 18:33:23,311 - INFO - Processed 75800000 reads so far
2011-05-19 18:33:32,133 - INFO - Processed 75900000 reads so far
2011-05-19 18:33:44,092 - INFO - Processed 76000000 reads so far
2011-05-19 18:33:53,041 - INFO - Processed 76100000 reads so far
2011-05-19 18:34:03,413 - INFO - Processed 76200000 reads so far
2011-05-19 18:34:13,577 - INFO - Processed 76300000 reads so far
2011-05-19 18:34:22,315 - INFO - Processed 76400000 reads so far
2011-05-19 18:34:31,304 - INFO - Processed 76500000 reads so far
2011-05-19 18:34:44,818 - INFO - Processed 76600000 reads so far
2011-05-19 18:34:53,115 - INFO - Processed 76700000 reads so far
2011-05-19 18:35:01,192 - INFO - Processed 76800000 reads so far
2011-05-19 18:35:08,840 - INFO - Processed 76900000 reads so far
2011-05-19 18:35:15,695 - INFO - Processed 77000000 reads so far
2011-05-19 18:35:23,557 - INFO - Processed 77100000 reads so far
2011-05-19 18:35:30,855 - INFO - Processed 77200000 reads so far
2011-05-19 18:35:38,099 - INFO - Processed 77300000 reads so far
2011-05-19 18:35:46,391 - INFO - Processed 77400000 reads so far
2011-05-19 18:35:57,951 - INFO - Processed 77500000 reads so far
2011-05-19 18:36:08,945 - INFO - Processed 77600000 reads so far
2011-05-19 18:36:19,425 - INFO - Processed 77700000 reads so far
2011-05-19 18:36:35,168 - INFO - Processed 77800000 reads so far
2011-05-19 18:36:44,095 - INFO - Processed 77900000 reads so far
2011-05-19 18:36:53,742 - INFO - Processed 78000000 reads so far
2011-05-19 18:37:04,407 - INFO - Processed 78100000 reads so far
2011-05-19 18:37:14,601 - INFO - Processed 78200000 reads so far
2011-05-19 18:37:23,997 - INFO - Processed 78300000 reads so far
2011-05-19 18:37:35,321 - INFO - Processed 78400000 reads so far
2011-05-19 18:37:44,472 - INFO - Processed 78500000 reads so far
2011-05-19 18:37:53,575 - INFO - Processed 78600000 reads so far
2011-05-19 18:38:03,273 - INFO - Processed 78700000 reads so far
2011-05-19 18:38:11,971 - INFO - Processed 78800000 reads so far
2011-05-19 18:38:22,778 - INFO - Processed 78900000 reads so far
2011-05-19 18:38:31,683 - INFO - Processed 79000000 reads so far
2011-05-19 18:38:41,041 - INFO - Processed 79100000 reads so far
2011-05-19 18:38:54,231 - INFO - Processed 79200000 reads so far
2011-05-19 18:39:03,047 - INFO - Processed 79300000 reads so far
2011-05-19 18:39:14,416 - INFO - Processed 79400000 reads so far
2011-05-19 18:39:26,593 - INFO - Processed 79500000 reads so far
2011-05-19 18:39:35,764 - INFO - Processed 79600000 reads so far
2011-05-19 18:39:45,226 - INFO - Processed 79700000 reads so far
2011-05-19 18:39:53,729 - INFO - Processed 79800000 reads so far
2011-05-19 18:40:03,989 - INFO - Processed 79900000 reads so far
2011-05-19 18:40:10,020 - INFO - Processed 80000000 reads so far
2011-05-19 18:40:18,084 - INFO - Processed 80100000 reads so far
2011-05-19 18:40:25,790 - INFO - Processed 80200000 reads so far
2011-05-19 18:40:36,550 - INFO - Processed 80300000 reads so far
2011-05-19 18:40:45,767 - INFO - Processed 80400000 reads so far
2011-05-19 18:40:57,387 - INFO - Processed 80500000 reads so far
2011-05-19 18:41:04,739 - INFO - Processed 80600000 reads so far
2011-05-19 18:41:10,619 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:102990042-123010042
2011-05-19 18:41:17,449 - INFO - Processed 80700000 reads so far
2011-05-19 18:41:29,175 - INFO - Processed 80800000 reads so far
2011-05-19 18:41:38,160 - INFO - Processed 80900000 reads so far
2011-05-19 18:41:49,770 - INFO - Processed 81000000 reads so far
2011-05-19 18:42:00,441 - INFO - Processed 81100000 reads so far
2011-05-19 18:42:09,926 - INFO - Processed 81200000 reads so far
2011-05-19 18:42:21,438 - INFO - Processed 81300000 reads so far
2011-05-19 18:42:31,981 - INFO - Processed 81400000 reads so far
2011-05-19 18:42:41,125 - INFO - Processed 81500000 reads so far
2011-05-19 18:42:51,596 - INFO - Processed 81600000 reads so far
2011-05-19 18:43:00,552 - INFO - Processed 81700000 reads so far
2011-05-19 18:43:01,787 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:122990136-143010136
2011-05-19 18:43:08,338 - INFO - Processed 81800000 reads so far
2011-05-19 18:43:17,084 - INFO - Processed 81900000 reads so far
2011-05-19 18:43:26,137 - INFO - Processed 82000000 reads so far
2011-05-19 18:43:37,077 - INFO - Processed 82100000 reads so far
2011-05-19 18:43:50,555 - INFO - Processed 82200000 reads so far
2011-05-19 18:44:00,241 - INFO - Processed 82300000 reads so far
2011-05-19 18:44:12,128 - INFO - Processed 82400000 reads so far
2011-05-19 18:44:22,577 - INFO - Processed 82500000 reads so far
2011-05-19 18:44:31,508 - INFO - Processed 82600000 reads so far
2011-05-19 18:44:42,425 - INFO - Processed 82700000 reads so far
2011-05-19 18:44:56,024 - INFO - Processed 82800000 reads so far
2011-05-19 18:44:57,200 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:142990185-163010185
2011-05-19 18:45:05,407 - INFO - Processed 82900000 reads so far
2011-05-19 18:45:12,411 - INFO - Processed 83000000 reads so far
2011-05-19 18:45:23,574 - INFO - Processed 83100000 reads so far
2011-05-19 18:45:33,120 - INFO - Processed 83200000 reads so far
2011-05-19 18:45:41,315 - INFO - Processed 83300000 reads so far
2011-05-19 18:45:52,795 - INFO - Processed 83400000 reads so far
2011-05-19 18:46:03,613 - INFO - Processed 83500000 reads so far
2011-05-19 18:46:14,601 - INFO - Processed 83600000 reads so far
2011-05-19 18:46:27,771 - INFO - Processed 83700000 reads so far
2011-05-19 18:46:38,440 - INFO - Processed 83800000 reads so far
2011-05-19 18:46:48,459 - INFO - Processed 83900000 reads so far
2011-05-19 18:46:48,499 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:162990228-183010228
2011-05-19 18:46:57,209 - INFO - Processed 84000000 reads so far
2011-05-19 18:47:09,586 - INFO - Processed 84100000 reads so far
2011-05-19 18:47:19,480 - INFO - Processed 84200000 reads so far
2011-05-19 18:47:27,597 - INFO - Processed 84300000 reads so far
2011-05-19 18:47:35,397 - INFO - Processed 84400000 reads so far
2011-05-19 18:47:45,616 - INFO - Processed 84500000 reads so far
2011-05-19 18:47:52,456 - INFO - Processed 84600000 reads so far
2011-05-19 18:48:03,586 - INFO - Processed 84700000 reads so far
2011-05-19 18:48:11,181 - INFO - Processed 84800000 reads so far
2011-05-19 18:48:20,281 - INFO - Processed 84900000 reads so far
2011-05-19 18:48:20,438 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:2989997-23009997
2011-05-19 18:48:28,438 - INFO - Processed 85000000 reads so far
2011-05-19 18:48:38,220 - INFO - Processed 85100000 reads so far
2011-05-19 18:48:48,430 - INFO - Processed 85200000 reads so far
2011-05-19 18:48:56,786 - INFO - Processed 85300000 reads so far
2011-05-19 18:49:05,176 - INFO - Processed 85400000 reads so far
2011-05-19 18:49:14,009 - INFO - Processed 85500000 reads so far
2011-05-19 18:49:22,208 - INFO - Processed 85600000 reads so far
2011-05-19 18:49:31,444 - INFO - Processed 85700000 reads so far
2011-05-19 18:49:43,459 - INFO - Processed 85800000 reads so far
2011-05-19 18:49:50,719 - INFO - Processed 85900000 reads so far
2011-05-19 18:49:57,974 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:22990035-43010035
2011-05-19 18:50:02,774 - INFO - Processed 86000000 reads so far
2011-05-19 18:50:11,330 - INFO - Processed 86100000 reads so far
2011-05-19 18:50:18,891 - INFO - Processed 86200000 reads so far
2011-05-19 18:50:27,341 - INFO - Processed 86300000 reads so far
2011-05-19 18:50:38,704 - INFO - Processed 86400000 reads so far
2011-05-19 18:50:49,416 - INFO - Processed 86500000 reads so far
2011-05-19 18:50:58,303 - INFO - Processed 86600000 reads so far
2011-05-19 18:51:09,408 - INFO - Processed 86700000 reads so far
2011-05-19 18:51:17,757 - INFO - Processed 86800000 reads so far
2011-05-19 18:51:27,762 - INFO - Processed 86900000 reads so far
2011-05-19 18:51:38,541 - INFO - Processed 87000000 reads so far
2011-05-19 18:51:42,612 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:42990036-63010036
2011-05-19 18:51:46,062 - INFO - Processed 87100000 reads so far
2011-05-19 18:51:53,796 - INFO - Processed 87200000 reads so far
2011-05-19 18:52:01,218 - INFO - Processed 87300000 reads so far
2011-05-19 18:52:10,236 - INFO - Processed 87400000 reads so far
2011-05-19 18:52:20,936 - INFO - Processed 87500000 reads so far
2011-05-19 18:52:29,382 - INFO - Processed 87600000 reads so far
2011-05-19 18:52:36,893 - INFO - Processed 87700000 reads so far
2011-05-19 18:52:45,177 - INFO - Processed 87800000 reads so far
2011-05-19 18:52:56,395 - INFO - Processed 87900000 reads so far
2011-05-19 18:53:05,572 - INFO - Processed 88000000 reads so far
2011-05-19 18:53:14,109 - INFO - Processed 88100000 reads so far
2011-05-19 18:53:14,433 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:62990088-83010088
2011-05-19 18:53:21,730 - INFO - Processed 88200000 reads so far
2011-05-19 18:53:34,053 - INFO - Processed 88300000 reads so far
2011-05-19 18:53:47,811 - INFO - Processed 88400000 reads so far
2011-05-19 18:53:56,869 - INFO - Processed 88500000 reads so far
2011-05-19 18:54:05,736 - INFO - Processed 88600000 reads so far
2011-05-19 18:54:15,373 - INFO - Processed 88700000 reads so far
2011-05-19 18:55:02,010 - INFO - Processed 88800000 reads so far
2011-05-19 18:55:11,863 - INFO - Processed 88900000 reads so far
2011-05-19 18:55:24,931 - INFO - Processed 89000000 reads so far
2011-05-19 18:55:35,911 - INFO - Processed 89100000 reads so far
2011-05-19 18:55:40,389 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:82990100-103010100
2011-05-19 18:55:44,888 - INFO - Processed 89200000 reads so far
2011-05-19 18:55:55,266 - INFO - Processed 89300000 reads so far
2011-05-19 18:56:06,995 - INFO - Processed 89400000 reads so far
2011-05-19 18:56:18,642 - INFO - Processed 89500000 reads so far
2011-05-19 18:56:34,399 - INFO - Processed 89600000 reads so far
2011-05-19 18:56:45,542 - INFO - Processed 89700000 reads so far
2011-05-19 18:56:57,051 - INFO - Processed 89800000 reads so far
2011-05-19 18:57:06,509 - INFO - Processed 89900000 reads so far
2011-05-19 18:57:18,347 - INFO - Processed 90000000 reads so far
2011-05-19 18:57:30,977 - INFO - Processed 90100000 reads so far
2011-05-19 18:57:42,283 - INFO - Processed 90200000 reads so far
2011-05-19 18:57:49,099 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:102990156-123010156
2011-05-19 18:57:56,236 - INFO - Processed 90300000 reads so far
2011-05-19 18:58:07,159 - INFO - Processed 90400000 reads so far
2011-05-19 18:58:18,598 - INFO - Processed 90500000 reads so far
2011-05-19 18:58:31,030 - INFO - Processed 90600000 reads so far
2011-05-19 18:58:42,508 - INFO - Processed 90700000 reads so far
2011-05-19 18:58:53,333 - INFO - Processed 90800000 reads so far
2011-05-19 18:59:01,544 - INFO - Processed 90900000 reads so far
2011-05-19 18:59:11,699 - INFO - Processed 91000000 reads so far
2011-05-19 18:59:22,342 - INFO - Processed 91100000 reads so far
2011-05-19 18:59:33,456 - INFO - Processed 91200000 reads so far
2011-05-19 18:59:44,326 - INFO - Processed 91300000 reads so far
2011-05-19 18:59:45,407 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:122990164-143010164
2011-05-19 18:59:54,993 - INFO - Processed 91400000 reads so far
2011-05-19 19:00:06,379 - INFO - Processed 91500000 reads so far
2011-05-19 19:00:15,483 - INFO - Processed 91600000 reads so far
2011-05-19 19:00:25,067 - INFO - Processed 91700000 reads so far
2011-05-19 19:00:35,328 - INFO - Processed 91800000 reads so far
2011-05-19 19:00:43,067 - INFO - Processed 91900000 reads so far
2011-05-19 19:00:53,919 - INFO - Processed 92000000 reads so far
2011-05-19 19:01:03,472 - INFO - Processed 92100000 reads so far
2011-05-19 19:01:15,957 - INFO - Processed 92200000 reads so far
2011-05-19 19:01:27,446 - INFO - Processed 92300000 reads so far
2011-05-19 19:01:39,972 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:142990180-163010180
2011-05-19 19:01:40,623 - INFO - Processed 92400000 reads so far
2011-05-19 19:01:49,157 - INFO - Processed 92500000 reads so far
2011-05-19 19:01:58,100 - INFO - Processed 92600000 reads so far
2011-05-19 19:02:11,651 - INFO - Processed 92700000 reads so far
2011-05-19 19:02:23,207 - INFO - Processed 92800000 reads so far
2011-05-19 19:02:31,670 - INFO - Processed 92900000 reads so far
2011-05-19 19:02:41,174 - INFO - Processed 93000000 reads so far
2011-05-19 19:02:53,613 - INFO - Processed 93100000 reads so far
2011-05-19 19:03:06,327 - INFO - Processed 93200000 reads so far
2011-05-19 19:03:17,450 - INFO - Processed 93300000 reads so far
2011-05-19 19:03:19,315 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3_random:0-20010136
2011-05-19 19:03:19,442 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:2989959-23009959
2011-05-19 19:03:30,332 - INFO - Processed 93400000 reads so far
2011-05-19 19:03:41,037 - INFO - Processed 93500000 reads so far
2011-05-19 19:03:53,060 - INFO - Processed 93600000 reads so far
2011-05-19 19:04:04,179 - INFO - Processed 93700000 reads so far
2011-05-19 19:04:15,505 - INFO - Processed 93800000 reads so far
2011-05-19 19:04:26,646 - INFO - Processed 93900000 reads so far
2011-05-19 19:04:39,092 - INFO - Processed 94000000 reads so far
2011-05-19 19:04:50,352 - INFO - Processed 94100000 reads so far
2011-05-19 19:05:03,158 - INFO - Processed 94200000 reads so far
2011-05-19 19:05:16,373 - INFO - Processed 94300000 reads so far
2011-05-19 19:05:29,588 - INFO - Processed 94400000 reads so far
2011-05-19 19:05:31,682 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:22989966-43009966
2011-05-19 19:05:40,697 - INFO - Processed 94500000 reads so far
2011-05-19 19:05:52,139 - INFO - Processed 94600000 reads so far
2011-05-19 19:06:03,384 - INFO - Processed 94700000 reads so far
2011-05-19 19:06:13,987 - INFO - Processed 94800000 reads so far
2011-05-19 19:06:29,281 - INFO - Processed 94900000 reads so far
2011-05-19 19:06:40,251 - INFO - Processed 95000000 reads so far
2011-05-19 19:06:51,282 - INFO - Processed 95100000 reads so far
2011-05-19 19:07:03,167 - INFO - Processed 95200000 reads so far
2011-05-19 19:07:15,063 - INFO - Processed 95300000 reads so far
2011-05-19 19:07:26,165 - INFO - Processed 95400000 reads so far
2011-05-19 19:07:30,759 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:42989982-63009982
2011-05-19 19:07:39,234 - INFO - Processed 95500000 reads so far
2011-05-19 19:07:47,511 - INFO - Processed 95600000 reads so far
2011-05-19 19:07:59,364 - INFO - Processed 95700000 reads so far
2011-05-19 19:08:12,384 - INFO - Processed 95800000 reads so far
2011-05-19 19:08:25,005 - INFO - Processed 95900000 reads so far
2011-05-19 19:08:36,164 - INFO - Processed 96000000 reads so far
2011-05-19 19:08:49,099 - INFO - Processed 96100000 reads so far
2011-05-19 19:08:59,953 - INFO - Processed 96200000 reads so far
2011-05-19 19:09:10,510 - INFO - Processed 96300000 reads so far
2011-05-19 19:09:21,935 - INFO - Processed 96400000 reads so far
2011-05-19 19:09:33,260 - INFO - Processed 96500000 reads so far
2011-05-19 19:09:36,407 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:62990005-83010005
2011-05-19 19:09:44,656 - INFO - Processed 96600000 reads so far
2011-05-19 19:09:57,385 - INFO - Processed 96700000 reads so far
2011-05-19 19:10:08,585 - INFO - Processed 96800000 reads so far
2011-05-19 19:10:48,261 - INFO - Processed 96900000 reads so far
2011-05-19 19:11:23,687 - INFO - Processed 97000000 reads so far
2011-05-19 19:11:41,307 - INFO - Processed 97100000 reads so far
2011-05-19 19:11:57,377 - INFO - Processed 97200000 reads so far
2011-05-19 19:12:05,675 - INFO - Processed 97300000 reads so far
2011-05-19 19:12:16,564 - INFO - Processed 97400000 reads so far
2011-05-19 19:12:28,859 - INFO - Processed 97500000 reads so far
2011-05-19 19:12:40,613 - INFO - Processed 97600000 reads so far
2011-05-19 19:12:41,931 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:82990044-103010044
2011-05-19 19:12:50,831 - INFO - Processed 97700000 reads so far
2011-05-19 19:13:00,839 - INFO - Processed 97800000 reads so far
2011-05-19 19:13:10,719 - INFO - Processed 97900000 reads so far
2011-05-19 19:13:19,641 - INFO - Processed 98000000 reads so far
2011-05-19 19:13:28,898 - INFO - Processed 98100000 reads so far
2011-05-19 19:13:39,769 - INFO - Processed 98200000 reads so far
2011-05-19 19:13:54,745 - INFO - Processed 98300000 reads so far
2011-05-19 19:14:05,948 - INFO - Processed 98400000 reads so far
2011-05-19 19:14:17,039 - INFO - Processed 98500000 reads so far
2011-05-19 19:14:28,083 - INFO - Processed 98600000 reads so far
2011-05-19 19:14:35,683 - INFO - Processed 98700000 reads so far
2011-05-19 19:14:36,566 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:102990078-123010078
2011-05-19 19:14:44,842 - INFO - Processed 98800000 reads so far
2011-05-19 19:14:55,621 - INFO - Processed 98900000 reads so far
2011-05-19 19:15:06,170 - INFO - Processed 99000000 reads so far
2011-05-19 19:15:14,282 - INFO - Processed 99100000 reads so far
2011-05-19 19:15:23,516 - INFO - Processed 99200000 reads so far
2011-05-19 19:15:32,100 - INFO - Processed 99300000 reads so far
2011-05-19 19:15:45,032 - INFO - Processed 99400000 reads so far
2011-05-19 19:15:53,891 - INFO - Processed 99500000 reads so far
2011-05-19 19:16:02,821 - INFO - Processed 99600000 reads so far
2011-05-19 19:16:12,823 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:122990111-143010111
2011-05-19 19:16:13,087 - INFO - Processed 99700000 reads so far
2011-05-19 19:16:27,846 - INFO - Processed 99800000 reads so far
2011-05-19 19:16:40,355 - INFO - Processed 99900000 reads so far
2011-05-19 19:16:52,361 - INFO - Processed 100000000 reads so far
2011-05-19 19:17:03,895 - INFO - Processed 100100000 reads so far
2011-05-19 19:17:16,176 - INFO - Processed 100200000 reads so far
2011-05-19 19:17:29,450 - INFO - Processed 100300000 reads so far
2011-05-19 19:17:40,469 - INFO - Processed 100400000 reads so far
2011-05-19 19:17:52,170 - INFO - Processed 100500000 reads so far
2011-05-19 19:18:03,869 - INFO - Processed 100600000 reads so far
2011-05-19 19:18:16,389 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:142990127-163010127
2011-05-19 19:18:16,617 - INFO - Processed 100700000 reads so far
2011-05-19 19:18:28,866 - INFO - Processed 100800000 reads so far
2011-05-19 19:18:38,649 - INFO - Processed 100900000 reads so far
2011-05-19 19:18:48,287 - INFO - Processed 101000000 reads so far
2011-05-19 19:18:57,904 - INFO - Processed 101100000 reads so far
2011-05-19 19:19:11,123 - INFO - Processed 101200000 reads so far
2011-05-19 19:19:21,833 - INFO - Processed 101300000 reads so far
2011-05-19 19:19:32,873 - INFO - Processed 101400000 reads so far
2011-05-19 19:19:45,571 - INFO - Processed 101500000 reads so far
2011-05-19 19:19:46,479 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4_random:0-20010008
2011-05-19 19:19:47,491 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:2990042-23010042
2011-05-19 19:20:00,222 - INFO - Processed 101600000 reads so far
2011-05-19 19:20:11,367 - INFO - Processed 101700000 reads so far
2011-05-19 19:20:22,546 - INFO - Processed 101800000 reads so far
2011-05-19 19:20:32,627 - INFO - Processed 101900000 reads so far
2011-05-19 19:20:42,684 - INFO - Processed 102000000 reads so far
2011-05-19 19:20:55,494 - INFO - Processed 102100000 reads so far
2011-05-19 19:21:05,003 - INFO - Processed 102200000 reads so far
2011-05-19 19:21:16,031 - INFO - Processed 102300000 reads so far
2011-05-19 19:21:27,759 - INFO - Processed 102400000 reads so far
2011-05-19 19:21:40,681 - INFO - Processed 102500000 reads so far
2011-05-19 19:21:49,882 - INFO - Processed 102600000 reads so far
2011-05-19 19:21:50,773 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:22990522-43010522
2011-05-19 19:22:01,170 - INFO - Processed 102700000 reads so far
2011-05-19 19:22:12,208 - INFO - Processed 102800000 reads so far
2011-05-19 19:22:23,230 - INFO - Processed 102900000 reads so far
2011-05-19 19:22:33,190 - INFO - Processed 103000000 reads so far
2011-05-19 19:22:44,165 - INFO - Processed 103100000 reads so far
2011-05-19 19:22:52,706 - INFO - Processed 103200000 reads so far
2011-05-19 19:23:02,914 - INFO - Processed 103300000 reads so far
2011-05-19 19:23:14,558 - INFO - Processed 103400000 reads so far
2011-05-19 19:23:26,718 - INFO - Processed 103500000 reads so far
2011-05-19 19:23:35,095 - INFO - Processed 103600000 reads so far
2011-05-19 19:23:41,000 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:42990573-63010573
2011-05-19 19:23:45,181 - INFO - Processed 103700000 reads so far
2011-05-19 19:23:53,470 - INFO - Processed 103800000 reads so far
2011-05-19 19:24:02,548 - INFO - Processed 103900000 reads so far
2011-05-19 19:24:11,919 - INFO - Processed 104000000 reads so far
2011-05-19 19:24:21,199 - INFO - Processed 104100000 reads so far
2011-05-19 19:24:32,211 - INFO - Processed 104200000 reads so far
2011-05-19 19:24:42,781 - INFO - Processed 104300000 reads so far
2011-05-19 19:24:51,933 - INFO - Processed 104400000 reads so far
2011-05-19 19:25:01,283 - INFO - Processed 104500000 reads so far
2011-05-19 19:25:11,048 - INFO - Processed 104600000 reads so far
2011-05-19 19:25:20,459 - INFO - Processed 104700000 reads so far
2011-05-19 19:25:21,851 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:62990584-83010584
2011-05-19 19:25:32,474 - INFO - Processed 104800000 reads so far
2011-05-19 19:25:47,738 - INFO - Processed 104900000 reads so far
2011-05-19 19:26:00,499 - INFO - Processed 105000000 reads so far
2011-05-19 19:26:12,244 - INFO - Processed 105100000 reads so far
2011-05-19 19:26:23,272 - INFO - Processed 105200000 reads so far
2011-05-19 19:26:31,692 - INFO - Processed 105300000 reads so far
2011-05-19 19:26:39,372 - INFO - Processed 105400000 reads so far
2011-05-19 19:26:48,550 - INFO - Processed 105500000 reads so far
2011-05-19 19:26:59,875 - INFO - Processed 105600000 reads so far
2011-05-19 19:27:08,255 - INFO - Processed 105700000 reads so far
2011-05-19 19:27:15,036 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:82990605-103010605
2011-05-19 19:27:17,405 - INFO - Processed 105800000 reads so far
2011-05-19 19:27:29,008 - INFO - Processed 105900000 reads so far
2011-05-19 19:27:36,988 - INFO - Processed 106000000 reads so far
2011-05-19 19:27:43,830 - INFO - Processed 106100000 reads so far
2011-05-19 19:27:52,632 - INFO - Processed 106200000 reads so far
2011-05-19 19:28:05,617 - INFO - Processed 106300000 reads so far
2011-05-19 19:28:16,366 - INFO - Processed 106400000 reads so far
2011-05-19 19:28:27,093 - INFO - Processed 106500000 reads so far
2011-05-19 19:28:38,310 - INFO - Processed 106600000 reads so far
2011-05-19 19:28:49,525 - INFO - Processed 106700000 reads so far
2011-05-19 19:28:59,157 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:102990620-123010620
2011-05-19 19:29:00,718 - INFO - Processed 106800000 reads so far
2011-05-19 19:29:14,591 - INFO - Processed 106900000 reads so far
2011-05-19 19:29:26,491 - INFO - Processed 107000000 reads so far
2011-05-19 19:29:37,694 - INFO - Processed 107100000 reads so far
2011-05-19 19:29:48,451 - INFO - Processed 107200000 reads so far
2011-05-19 19:29:59,816 - INFO - Processed 107300000 reads so far
2011-05-19 19:30:11,209 - INFO - Processed 107400000 reads so far
2011-05-19 19:30:25,458 - INFO - Processed 107500000 reads so far
2011-05-19 19:30:36,617 - INFO - Processed 107600000 reads so far
2011-05-19 19:30:48,369 - INFO - Processed 107700000 reads so far
2011-05-19 19:31:01,313 - INFO - Processed 107800000 reads so far
2011-05-19 19:31:04,531 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:122990642-143010642
2011-05-19 19:31:12,038 - INFO - Processed 107900000 reads so far
2011-05-19 19:31:23,695 - INFO - Processed 108000000 reads so far
2011-05-19 19:31:40,201 - INFO - Processed 108100000 reads so far
2011-05-19 19:31:51,160 - INFO - Processed 108200000 reads so far
2011-05-19 19:32:01,893 - INFO - Processed 108300000 reads so far
2011-05-19 19:32:18,243 - INFO - Processed 108400000 reads so far
2011-05-19 19:32:29,959 - INFO - Processed 108500000 reads so far
2011-05-19 19:32:46,728 - INFO - Processed 108600000 reads so far
2011-05-19 19:33:00,355 - INFO - Processed 108700000 reads so far
2011-05-19 19:33:11,423 - INFO - Processed 108800000 reads so far
2011-05-19 19:33:21,335 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:142990682-163010682
2011-05-19 19:33:23,391 - INFO - Processed 108900000 reads so far
2011-05-19 19:33:31,067 - INFO - Processed 109000000 reads so far
2011-05-19 19:33:42,152 - INFO - Processed 109100000 reads so far
2011-05-19 19:33:53,871 - INFO - Processed 109200000 reads so far
2011-05-19 19:34:05,850 - INFO - Processed 109300000 reads so far
2011-05-19 19:34:15,907 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5_random:0-20010083
2011-05-19 19:34:16,287 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:2989998-23009998
2011-05-19 19:34:16,928 - INFO - Processed 109400000 reads so far
2011-05-19 19:34:29,010 - INFO - Processed 109500000 reads so far
2011-05-19 19:34:38,834 - INFO - Processed 109600000 reads so far
2011-05-19 19:34:47,760 - INFO - Processed 109700000 reads so far
2011-05-19 19:34:55,528 - INFO - Processed 109800000 reads so far
2011-05-19 19:35:04,782 - INFO - Processed 109900000 reads so far
2011-05-19 19:35:14,096 - INFO - Processed 110000000 reads so far
2011-05-19 19:35:23,124 - INFO - Processed 110100000 reads so far
2011-05-19 19:35:35,148 - INFO - Processed 110200000 reads so far
2011-05-19 19:35:46,460 - INFO - Processed 110300000 reads so far
2011-05-19 19:35:57,558 - INFO - Processed 110400000 reads so far
2011-05-19 19:36:04,751 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:22990005-43010005
2011-05-19 19:36:09,616 - INFO - Processed 110500000 reads so far
2011-05-19 19:36:19,801 - INFO - Processed 110600000 reads so far
2011-05-19 19:36:30,794 - INFO - Processed 110700000 reads so far
2011-05-19 19:36:42,508 - INFO - Processed 110800000 reads so far
2011-05-19 19:36:52,817 - INFO - Processed 110900000 reads so far
2011-05-19 19:37:01,494 - INFO - Processed 111000000 reads so far
2011-05-19 19:37:12,586 - INFO - Processed 111100000 reads so far
2011-05-19 19:37:21,404 - INFO - Processed 111200000 reads so far
2011-05-19 19:37:29,699 - INFO - Processed 111300000 reads so far
2011-05-19 19:37:38,623 - INFO - Processed 111400000 reads so far
2011-05-19 19:37:47,890 - INFO - Processed 111500000 reads so far
2011-05-19 19:37:52,142 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:42990021-63010021
2011-05-19 19:37:58,099 - INFO - Processed 111600000 reads so far
2011-05-19 19:38:06,885 - INFO - Processed 111700000 reads so far
2011-05-19 19:38:17,209 - INFO - Processed 111800000 reads so far
2011-05-19 19:38:27,314 - INFO - Processed 111900000 reads so far
2011-05-19 19:38:38,101 - INFO - Processed 112000000 reads so far
2011-05-19 19:38:47,632 - INFO - Processed 112100000 reads so far
2011-05-19 19:38:56,195 - INFO - Processed 112200000 reads so far
2011-05-19 19:39:05,606 - INFO - Processed 112300000 reads so far
2011-05-19 19:39:15,408 - INFO - Processed 112400000 reads so far
2011-05-19 19:39:25,420 - INFO - Processed 112500000 reads so far
2011-05-19 19:39:34,415 - INFO - Processed 112600000 reads so far
2011-05-19 19:39:40,350 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:62990035-83010035
2011-05-19 19:39:42,496 - INFO - Processed 112700000 reads so far
2011-05-19 19:39:51,325 - INFO - Processed 112800000 reads so far
2011-05-19 19:39:58,805 - INFO - Processed 112900000 reads so far
2011-05-19 19:40:36,334 - INFO - Processed 113000000 reads so far
2011-05-19 19:40:45,179 - INFO - Processed 113100000 reads so far
2011-05-19 19:40:53,735 - INFO - Processed 113200000 reads so far
2011-05-19 19:41:03,416 - INFO - Processed 113300000 reads so far
2011-05-19 19:41:13,000 - INFO - Processed 113400000 reads so far
2011-05-19 19:41:21,274 - INFO - Processed 113500000 reads so far
2011-05-19 19:41:31,238 - INFO - Processed 113600000 reads so far
2011-05-19 19:41:42,530 - INFO - Processed 113700000 reads so far
2011-05-19 19:41:43,892 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:82990037-103010037
2011-05-19 19:41:51,557 - INFO - Processed 113800000 reads so far
2011-05-19 19:42:00,750 - INFO - Processed 113900000 reads so far
2011-05-19 19:42:11,566 - INFO - Processed 114000000 reads so far
2011-05-19 19:42:20,097 - INFO - Processed 114100000 reads so far
2011-05-19 19:42:33,015 - INFO - Processed 114200000 reads so far
2011-05-19 19:42:42,112 - INFO - Processed 114300000 reads so far
2011-05-19 19:42:55,199 - INFO - Processed 114400000 reads so far
2011-05-19 19:43:04,426 - INFO - Processed 114500000 reads so far
2011-05-19 19:43:13,236 - INFO - Processed 114600000 reads so far
2011-05-19 19:43:23,461 - INFO - Processed 114700000 reads so far
2011-05-19 19:43:31,860 - INFO - Processed 114800000 reads so far
2011-05-19 19:43:32,356 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:102990046-123010046
2011-05-19 19:43:42,608 - INFO - Processed 114900000 reads so far
2011-05-19 19:43:54,260 - INFO - Processed 115000000 reads so far
2011-05-19 19:44:05,368 - INFO - Processed 115100000 reads so far
2011-05-19 19:44:12,962 - INFO - Processed 115200000 reads so far
2011-05-19 19:44:22,873 - INFO - Processed 115300000 reads so far
2011-05-19 19:44:33,493 - INFO - Processed 115400000 reads so far
2011-05-19 19:44:44,619 - INFO - Processed 115500000 reads so far
2011-05-19 19:44:53,885 - INFO - Processed 115600000 reads so far
2011-05-19 19:45:03,359 - INFO - Processed 115700000 reads so far
2011-05-19 19:45:16,911 - INFO - Processed 115800000 reads so far
2011-05-19 19:45:27,754 - INFO - Processed 115900000 reads so far
2011-05-19 19:45:41,678 - INFO - Processed 116000000 reads so far
2011-05-19 19:45:53,488 - INFO - Processed 116100000 reads so far
2011-05-19 19:46:03,402 - INFO - Processed 116200000 reads so far
2011-05-19 19:46:17,396 - INFO - Processed 116300000 reads so far
2011-05-19 19:46:33,810 - INFO - Processed 116400000 reads so far
2011-05-19 19:46:46,331 - INFO - Processed 116500000 reads so far
2011-05-19 19:46:57,478 - INFO - Processed 116600000 reads so far
2011-05-19 19:47:08,970 - INFO - Processed 116700000 reads so far
2011-05-19 19:47:22,171 - INFO - Processed 116800000 reads so far
2011-05-19 19:47:26,015 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:122990048-143010048
2011-05-19 19:47:30,539 - INFO - Processed 116900000 reads so far
2011-05-19 19:47:39,730 - INFO - Processed 117000000 reads so far
2011-05-19 19:47:49,228 - INFO - Processed 117100000 reads so far
2011-05-19 19:48:00,524 - INFO - Processed 117200000 reads so far
2011-05-19 19:48:12,312 - INFO - Processed 117300000 reads so far
2011-05-19 19:48:22,290 - INFO - Processed 117400000 reads so far
2011-05-19 19:48:33,165 - INFO - Processed 117500000 reads so far
2011-05-19 19:48:42,917 - INFO - Processed 117600000 reads so far
2011-05-19 19:48:51,676 - INFO - Processed 117700000 reads so far
2011-05-19 19:49:01,256 - INFO - Processed 117800000 reads so far
2011-05-19 19:49:11,813 - INFO - Processed 117900000 reads so far
2011-05-19 19:49:18,650 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:142990050-163010050
2011-05-19 19:49:19,213 - INFO - Processed 118000000 reads so far
2011-05-19 19:49:27,025 - INFO - Processed 118100000 reads so far
2011-05-19 19:49:38,445 - INFO - Processed 118200000 reads so far
2011-05-19 19:49:49,452 - INFO - Processed 118300000 reads so far
2011-05-19 19:49:53,880 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:2990057-23010057
2011-05-19 19:49:58,219 - INFO - Processed 118400000 reads so far
2011-05-19 19:50:06,196 - INFO - Processed 118500000 reads so far
2011-05-19 19:50:15,279 - INFO - Processed 118600000 reads so far
2011-05-19 19:50:23,780 - INFO - Processed 118700000 reads so far
2011-05-19 19:50:31,622 - INFO - Processed 118800000 reads so far
2011-05-19 19:50:41,681 - INFO - Processed 118900000 reads so far
2011-05-19 19:50:50,336 - INFO - Processed 119000000 reads so far
2011-05-19 19:50:58,201 - INFO - Processed 119100000 reads so far
2011-05-19 19:51:11,268 - INFO - Processed 119200000 reads so far
2011-05-19 19:51:15,986 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:22990173-43010173
2011-05-19 19:51:20,510 - INFO - Processed 119300000 reads so far
2011-05-19 19:51:31,002 - INFO - Processed 119400000 reads so far
2011-05-19 19:51:40,050 - INFO - Processed 119500000 reads so far
2011-05-19 19:51:50,761 - INFO - Processed 119600000 reads so far
2011-05-19 19:52:02,041 - INFO - Processed 119700000 reads so far
2011-05-19 19:52:10,535 - INFO - Processed 119800000 reads so far
2011-05-19 19:52:20,293 - INFO - Processed 119900000 reads so far
2011-05-19 19:52:29,555 - INFO - Processed 120000000 reads so far
2011-05-19 19:52:33,979 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:46351716-66371716
2011-05-19 19:52:39,225 - INFO - Processed 120100000 reads so far
2011-05-19 19:52:47,317 - INFO - Processed 120200000 reads so far
2011-05-19 19:52:55,732 - INFO - Processed 120300000 reads so far
2011-05-19 19:53:06,458 - INFO - Processed 120400000 reads so far
2011-05-19 19:53:18,121 - INFO - Processed 120500000 reads so far
2011-05-19 19:53:27,009 - INFO - Processed 120600000 reads so far
2011-05-19 19:53:36,322 - INFO - Processed 120700000 reads so far
2011-05-19 19:53:46,662 - INFO - Processed 120800000 reads so far
2011-05-19 19:53:56,397 - INFO - Processed 120900000 reads so far
2011-05-19 19:54:03,913 - INFO - Processed 121000000 reads so far
2011-05-19 19:54:11,786 - INFO - Processed 121100000 reads so far
2011-05-19 19:54:12,889 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:66351728-86371728
2011-05-19 19:54:21,998 - INFO - Processed 121200000 reads so far
2011-05-19 19:54:29,921 - INFO - Processed 121300000 reads so far
2011-05-19 19:54:38,994 - INFO - Processed 121400000 reads so far
2011-05-19 19:54:47,445 - INFO - Processed 121500000 reads so far
2011-05-19 19:54:58,121 - INFO - Processed 121600000 reads so far
2011-05-19 19:55:07,055 - INFO - Processed 121700000 reads so far
2011-05-19 19:55:14,154 - INFO - Processed 121800000 reads so far
2011-05-19 19:55:24,031 - INFO - Processed 121900000 reads so far
2011-05-19 19:55:34,789 - INFO - Processed 122000000 reads so far
2011-05-19 19:55:42,449 - INFO - Processed 122100000 reads so far
2011-05-19 19:55:49,878 - INFO - Processed 122200000 reads so far
2011-05-19 19:55:52,093 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:86351762-106371762
2011-05-19 19:55:59,803 - INFO - Processed 122300000 reads so far
2011-05-19 19:56:10,356 - INFO - Processed 122400000 reads so far
2011-05-19 19:56:19,964 - INFO - Processed 122500000 reads so far
2011-05-19 19:56:28,375 - INFO - Processed 122600000 reads so far
2011-05-19 19:56:36,651 - INFO - Processed 122700000 reads so far
2011-05-19 19:56:44,088 - INFO - Processed 122800000 reads so far
2011-05-19 19:56:50,856 - INFO - Processed 122900000 reads so far
2011-05-19 19:56:59,034 - INFO - Processed 123000000 reads so far
2011-05-19 19:57:07,301 - INFO - Processed 123100000 reads so far
2011-05-19 19:57:16,081 - INFO - Processed 123200000 reads so far
2011-05-19 19:57:26,723 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:106351775-126371775
2011-05-19 19:57:27,409 - INFO - Processed 123300000 reads so far
2011-05-19 19:57:38,413 - INFO - Processed 123400000 reads so far
2011-05-19 19:57:50,177 - INFO - Processed 123500000 reads so far
2011-05-19 19:58:01,646 - INFO - Processed 123600000 reads so far
2011-05-19 19:58:11,733 - INFO - Processed 123700000 reads so far
2011-05-19 19:58:21,796 - INFO - Processed 123800000 reads so far
2011-05-19 19:58:32,999 - INFO - Processed 123900000 reads so far
2011-05-19 19:58:43,998 - INFO - Processed 124000000 reads so far
2011-05-19 19:58:56,132 - INFO - Processed 124100000 reads so far
2011-05-19 19:59:07,813 - INFO - Processed 124200000 reads so far
2011-05-19 19:59:18,453 - INFO - Processed 124300000 reads so far
2011-05-19 19:59:25,430 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:126351786-146371786
2011-05-19 19:59:29,540 - INFO - Processed 124400000 reads so far
2011-05-19 19:59:42,627 - INFO - Processed 124500000 reads so far
2011-05-19 19:59:52,745 - INFO - Processed 124600000 reads so far
2011-05-19 20:00:02,681 - INFO - Processed 124700000 reads so far
2011-05-19 20:00:13,414 - INFO - Processed 124800000 reads so far
2011-05-19 20:00:25,654 - INFO - Processed 124900000 reads so far
2011-05-19 20:00:38,848 - INFO - Processed 125000000 reads so far
2011-05-19 20:00:50,094 - INFO - Processed 125100000 reads so far
2011-05-19 20:01:00,707 - INFO - Processed 125200000 reads so far
2011-05-19 20:01:11,715 - INFO - Processed 125300000 reads so far
2011-05-19 20:01:24,124 - INFO - Processed 125400000 reads so far
2011-05-19 20:01:34,352 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:146351787-166371787
2011-05-19 20:01:38,739 - INFO - Processed 125500000 reads so far
2011-05-19 20:01:54,962 - INFO - Processed 125600000 reads so far
2011-05-19 20:02:08,608 - INFO - Processed 125700000 reads so far
2011-05-19 20:02:18,642 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7_random:0-20010061
2011-05-19 20:02:19,161 - INFO - Processed 125800000 reads so far
2011-05-19 20:02:20,165 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:2990021-23010021
2011-05-19 20:02:28,402 - INFO - Processed 125900000 reads so far
2011-05-19 20:02:42,193 - INFO - Processed 126000000 reads so far
2011-05-19 20:02:54,432 - INFO - Processed 126100000 reads so far
2011-05-19 20:03:05,077 - INFO - Processed 126200000 reads so far
2011-05-19 20:03:16,788 - INFO - Processed 126300000 reads so far
2011-05-19 20:03:32,262 - INFO - Processed 126400000 reads so far
2011-05-19 20:03:45,568 - INFO - Processed 126500000 reads so far
2011-05-19 20:03:59,522 - INFO - Processed 126600000 reads so far
2011-05-19 20:04:09,901 - INFO - Processed 126700000 reads so far
2011-05-19 20:04:19,545 - INFO - Processed 126800000 reads so far
2011-05-19 20:04:31,581 - INFO - Processed 126900000 reads so far
2011-05-19 20:04:40,300 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:22990028-43010028
2011-05-19 20:04:42,837 - INFO - Processed 127000000 reads so far
2011-05-19 20:04:55,459 - INFO - Processed 127100000 reads so far
2011-05-19 20:05:04,665 - INFO - Processed 127200000 reads so far
2011-05-19 20:05:16,448 - INFO - Processed 127300000 reads so far
2011-05-19 20:05:27,015 - INFO - Processed 127400000 reads so far
2011-05-19 20:05:39,362 - INFO - Processed 127500000 reads so far
2011-05-19 20:05:48,217 - INFO - Processed 127600000 reads so far
2011-05-19 20:05:59,303 - INFO - Processed 127700000 reads so far
2011-05-19 20:06:09,281 - INFO - Processed 127800000 reads so far
2011-05-19 20:06:21,098 - INFO - Processed 127900000 reads so far
2011-05-19 20:06:31,515 - INFO - Processed 128000000 reads so far
2011-05-19 20:06:35,794 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:42990050-63010050
2011-05-19 20:06:39,915 - INFO - Processed 128100000 reads so far
2011-05-19 20:06:48,412 - INFO - Processed 128200000 reads so far
2011-05-19 20:06:57,119 - INFO - Processed 128300000 reads so far
2011-05-19 20:07:05,893 - INFO - Processed 128400000 reads so far
2011-05-19 20:07:13,343 - INFO - Processed 128500000 reads so far
2011-05-19 20:07:23,833 - INFO - Processed 128600000 reads so far
2011-05-19 20:07:32,110 - INFO - Processed 128700000 reads so far
2011-05-19 20:07:40,790 - INFO - Processed 128800000 reads so far
2011-05-19 20:07:47,546 - INFO - Processed 128900000 reads so far
2011-05-19 20:07:55,943 - INFO - Processed 129000000 reads so far
2011-05-19 20:07:56,528 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:62990063-83010063
2011-05-19 20:08:03,562 - INFO - Processed 129100000 reads so far
2011-05-19 20:08:10,429 - INFO - Processed 129200000 reads so far
2011-05-19 20:08:19,077 - INFO - Processed 129300000 reads so far
2011-05-19 20:08:29,741 - INFO - Processed 129400000 reads so far
2011-05-19 20:08:41,442 - INFO - Processed 129500000 reads so far
2011-05-19 20:08:55,070 - INFO - Processed 129600000 reads so far
2011-05-19 20:09:07,391 - INFO - Processed 129700000 reads so far
2011-05-19 20:09:18,628 - INFO - Processed 129800000 reads so far
2011-05-19 20:09:29,136 - INFO - Processed 129900000 reads so far
2011-05-19 20:09:41,515 - INFO - Processed 130000000 reads so far
2011-05-19 20:09:51,515 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:82990069-103010069
2011-05-19 20:09:52,402 - INFO - Processed 130100000 reads so far
2011-05-19 20:10:04,504 - INFO - Processed 130200000 reads so far
2011-05-19 20:10:17,230 - INFO - Processed 130300000 reads so far
2011-05-19 20:10:27,606 - INFO - Processed 130400000 reads so far
2011-05-19 20:10:42,049 - INFO - Processed 130500000 reads so far
2011-05-19 20:10:56,811 - INFO - Processed 130600000 reads so far
2011-05-19 20:11:06,637 - INFO - Processed 130700000 reads so far
2011-05-19 20:11:17,649 - INFO - Processed 130800000 reads so far
2011-05-19 20:11:29,214 - INFO - Processed 130900000 reads so far
2011-05-19 20:11:40,505 - INFO - Processed 131000000 reads so far
2011-05-19 20:11:53,945 - INFO - Processed 131100000 reads so far
2011-05-19 20:12:00,589 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:102990072-123010072
2011-05-19 20:12:05,195 - INFO - Processed 131200000 reads so far
2011-05-19 20:12:16,184 - INFO - Processed 131300000 reads so far
2011-05-19 20:12:26,827 - INFO - Processed 131400000 reads so far
2011-05-19 20:12:38,977 - INFO - Processed 131500000 reads so far
2011-05-19 20:12:49,856 - INFO - Processed 131600000 reads so far
2011-05-19 20:13:04,920 - INFO - Processed 131700000 reads so far
2011-05-19 20:13:15,940 - INFO - Processed 131800000 reads so far
2011-05-19 20:13:25,912 - INFO - Processed 131900000 reads so far
2011-05-19 20:13:37,811 - INFO - Processed 132000000 reads so far
2011-05-19 20:13:49,471 - INFO - Processed 132100000 reads so far
2011-05-19 20:14:00,374 - INFO - Processed 132200000 reads so far
2011-05-19 20:14:02,858 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:122990083-143010083
2011-05-19 20:14:12,630 - INFO - Processed 132300000 reads so far
2011-05-19 20:14:23,350 - INFO - Processed 132400000 reads so far
2011-05-19 20:14:34,455 - INFO - Processed 132500000 reads so far
2011-05-19 20:14:44,550 - INFO - Processed 132600000 reads so far
2011-05-19 20:14:53,539 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8_random:0-20010005
2011-05-19 20:14:55,317 - INFO - Processed 132700000 reads so far
2011-05-19 20:15:02,335 - INFO - Processed 132800000 reads so far
2011-05-19 20:15:05,031 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:2989968-23009968
2011-05-19 20:15:09,421 - INFO - Processed 132900000 reads so far
2011-05-19 20:15:17,954 - INFO - Processed 133000000 reads so far
2011-05-19 20:15:23,593 - INFO - Processed 133100000 reads so far
2011-05-19 20:15:29,218 - INFO - Processed 133200000 reads so far
2011-05-19 20:15:36,039 - INFO - Processed 133300000 reads so far
2011-05-19 20:15:43,814 - INFO - Processed 133400000 reads so far
2011-05-19 20:15:58,441 - INFO - Processed 133500000 reads so far
2011-05-19 20:16:07,451 - INFO - Processed 133600000 reads so far
2011-05-19 20:16:13,670 - INFO - Processed 133700000 reads so far
2011-05-19 20:16:20,646 - INFO - Processed 133800000 reads so far
2011-05-19 20:16:33,523 - INFO - Processed 133900000 reads so far
2011-05-19 20:16:43,804 - INFO - Processed 134000000 reads so far
2011-05-19 20:16:51,121 - INFO - Processed 134100000 reads so far
2011-05-19 20:16:57,844 - INFO - Processed 134200000 reads so far
2011-05-19 20:17:06,951 - INFO - Processed 134300000 reads so far
2011-05-19 20:17:14,256 - INFO - Processed 134400000 reads so far
2011-05-19 20:17:21,171 - INFO - Processed 134500000 reads so far
2011-05-19 20:17:27,817 - INFO - Processed 134600000 reads so far
2011-05-19 20:17:35,364 - INFO - Processed 134700000 reads so far
2011-05-19 20:17:43,483 - INFO - Processed 134800000 reads so far
2011-05-19 20:17:51,635 - INFO - Processed 134900000 reads so far
2011-05-19 20:18:00,238 - INFO - Processed 135000000 reads so far
2011-05-19 20:18:09,174 - INFO - Processed 135100000 reads so far
2011-05-19 20:18:17,239 - INFO - Processed 135200000 reads so far
2011-05-19 20:18:23,154 - INFO - Processed 135300000 reads so far
2011-05-19 20:18:29,559 - INFO - Processed 135400000 reads so far
2011-05-19 20:18:38,438 - INFO - Processed 135500000 reads so far
2011-05-19 20:18:45,710 - INFO - Processed 135600000 reads so far
2011-05-19 20:18:52,645 - INFO - Processed 135700000 reads so far
2011-05-19 20:18:58,379 - INFO - Processed 135800000 reads so far
2011-05-19 20:19:05,260 - INFO - Processed 135900000 reads so far
2011-05-19 20:19:12,301 - INFO - Processed 136000000 reads so far
2011-05-19 20:19:19,494 - INFO - Processed 136100000 reads so far
2011-05-19 20:19:26,689 - INFO - Processed 136200000 reads so far
2011-05-19 20:19:33,260 - INFO - Processed 136300000 reads so far
2011-05-19 20:19:39,442 - INFO - Processed 136400000 reads so far
2011-05-19 20:19:45,385 - INFO - Processed 136500000 reads so far
2011-05-19 20:19:52,483 - INFO - Processed 136600000 reads so far
2011-05-19 20:19:59,189 - INFO - Processed 136700000 reads so far
2011-05-19 20:20:06,350 - INFO - Processed 136800000 reads so far
2011-05-19 20:20:12,864 - INFO - Processed 136900000 reads so far
2011-05-19 20:20:20,361 - INFO - Processed 137000000 reads so far
2011-05-19 20:20:27,895 - INFO - Processed 137100000 reads so far
2011-05-19 20:20:37,609 - INFO - Processed 137200000 reads so far
2011-05-19 20:20:46,473 - INFO - Processed 137300000 reads so far
2011-05-19 20:20:55,532 - INFO - Processed 137400000 reads so far
2011-05-19 20:21:03,822 - INFO - Processed 137500000 reads so far
2011-05-19 20:21:21,522 - INFO - Processed 137600000 reads so far
2011-05-19 20:21:30,774 - INFO - Processed 137700000 reads so far
2011-05-19 20:21:40,272 - INFO - Processed 137800000 reads so far
2011-05-19 20:21:53,494 - INFO - Processed 137900000 reads so far
2011-05-19 20:22:03,297 - INFO - Processed 138000000 reads so far
2011-05-19 20:22:12,374 - INFO - Processed 138100000 reads so far
2011-05-19 20:22:22,470 - INFO - Processed 138200000 reads so far
2011-05-19 20:22:31,458 - INFO - Processed 138300000 reads so far
2011-05-19 20:22:39,933 - INFO - Processed 138400000 reads so far
2011-05-19 20:22:48,565 - INFO - Processed 138500000 reads so far
2011-05-19 20:23:02,384 - INFO - Processed 138600000 reads so far
2011-05-19 20:23:13,304 - INFO - Processed 138700000 reads so far
2011-05-19 20:23:24,485 - INFO - Processed 138800000 reads so far
2011-05-19 20:23:35,711 - INFO - Processed 138900000 reads so far
2011-05-19 20:23:46,381 - INFO - Processed 139000000 reads so far
2011-05-19 20:23:57,443 - INFO - Processed 139100000 reads so far
2011-05-19 20:24:13,125 - INFO - Processed 139200000 reads so far
2011-05-19 20:24:24,019 - INFO - Processed 139300000 reads so far
2011-05-19 20:24:34,854 - INFO - Processed 139400000 reads so far
2011-05-19 20:24:49,081 - INFO - Processed 139500000 reads so far
2011-05-19 20:25:03,559 - INFO - Processed 139600000 reads so far
2011-05-19 20:25:04,292 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:22989999-43009999
2011-05-19 20:25:16,484 - INFO - Processed 139700000 reads so far
2011-05-19 20:25:29,151 - INFO - Processed 139800000 reads so far
2011-05-19 20:25:40,253 - INFO - Processed 139900000 reads so far
2011-05-19 20:25:51,407 - INFO - Processed 140000000 reads so far
2011-05-19 20:26:02,890 - INFO - Processed 140100000 reads so far
2011-05-19 20:26:16,226 - INFO - Processed 140200000 reads so far
2011-05-19 20:26:27,949 - INFO - Processed 140300000 reads so far
2011-05-19 20:26:39,225 - INFO - Processed 140400000 reads so far
2011-05-19 20:26:53,009 - INFO - Processed 140500000 reads so far
2011-05-19 20:27:04,027 - INFO - Processed 140600000 reads so far
2011-05-19 20:27:19,384 - INFO - Processed 140700000 reads so far
2011-05-19 20:27:30,742 - INFO - Processed 140800000 reads so far
2011-05-19 20:27:34,556 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:42990000-63010000
2011-05-19 20:27:42,611 - INFO - Processed 140900000 reads so far
2011-05-19 20:28:02,427 - INFO - Processed 141000000 reads so far
2011-05-19 20:28:13,692 - INFO - Processed 141100000 reads so far
2011-05-19 20:28:24,784 - INFO - Processed 141200000 reads so far
2011-05-19 20:28:39,869 - INFO - Processed 141300000 reads so far
2011-05-19 20:28:52,491 - INFO - Processed 141400000 reads so far
2011-05-19 20:29:04,055 - INFO - Processed 141500000 reads so far
2011-05-19 20:29:14,748 - INFO - Processed 141600000 reads so far
2011-05-19 20:29:25,840 - INFO - Processed 141700000 reads so far
2011-05-19 20:29:36,390 - INFO - Processed 141800000 reads so far
2011-05-19 20:29:47,455 - INFO - Processed 141900000 reads so far
2011-05-19 20:29:49,808 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:62990014-83010014
2011-05-19 20:29:58,582 - INFO - Processed 142000000 reads so far
2011-05-19 20:30:09,363 - INFO - Processed 142100000 reads so far
2011-05-19 20:30:19,267 - INFO - Processed 142200000 reads so far
2011-05-19 20:30:30,315 - INFO - Processed 142300000 reads so far
2011-05-19 20:30:42,501 - INFO - Processed 142400000 reads so far
2011-05-19 20:30:53,094 - INFO - Processed 142500000 reads so far
2011-05-19 20:31:04,251 - INFO - Processed 142600000 reads so far
2011-05-19 20:31:16,080 - INFO - Processed 142700000 reads so far
2011-05-19 20:31:27,445 - INFO - Processed 142800000 reads so far
2011-05-19 20:31:39,212 - INFO - Processed 142900000 reads so far
2011-05-19 20:31:51,584 - INFO - Processed 143000000 reads so far
2011-05-19 20:31:51,810 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:82990098-103010098
2011-05-19 20:32:05,478 - INFO - Processed 143100000 reads so far
2011-05-19 20:32:16,408 - INFO - Processed 143200000 reads so far
2011-05-19 20:32:28,032 - INFO - Processed 143300000 reads so far
2011-05-19 20:32:39,322 - INFO - Processed 143400000 reads so far
2011-05-19 20:32:50,499 - INFO - Processed 143500000 reads so far
2011-05-19 20:33:00,981 - INFO - Processed 143600000 reads so far
2011-05-19 20:33:14,506 - INFO - Processed 143700000 reads so far
2011-05-19 20:33:26,661 - INFO - Processed 143800000 reads so far
2011-05-19 20:33:37,355 - INFO - Processed 143900000 reads so far
2011-05-19 20:33:48,242 - INFO - Processed 144000000 reads so far
2011-05-19 20:33:54,911 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:102990101-123010101
2011-05-19 20:33:55,506 - INFO - Processed 144100000 reads so far
2011-05-19 20:34:04,059 - INFO - Processed 144200000 reads so far
2011-05-19 20:34:15,522 - INFO - Processed 144300000 reads so far
2011-05-19 20:34:24,662 - INFO - Processed 144400000 reads so far
2011-05-19 20:34:34,286 - INFO - Processed 144500000 reads so far
2011-05-19 20:34:43,044 - INFO - Processed 144600000 reads so far
2011-05-19 20:34:55,980 - INFO - Processed 144700000 reads so far
2011-05-19 20:35:05,709 - INFO - Processed 144800000 reads so far
2011-05-19 20:35:15,535 - INFO - Processed 144900000 reads so far
2011-05-19 20:35:26,286 - INFO - Processed 145000000 reads so far
2011-05-19 20:35:36,062 - INFO - Processed 145100000 reads so far
2011-05-19 20:35:42,112 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:122990105-143010105
2011-05-19 20:35:44,795 - INFO - Processed 145200000 reads so far
2011-05-19 20:35:48,257 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9_random:0-20010005
2011-05-19 20:35:50,209 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrM:0-20010000
2011-05-19 20:35:53,127 - INFO - Processed 145300000 reads so far
2011-05-19 20:36:00,659 - INFO - Processed 145400000 reads so far
2011-05-19 20:36:00,848 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrUn_random:0-20010000
2011-05-19 20:36:11,602 - INFO - Processed 145500000 reads so far
2011-05-19 20:36:21,400 - INFO - Processed 145600000 reads so far
2011-05-19 20:36:27,928 - INFO - Processed 145700000 reads so far
2011-05-19 20:36:36,655 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:2989998-23009998
2011-05-19 20:36:36,904 - INFO - Processed 145800000 reads so far
2011-05-19 20:36:45,112 - INFO - Processed 145900000 reads so far
2011-05-19 20:36:54,524 - INFO - Processed 146000000 reads so far
2011-05-19 20:37:01,792 - INFO - Processed 146100000 reads so far
2011-05-19 20:37:09,369 - INFO - Processed 146200000 reads so far
2011-05-19 20:37:19,577 - INFO - Processed 146300000 reads so far
2011-05-19 20:37:28,459 - INFO - Processed 146400000 reads so far
2011-05-19 20:37:37,796 - INFO - Processed 146500000 reads so far
2011-05-19 20:37:47,519 - INFO - Processed 146600000 reads so far
2011-05-19 20:37:58,063 - INFO - Processed 146700000 reads so far
2011-05-19 20:38:08,482 - INFO - Processed 146800000 reads so far
2011-05-19 20:38:18,663 - INFO - Processed 146900000 reads so far
2011-05-19 20:38:28,419 - INFO - Processed 147000000 reads so far
2011-05-19 20:38:38,070 - INFO - Processed 147100000 reads so far
2011-05-19 20:38:43,441 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:22990003-43010003
2011-05-19 20:38:47,437 - INFO - Processed 147200000 reads so far
2011-05-19 20:38:57,829 - INFO - Processed 147300000 reads so far
2011-05-19 20:39:07,547 - INFO - Processed 147400000 reads so far
2011-05-19 20:39:16,719 - INFO - Processed 147500000 reads so far
2011-05-19 20:39:25,176 - INFO - Processed 147600000 reads so far
2011-05-19 20:39:34,059 - INFO - Processed 147700000 reads so far
2011-05-19 20:39:43,857 - INFO - Processed 147800000 reads so far
2011-05-19 20:39:51,400 - INFO - Processed 147900000 reads so far
2011-05-19 20:39:58,970 - INFO - Processed 148000000 reads so far
2011-05-19 20:40:09,312 - INFO - Processed 148100000 reads so far
2011-05-19 20:40:21,128 - INFO - Processed 148200000 reads so far
2011-05-19 20:40:29,514 - INFO - Processed 148300000 reads so far
2011-05-19 20:40:36,950 - INFO - Processed 148400000 reads so far
2011-05-19 20:40:46,268 - INFO - Processed 148500000 reads so far
2011-05-19 20:40:54,502 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:42990004-63010004
2011-05-19 20:40:58,319 - INFO - Processed 148600000 reads so far
2011-05-19 20:41:07,054 - INFO - Processed 148700000 reads so far
2011-05-19 20:41:15,716 - INFO - Processed 148800000 reads so far
2011-05-19 20:41:22,369 - INFO - Processed 148900000 reads so far
2011-05-19 20:41:31,316 - INFO - Processed 149000000 reads so far
2011-05-19 20:41:40,590 - INFO - Processed 149100000 reads so far
2011-05-19 20:41:52,730 - INFO - Processed 149200000 reads so far
2011-05-19 20:42:04,036 - INFO - Processed 149300000 reads so far
2011-05-19 20:42:15,347 - INFO - Processed 149400000 reads so far
2011-05-19 20:42:25,189 - INFO - Processed 149500000 reads so far
2011-05-19 20:42:34,067 - INFO - Processed 149600000 reads so far
2011-05-19 20:42:37,881 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:62990020-83010020
2011-05-19 20:42:44,702 - INFO - Processed 149700000 reads so far
2011-05-19 20:42:55,156 - INFO - Processed 149800000 reads so far
2011-05-19 20:43:03,149 - INFO - Processed 149900000 reads so far
2011-05-19 20:43:12,200 - INFO - Processed 150000000 reads so far
2011-05-19 20:43:24,875 - INFO - Processed 150100000 reads so far
2011-05-19 20:43:34,467 - INFO - Processed 150200000 reads so far
2011-05-19 20:43:44,545 - INFO - Processed 150300000 reads so far
2011-05-19 20:43:56,885 - INFO - Processed 150400000 reads so far
2011-05-19 20:44:07,584 - INFO - Processed 150500000 reads so far
2011-05-19 20:44:17,315 - INFO - Processed 150600000 reads so far
2011-05-19 20:44:27,332 - INFO - Processed 150700000 reads so far
2011-05-19 20:44:27,384 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:82990028-103010028
2011-05-19 20:44:38,559 - INFO - Processed 150800000 reads so far
2011-05-19 20:44:50,431 - INFO - Processed 150900000 reads so far
2011-05-19 20:44:59,657 - INFO - Processed 151000000 reads so far
2011-05-19 20:45:10,887 - INFO - Processed 151100000 reads so far
2011-05-19 20:45:22,024 - INFO - Processed 151200000 reads so far
2011-05-19 20:45:33,183 - INFO - Processed 151300000 reads so far
2011-05-19 20:45:43,741 - INFO - Processed 151400000 reads so far
2011-05-19 20:45:52,258 - INFO - Processed 151500000 reads so far
2011-05-19 20:46:00,725 - INFO - Processed 151600000 reads so far
2011-05-19 20:46:10,509 - INFO - Processed 151700000 reads so far
2011-05-19 20:46:16,476 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:102990061-123010061
2011-05-19 20:46:22,124 - INFO - Processed 151800000 reads so far
2011-05-19 20:46:32,681 - INFO - Processed 151900000 reads so far
2011-05-19 20:46:42,729 - INFO - Processed 152000000 reads so far
2011-05-19 20:46:55,705 - INFO - Processed 152100000 reads so far
2011-05-19 20:47:04,660 - INFO - Processed 152200000 reads so far
2011-05-19 20:47:15,514 - INFO - Processed 152300000 reads so far
2011-05-19 20:47:26,062 - INFO - Processed 152400000 reads so far
2011-05-19 20:47:36,347 - INFO - Processed 152500000 reads so far
2011-05-19 20:47:46,768 - INFO - Processed 152600000 reads so far
2011-05-19 20:47:53,742 - INFO - Processed 152700000 reads so far
2011-05-19 20:47:58,973 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:122990062-143010062
2011-05-19 20:48:03,930 - INFO - Processed 152800000 reads so far
2011-05-19 20:48:13,641 - INFO - Processed 152900000 reads so far
2011-05-19 20:48:24,033 - INFO - Processed 153000000 reads so far
2011-05-19 20:48:32,955 - INFO - Processed 153100000 reads so far
2011-05-19 20:48:58,787 - INFO - Processed 153200000 reads so far
2011-05-19 20:49:09,439 - INFO - Processed 153300000 reads so far
2011-05-19 20:49:21,707 - INFO - Processed 153400000 reads so far
2011-05-19 20:49:31,045 - INFO - Processed 153500000 reads so far
2011-05-19 20:49:39,421 - INFO - Processed 153600000 reads so far
2011-05-19 20:49:46,335 - INFO - Processed 153700000 reads so far
2011-05-19 20:49:55,380 - INFO - Processed 153800000 reads so far
2011-05-19 20:50:00,246 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:142990078-163010078
2011-05-19 20:50:02,737 - INFO - Processed 153900000 reads so far
2011-05-19 20:50:10,402 - INFO - Processed 154000000 reads so far
2011-05-19 20:50:19,068 - INFO - Processed 154100000 reads so far
2011-05-19 20:50:29,576 - INFO - Processed 154200000 reads so far
2011-05-19 20:50:40,185 - INFO - Processed 154300000 reads so far
2011-05-19 20:50:48,539 - INFO - Processed 154400000 reads so far
2011-05-19 20:50:58,061 - INFO - Processed 154500000 reads so far
2011-05-19 20:51:08,031 - INFO - Processed 154600000 reads so far
2011-05-19 20:51:16,493 - INFO - Processed 154700000 reads so far
2011-05-19 20:51:27,976 - INFO - Processed 154800000 reads so far
2011-05-19 20:51:38,074 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:162990093-183010093
2011-05-19 20:51:38,916 - INFO - Processed 154900000 reads so far
2011-05-19 20:51:46,733 - INFO - Processed 155000000 reads so far
2011-05-19 20:51:55,857 - INFO - Processed 155100000 reads so far
2011-05-19 20:51:57,909 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX_random:0-20010000
2011-05-19 20:52:01,784 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY:10325-20030325
2011-05-19 20:52:02,842 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:50693-20070693
2011-05-19 20:52:03,460 - INFO - Processed 155200000 reads so far
2011-05-19 20:52:05,147 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:20162385-40182385
2011-05-19 20:52:06,870 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:40170932-60190932
2011-05-19 20:52:11,047 - INFO - Processed 155300000 reads so far
2011-05-19 20:52:16,909 - INFO - Processed 155400000 reads so far
2011-05-19 20:52:20,848 - INFO - Processed 155500000 reads so far
2011-05-19 20:52:24,709 - INFO - Processed 155600000 reads so far
2011-05-19 20:52:28,195 - INFO - Processed 155700000 reads so far
2011-05-19 20:52:31,571 - INFO - Processed 155800000 reads so far
2011-05-19 20:52:36,757 - INFO - Processed 155900000 reads so far
2011-05-19 20:52:39,373 - INFO - Processed 156000000 reads so far
2011-05-19 20:52:42,079 - INFO - Processed 156100000 reads so far
2011-05-19 20:52:47,431 - INFO - Processed 156200000 reads so far
2011-05-19 20:52:50,820 - INFO - Processed 156300000 reads so far
2011-05-19 20:52:54,890 - INFO - Processed 156400000 reads so far
2011-05-19 20:52:58,838 - INFO - Processed 156500000 reads so far
2011-05-19 20:53:02,939 - INFO - Processed 156600000 reads so far
2011-05-19 20:53:06,946 - INFO - Processed 156700000 reads so far
2011-05-19 20:53:11,309 - INFO - Processed 156800000 reads so far
2011-05-19 20:53:15,417 - INFO - Processed 156900000 reads so far
2011-05-19 20:53:19,594 - INFO - Processed 157000000 reads so far
2011-05-19 20:53:25,219 - INFO - Processed 157100000 reads so far
2011-05-19 20:53:30,390 - INFO - Processed 157200000 reads so far
2011-05-19 20:53:34,227 - INFO - Processed 157300000 reads so far
2011-05-19 20:53:37,455 - INFO - Processed 157400000 reads so far
2011-05-19 20:53:41,402 - INFO - Processed 157500000 reads so far
2011-05-19 20:53:44,584 - INFO - Processed 157600000 reads so far
2011-05-19 20:53:48,551 - INFO - Processed 157700000 reads so far
2011-05-19 20:53:50,665 - INFO - Finished loading data. Outputting QC metrics
2011-05-19 20:54:10,847 - INFO - Finished outputting QC metrics
2011-05-19 20:54:10,949 - INFO - Finished generating QC metrics