2011-05-20 09:31:28,193 - INFO - Generating QC metrics for BAM File ['WTCHG_11896.bam']
2011-05-20 09:31:28,193 - INFO - Output will go to WTCHG_11896.qc.txt.tmp
2011-05-20 09:31:28,193 - INFO - Reading GC Map from file /data/Genomes/gcMap/Mouse37.gcMap.gz
2011-05-20 09:33:45,317 - INFO - Finished reading GC Map
2011-05-20 09:33:45,318 - INFO - Reading CDS from exon definition file /data/Genomes/annotation/Mouse37.refGene.txt.gz
2011-05-20 09:33:47,327 - INFO - Read 382138 exons (33804740 nucleotides) for 32 chromosomes
2011-05-20 09:33:47,328 - INFO - Computing coverage cut-off
2011-05-20 09:33:47,328 - INFO - Retrieving BAM file coverage info from samtools pileup
2011-05-20 09:33:54,180 - INFO - Processed 1000000 pile-up sites
2011-05-20 09:33:56,515 - INFO - Processed 2000000 pile-up sites
2011-05-20 09:33:58,856 - INFO - Processed 3000000 pile-up sites
2011-05-20 09:34:01,231 - INFO - Processed 4000000 pile-up sites
2011-05-20 09:34:04,226 - INFO - Processed 5000000 pile-up sites
2011-05-20 09:34:08,232 - INFO - Processed 6000000 pile-up sites
2011-05-20 09:34:12,057 - INFO - Processed 7000000 pile-up sites
2011-05-20 09:34:15,983 - INFO - Processed 8000000 pile-up sites
2011-05-20 09:34:20,019 - INFO - Processed 9000000 pile-up sites
2011-05-20 09:34:23,997 - INFO - Processed 10000000 pile-up sites
2011-05-20 09:34:30,578 - INFO - Processed 11000000 pile-up sites
2011-05-20 09:34:35,005 - INFO - Processed 12000000 pile-up sites
2011-05-20 09:34:39,120 - INFO - Processed 13000000 pile-up sites
2011-05-20 09:34:43,239 - INFO - Processed 14000000 pile-up sites
2011-05-20 09:34:47,066 - INFO - Processed 15000000 pile-up sites
2011-05-20 09:34:52,423 - INFO - Processed 16000000 pile-up sites
2011-05-20 09:34:56,274 - INFO - Processed 17000000 pile-up sites
2011-05-20 09:35:00,508 - INFO - Processed 18000000 pile-up sites
2011-05-20 09:35:04,471 - INFO - Processed 19000000 pile-up sites
2011-05-20 09:35:08,464 - INFO - Processed 20000000 pile-up sites
2011-05-20 09:35:12,523 - INFO - Processed 21000000 pile-up sites
2011-05-20 09:35:16,541 - INFO - Processed 22000000 pile-up sites
2011-05-20 09:35:20,373 - INFO - Processed 23000000 pile-up sites
2011-05-20 09:35:24,457 - INFO - Processed 24000000 pile-up sites
2011-05-20 09:35:28,288 - INFO - Processed 25000000 pile-up sites
2011-05-20 09:35:32,197 - INFO - Processed 26000000 pile-up sites
2011-05-20 09:35:37,254 - INFO - Processed 27000000 pile-up sites
2011-05-20 09:35:41,252 - INFO - Processed 28000000 pile-up sites
2011-05-20 09:35:45,956 - INFO - Processed 29000000 pile-up sites
2011-05-20 09:35:52,035 - INFO - Processed 30000000 pile-up sites
2011-05-20 09:35:55,939 - INFO - Processed 31000000 pile-up sites
2011-05-20 09:36:00,060 - INFO - Processed 32000000 pile-up sites
2011-05-20 09:36:04,335 - INFO - Processed 33000000 pile-up sites
2011-05-20 09:36:08,112 - INFO - Processed 34000000 pile-up sites
2011-05-20 09:36:11,703 - INFO - Processed 35000000 pile-up sites
2011-05-20 09:36:15,555 - INFO - Processed 36000000 pile-up sites
2011-05-20 09:36:19,665 - INFO - Processed 37000000 pile-up sites
2011-05-20 09:36:23,427 - INFO - Processed 38000000 pile-up sites
2011-05-20 09:36:28,416 - INFO - Processed 39000000 pile-up sites
2011-05-20 09:36:31,921 - INFO - Processed 40000000 pile-up sites
2011-05-20 09:36:33,487 - INFO - Finished processing pile-up on 40617488 sites (200000003 nucleotides)
2011-05-20 09:36:33,487 - INFO - Coverage cut-off value is 18
2011-05-20 09:36:33,487 - INFO - Loading data into QC data manager
2011-05-20 09:36:33,755 - INFO - Reading data from BAM file WTCHG_11896.bam. All reads in file will be read
2011-05-20 09:36:33,797 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:2990070-23010070
2011-05-20 09:36:43,507 - INFO - Processed 100000 reads so far
2011-05-20 09:36:51,164 - INFO - Processed 200000 reads so far
2011-05-20 09:37:00,015 - INFO - Processed 300000 reads so far
2011-05-20 09:37:08,675 - INFO - Processed 400000 reads so far
2011-05-20 09:37:16,597 - INFO - Processed 500000 reads so far
2011-05-20 09:37:24,905 - INFO - Processed 600000 reads so far
2011-05-20 09:37:32,885 - INFO - Processed 700000 reads so far
2011-05-20 09:37:41,130 - INFO - Processed 800000 reads so far
2011-05-20 09:37:49,681 - INFO - Processed 900000 reads so far
2011-05-20 09:37:54,506 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:22990072-43010072
2011-05-20 09:37:58,169 - INFO - Processed 1000000 reads so far
2011-05-20 09:38:06,030 - INFO - Processed 1100000 reads so far
2011-05-20 09:38:16,147 - INFO - Processed 1200000 reads so far
2011-05-20 09:38:23,846 - INFO - Processed 1300000 reads so far
2011-05-20 09:38:31,053 - INFO - Processed 1400000 reads so far
2011-05-20 09:38:41,154 - INFO - Processed 1500000 reads so far
2011-05-20 09:38:51,178 - INFO - Processed 1600000 reads so far
2011-05-20 09:39:01,168 - INFO - Processed 1700000 reads so far
2011-05-20 09:39:11,764 - INFO - Processed 1800000 reads so far
2011-05-20 09:39:19,215 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:42990087-63010087
2011-05-20 09:39:19,892 - INFO - Processed 1900000 reads so far
2011-05-20 09:39:28,312 - INFO - Processed 2000000 reads so far
2011-05-20 09:39:38,702 - INFO - Processed 2100000 reads so far
2011-05-20 09:39:50,014 - INFO - Processed 2200000 reads so far
2011-05-20 09:40:01,761 - INFO - Processed 2300000 reads so far
2011-05-20 09:40:12,871 - INFO - Processed 2400000 reads so far
2011-05-20 09:40:24,308 - INFO - Processed 2500000 reads so far
2011-05-20 09:40:35,623 - INFO - Processed 2600000 reads so far
2011-05-20 09:40:48,313 - INFO - Processed 2700000 reads so far
2011-05-20 09:40:58,709 - INFO - Processed 2800000 reads so far
2011-05-20 09:41:01,349 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:62990105-83010105
2011-05-20 09:41:09,918 - INFO - Processed 2900000 reads so far
2011-05-20 09:41:21,807 - INFO - Processed 3000000 reads so far
2011-05-20 09:41:33,164 - INFO - Processed 3100000 reads so far
2011-05-20 09:41:45,439 - INFO - Processed 3200000 reads so far
2011-05-20 09:41:57,430 - INFO - Processed 3300000 reads so far
2011-05-20 09:42:09,205 - INFO - Processed 3400000 reads so far
2011-05-20 09:42:20,832 - INFO - Processed 3500000 reads so far
2011-05-20 09:42:32,935 - INFO - Processed 3600000 reads so far
2011-05-20 09:42:45,478 - INFO - Processed 3700000 reads so far
2011-05-20 09:42:51,947 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:82990110-103010110
2011-05-20 09:42:58,755 - INFO - Processed 3800000 reads so far
2011-05-20 09:43:09,697 - INFO - Processed 3900000 reads so far
2011-05-20 09:43:18,997 - INFO - Processed 4000000 reads so far
2011-05-20 09:43:31,486 - INFO - Processed 4100000 reads so far
2011-05-20 09:43:39,981 - INFO - Processed 4200000 reads so far
2011-05-20 09:43:48,043 - INFO - Processed 4300000 reads so far
2011-05-20 09:43:58,949 - INFO - Processed 4400000 reads so far
2011-05-20 09:44:07,638 - INFO - Processed 4500000 reads so far
2011-05-20 09:44:16,248 - INFO - Processed 4600000 reads so far
2011-05-20 09:44:24,774 - INFO - Processed 4700000 reads so far
2011-05-20 09:44:26,472 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:102990112-123010112
2011-05-20 09:44:33,954 - INFO - Processed 4800000 reads so far
2011-05-20 09:44:43,913 - INFO - Processed 4900000 reads so far
2011-05-20 09:44:54,531 - INFO - Processed 5000000 reads so far
2011-05-20 09:45:02,525 - INFO - Processed 5100000 reads so far
2011-05-20 09:45:11,240 - INFO - Processed 5200000 reads so far
2011-05-20 09:45:21,650 - INFO - Processed 5300000 reads so far
2011-05-20 09:45:31,829 - INFO - Processed 5400000 reads so far
2011-05-20 09:45:55,747 - INFO - Processed 5500000 reads so far
2011-05-20 09:46:05,492 - INFO - Processed 5600000 reads so far
2011-05-20 09:46:11,776 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:122990126-143010126
2011-05-20 09:46:17,289 - INFO - Processed 5700000 reads so far
2011-05-20 09:46:29,549 - INFO - Processed 5800000 reads so far
2011-05-20 09:46:39,384 - INFO - Processed 5900000 reads so far
2011-05-20 09:46:47,962 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:2990004-23010004
2011-05-20 09:46:50,156 - INFO - Processed 6000000 reads so far
2011-05-20 09:46:58,843 - INFO - Processed 6100000 reads so far
2011-05-20 09:47:05,896 - INFO - Processed 6200000 reads so far
2011-05-20 09:47:16,503 - INFO - Processed 6300000 reads so far
2011-05-20 09:47:27,818 - INFO - Processed 6400000 reads so far
2011-05-20 09:47:36,836 - INFO - Processed 6500000 reads so far
2011-05-20 09:47:45,273 - INFO - Processed 6600000 reads so far
2011-05-20 09:47:54,203 - INFO - Processed 6700000 reads so far
2011-05-20 09:48:02,551 - INFO - Processed 6800000 reads so far
2011-05-20 09:48:12,745 - INFO - Processed 6900000 reads so far
2011-05-20 09:48:22,412 - INFO - Processed 7000000 reads so far
2011-05-20 09:48:31,307 - INFO - Processed 7100000 reads so far
2011-05-20 09:48:31,356 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:22990027-43010027
2011-05-20 09:48:39,569 - INFO - Processed 7200000 reads so far
2011-05-20 09:48:47,630 - INFO - Processed 7300000 reads so far
2011-05-20 09:48:57,240 - INFO - Processed 7400000 reads so far
2011-05-20 09:49:09,868 - INFO - Processed 7500000 reads so far
2011-05-20 09:49:21,172 - INFO - Processed 7600000 reads so far
2011-05-20 09:49:32,500 - INFO - Processed 7700000 reads so far
2011-05-20 09:49:43,795 - INFO - Processed 7800000 reads so far
2011-05-20 09:49:55,399 - INFO - Processed 7900000 reads so far
2011-05-20 09:50:10,408 - INFO - Processed 8000000 reads so far
2011-05-20 09:50:14,182 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:42990063-63010063
2011-05-20 09:50:19,088 - INFO - Processed 8100000 reads so far
2011-05-20 09:50:28,644 - INFO - Processed 8200000 reads so far
2011-05-20 09:50:38,729 - INFO - Processed 8300000 reads so far
2011-05-20 09:50:49,704 - INFO - Processed 8400000 reads so far
2011-05-20 09:51:01,523 - INFO - Processed 8500000 reads so far
2011-05-20 09:51:12,754 - INFO - Processed 8600000 reads so far
2011-05-20 09:51:22,289 - INFO - Processed 8700000 reads so far
2011-05-20 09:51:32,956 - INFO - Processed 8800000 reads so far
2011-05-20 09:51:42,040 - INFO - Processed 8900000 reads so far
2011-05-20 09:51:51,552 - INFO - Processed 9000000 reads so far
2011-05-20 09:51:52,736 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:62990066-83010066
2011-05-20 09:52:02,678 - INFO - Processed 9100000 reads so far
2011-05-20 09:52:13,843 - INFO - Processed 9200000 reads so far
2011-05-20 09:52:24,272 - INFO - Processed 9300000 reads so far
2011-05-20 09:52:34,207 - INFO - Processed 9400000 reads so far
2011-05-20 09:52:46,111 - INFO - Processed 9500000 reads so far
2011-05-20 09:52:55,870 - INFO - Processed 9600000 reads so far
2011-05-20 09:53:05,286 - INFO - Processed 9700000 reads so far
2011-05-20 09:53:12,870 - INFO - Processed 9800000 reads so far
2011-05-20 09:53:24,389 - INFO - Processed 9900000 reads so far
2011-05-20 09:53:30,883 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:82990078-103010078
2011-05-20 09:53:33,276 - INFO - Processed 10000000 reads so far
2011-05-20 09:53:42,796 - INFO - Processed 10100000 reads so far
2011-05-20 09:53:53,352 - INFO - Processed 10200000 reads so far
2011-05-20 09:54:04,382 - INFO - Processed 10300000 reads so far
2011-05-20 09:54:15,143 - INFO - Processed 10400000 reads so far
2011-05-20 09:54:27,764 - INFO - Processed 10500000 reads so far
2011-05-20 09:54:40,273 - INFO - Processed 10600000 reads so far
2011-05-20 09:54:51,612 - INFO - Processed 10700000 reads so far
2011-05-20 09:55:04,361 - INFO - Processed 10800000 reads so far
2011-05-20 09:55:15,195 - INFO - Processed 10900000 reads so far
2011-05-20 09:55:15,629 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:102990114-123010114
2011-05-20 09:55:25,657 - INFO - Processed 11000000 reads so far
2011-05-20 09:55:35,393 - INFO - Processed 11100000 reads so far
2011-05-20 09:55:44,669 - INFO - Processed 11200000 reads so far
2011-05-20 09:55:54,513 - INFO - Processed 11300000 reads so far
2011-05-20 09:56:03,672 - INFO - Processed 11400000 reads so far
2011-05-20 09:56:13,984 - INFO - Processed 11500000 reads so far
2011-05-20 09:56:25,113 - INFO - Processed 11600000 reads so far
2011-05-20 09:56:34,353 - INFO - Processed 11700000 reads so far
2011-05-20 09:56:47,200 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:2990001-23010001
2011-05-20 09:56:47,457 - INFO - Processed 11800000 reads so far
2011-05-20 09:56:56,214 - INFO - Processed 11900000 reads so far
2011-05-20 09:57:06,835 - INFO - Processed 12000000 reads so far
2011-05-20 09:57:18,959 - INFO - Processed 12100000 reads so far
2011-05-20 09:57:29,867 - INFO - Processed 12200000 reads so far
2011-05-20 09:57:40,333 - INFO - Processed 12300000 reads so far
2011-05-20 09:57:50,229 - INFO - Processed 12400000 reads so far
2011-05-20 09:58:02,647 - INFO - Processed 12500000 reads so far
2011-05-20 09:58:13,748 - INFO - Processed 12600000 reads so far
2011-05-20 09:58:24,705 - INFO - Processed 12700000 reads so far
2011-05-20 09:58:36,778 - INFO - Processed 12800000 reads so far
2011-05-20 09:58:48,097 - INFO - Processed 12900000 reads so far
2011-05-20 09:58:50,622 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:22990021-43010021
2011-05-20 09:58:59,455 - INFO - Processed 13000000 reads so far
2011-05-20 09:59:10,637 - INFO - Processed 13100000 reads so far
2011-05-20 09:59:21,819 - INFO - Processed 13200000 reads so far
2011-05-20 09:59:31,325 - INFO - Processed 13300000 reads so far
2011-05-20 09:59:41,515 - INFO - Processed 13400000 reads so far
2011-05-20 09:59:51,765 - INFO - Processed 13500000 reads so far
2011-05-20 10:00:00,518 - INFO - Processed 13600000 reads so far
2011-05-20 10:00:10,145 - INFO - Processed 13700000 reads so far
2011-05-20 10:00:19,807 - INFO - Processed 13800000 reads so far
2011-05-20 10:00:22,959 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:42990051-63010051
2011-05-20 10:00:28,500 - INFO - Processed 13900000 reads so far
2011-05-20 10:00:36,813 - INFO - Processed 14000000 reads so far
2011-05-20 10:00:48,500 - INFO - Processed 14100000 reads so far
2011-05-20 10:00:58,940 - INFO - Processed 14200000 reads so far
2011-05-20 10:01:08,995 - INFO - Processed 14300000 reads so far
2011-05-20 10:01:19,214 - INFO - Processed 14400000 reads so far
2011-05-20 10:01:30,144 - INFO - Processed 14500000 reads so far
2011-05-20 10:01:41,573 - INFO - Processed 14600000 reads so far
2011-05-20 10:01:53,431 - INFO - Processed 14700000 reads so far
2011-05-20 10:01:57,896 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:62990053-83010053
2011-05-20 10:02:04,312 - INFO - Processed 14800000 reads so far
2011-05-20 10:02:15,589 - INFO - Processed 14900000 reads so far
2011-05-20 10:02:27,833 - INFO - Processed 15000000 reads so far
2011-05-20 10:02:39,819 - INFO - Processed 15100000 reads so far
2011-05-20 10:02:51,587 - INFO - Processed 15200000 reads so far
2011-05-20 10:03:03,016 - INFO - Processed 15300000 reads so far
2011-05-20 10:03:15,413 - INFO - Processed 15400000 reads so far
2011-05-20 10:03:25,271 - INFO - Processed 15500000 reads so far
2011-05-20 10:03:35,049 - INFO - Processed 15600000 reads so far
2011-05-20 10:03:43,827 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:82990080-103010080
2011-05-20 10:03:45,761 - INFO - Processed 15700000 reads so far
2011-05-20 10:03:57,647 - INFO - Processed 15800000 reads so far
2011-05-20 10:04:07,951 - INFO - Processed 15900000 reads so far
2011-05-20 10:04:19,397 - INFO - Processed 16000000 reads so far
2011-05-20 10:04:31,113 - INFO - Processed 16100000 reads so far
2011-05-20 10:04:43,628 - INFO - Processed 16200000 reads so far
2011-05-20 10:04:51,972 - INFO - Processed 16300000 reads so far
2011-05-20 10:05:02,001 - INFO - Processed 16400000 reads so far
2011-05-20 10:05:12,520 - INFO - Processed 16500000 reads so far
2011-05-20 10:05:23,113 - INFO - Processed 16600000 reads so far
2011-05-20 10:05:25,653 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:102990101-123010101
2011-05-20 10:05:33,886 - INFO - Processed 16700000 reads so far
2011-05-20 10:05:44,987 - INFO - Processed 16800000 reads so far
2011-05-20 10:05:52,889 - INFO - Processed 16900000 reads so far
2011-05-20 10:06:03,351 - INFO - Processed 17000000 reads so far
2011-05-20 10:06:14,885 - INFO - Processed 17100000 reads so far
2011-05-20 10:06:26,300 - INFO - Processed 17200000 reads so far
2011-05-20 10:06:37,498 - INFO - Processed 17300000 reads so far
2011-05-20 10:06:46,122 - INFO - Processed 17400000 reads so far
2011-05-20 10:06:55,659 - INFO - Processed 17500000 reads so far
2011-05-20 10:07:02,662 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:2990099-23010099
2011-05-20 10:07:07,489 - INFO - Processed 17600000 reads so far
2011-05-20 10:07:18,283 - INFO - Processed 17700000 reads so far
2011-05-20 10:07:28,555 - INFO - Processed 17800000 reads so far
2011-05-20 10:07:37,106 - INFO - Processed 17900000 reads so far
2011-05-20 10:07:50,733 - INFO - Processed 18000000 reads so far
2011-05-20 10:08:02,757 - INFO - Processed 18100000 reads so far
2011-05-20 10:08:12,203 - INFO - Processed 18200000 reads so far
2011-05-20 10:08:22,272 - INFO - Processed 18300000 reads so far
2011-05-20 10:08:32,226 - INFO - Processed 18400000 reads so far
2011-05-20 10:08:39,113 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:22990143-43010143
2011-05-20 10:08:40,705 - INFO - Processed 18500000 reads so far
2011-05-20 10:08:51,693 - INFO - Processed 18600000 reads so far
2011-05-20 10:09:02,472 - INFO - Processed 18700000 reads so far
2011-05-20 10:09:11,866 - INFO - Processed 18800000 reads so far
2011-05-20 10:09:26,877 - INFO - Processed 18900000 reads so far
2011-05-20 10:09:41,451 - INFO - Processed 19000000 reads so far
2011-05-20 10:09:52,916 - INFO - Processed 19100000 reads so far
2011-05-20 10:10:18,869 - INFO - Processed 19200000 reads so far
2011-05-20 10:10:27,536 - INFO - Processed 19300000 reads so far
2011-05-20 10:10:41,230 - INFO - Processed 19400000 reads so far
2011-05-20 10:10:58,920 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:42990207-63010207
2011-05-20 10:11:10,999 - INFO - Processed 19500000 reads so far
2011-05-20 10:11:24,714 - INFO - Processed 19600000 reads so far
2011-05-20 10:11:37,587 - INFO - Processed 19700000 reads so far
2011-05-20 10:11:49,553 - INFO - Processed 19800000 reads so far
2011-05-20 10:11:58,499 - INFO - Processed 19900000 reads so far
2011-05-20 10:12:06,767 - INFO - Processed 20000000 reads so far
2011-05-20 10:12:15,188 - INFO - Processed 20100000 reads so far
2011-05-20 10:12:23,628 - INFO - Processed 20200000 reads so far
2011-05-20 10:12:32,669 - INFO - Processed 20300000 reads so far
2011-05-20 10:12:40,980 - INFO - Processed 20400000 reads so far
2011-05-20 10:12:44,660 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:62990225-83010225
2011-05-20 10:12:49,453 - INFO - Processed 20500000 reads so far
2011-05-20 10:12:57,462 - INFO - Processed 20600000 reads so far
2011-05-20 10:13:05,433 - INFO - Processed 20700000 reads so far
2011-05-20 10:13:19,468 - INFO - Processed 20800000 reads so far
2011-05-20 10:13:28,094 - INFO - Processed 20900000 reads so far
2011-05-20 10:13:39,187 - INFO - Processed 21000000 reads so far
2011-05-20 10:13:50,021 - INFO - Processed 21100000 reads so far
2011-05-20 10:14:00,914 - INFO - Processed 21200000 reads so far
2011-05-20 10:14:12,305 - INFO - Processed 21300000 reads so far
2011-05-20 10:14:23,683 - INFO - Processed 21400000 reads so far
2011-05-20 10:14:25,185 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:82990281-103010281
2011-05-20 10:14:35,363 - INFO - Processed 21500000 reads so far
2011-05-20 10:14:46,929 - INFO - Processed 21600000 reads so far
2011-05-20 10:14:58,226 - INFO - Processed 21700000 reads so far
2011-05-20 10:15:09,072 - INFO - Processed 21800000 reads so far
2011-05-20 10:15:20,370 - INFO - Processed 21900000 reads so far
2011-05-20 10:15:31,564 - INFO - Processed 22000000 reads so far
2011-05-20 10:15:42,829 - INFO - Processed 22100000 reads so far
2011-05-20 10:15:54,042 - INFO - Processed 22200000 reads so far
2011-05-20 10:16:05,237 - INFO - Processed 22300000 reads so far
2011-05-20 10:16:07,213 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:102990299-123010299
2011-05-20 10:16:20,101 - INFO - Processed 22400000 reads so far
2011-05-20 10:16:29,798 - INFO - Processed 22500000 reads so far
2011-05-20 10:16:41,903 - INFO - Processed 22600000 reads so far
2011-05-20 10:16:52,960 - INFO - Processed 22700000 reads so far
2011-05-20 10:17:04,449 - INFO - Processed 22800000 reads so far
2011-05-20 10:17:15,969 - INFO - Processed 22900000 reads so far
2011-05-20 10:17:27,067 - INFO - Processed 23000000 reads so far
2011-05-20 10:17:39,293 - INFO - Processed 23100000 reads so far
2011-05-20 10:17:44,502 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13_random:0-20010000
2011-05-20 10:17:45,638 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:2990062-23010062
2011-05-20 10:17:50,552 - INFO - Processed 23200000 reads so far
2011-05-20 10:18:01,187 - INFO - Processed 23300000 reads so far
2011-05-20 10:18:12,163 - INFO - Processed 23400000 reads so far
2011-05-20 10:18:25,051 - INFO - Processed 23500000 reads so far
2011-05-20 10:18:40,180 - INFO - Processed 23600000 reads so far
2011-05-20 10:18:51,583 - INFO - Processed 23700000 reads so far
2011-05-20 10:18:58,886 - INFO - Processed 23800000 reads so far
2011-05-20 10:19:07,272 - INFO - Processed 23900000 reads so far
2011-05-20 10:19:16,214 - INFO - Processed 24000000 reads so far
2011-05-20 10:19:21,935 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:22990091-43010091
2011-05-20 10:19:25,097 - INFO - Processed 24100000 reads so far
2011-05-20 10:19:35,019 - INFO - Processed 24200000 reads so far
2011-05-20 10:19:43,174 - INFO - Processed 24300000 reads so far
2011-05-20 10:19:52,838 - INFO - Processed 24400000 reads so far
2011-05-20 10:20:03,170 - INFO - Processed 24500000 reads so far
2011-05-20 10:20:12,936 - INFO - Processed 24600000 reads so far
2011-05-20 10:20:21,410 - INFO - Processed 24700000 reads so far
2011-05-20 10:20:30,260 - INFO - Processed 24800000 reads so far
2011-05-20 10:20:39,280 - INFO - Processed 24900000 reads so far
2011-05-20 10:20:49,782 - INFO - Processed 25000000 reads so far
2011-05-20 10:20:55,854 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:42990111-63010111
2011-05-20 10:21:00,153 - INFO - Processed 25100000 reads so far
2011-05-20 10:21:10,153 - INFO - Processed 25200000 reads so far
2011-05-20 10:21:21,970 - INFO - Processed 25300000 reads so far
2011-05-20 10:21:32,175 - INFO - Processed 25400000 reads so far
2011-05-20 10:21:42,894 - INFO - Processed 25500000 reads so far
2011-05-20 10:21:52,242 - INFO - Processed 25600000 reads so far
2011-05-20 10:22:00,477 - INFO - Processed 25700000 reads so far
2011-05-20 10:22:13,493 - INFO - Processed 25800000 reads so far
2011-05-20 10:22:25,239 - INFO - Processed 25900000 reads so far
2011-05-20 10:22:36,533 - INFO - Processed 26000000 reads so far
2011-05-20 10:22:46,696 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:62990112-83010112
2011-05-20 10:22:47,920 - INFO - Processed 26100000 reads so far
2011-05-20 10:23:00,089 - INFO - Processed 26200000 reads so far
2011-05-20 10:23:11,310 - INFO - Processed 26300000 reads so far
2011-05-20 10:23:23,145 - INFO - Processed 26400000 reads so far
2011-05-20 10:23:34,383 - INFO - Processed 26500000 reads so far
2011-05-20 10:23:45,509 - INFO - Processed 26600000 reads so far
2011-05-20 10:23:58,493 - INFO - Processed 26700000 reads so far
2011-05-20 10:24:08,202 - INFO - Processed 26800000 reads so far
2011-05-20 10:24:16,361 - INFO - Processed 26900000 reads so far
2011-05-20 10:24:25,887 - INFO - Processed 27000000 reads so far
2011-05-20 10:24:32,226 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:82990113-103010113
2011-05-20 10:24:35,478 - INFO - Processed 27100000 reads so far
2011-05-20 10:24:45,243 - INFO - Processed 27200000 reads so far
2011-05-20 10:24:54,618 - INFO - Processed 27300000 reads so far
2011-05-20 10:25:04,654 - INFO - Processed 27400000 reads so far
2011-05-20 10:25:13,918 - INFO - Processed 27500000 reads so far
2011-05-20 10:25:24,285 - INFO - Processed 27600000 reads so far
2011-05-20 10:25:35,067 - INFO - Processed 27700000 reads so far
2011-05-20 10:25:46,367 - INFO - Processed 27800000 reads so far
2011-05-20 10:25:58,899 - INFO - Processed 27900000 reads so far
2011-05-20 10:26:01,351 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:102990114-123010114
2011-05-20 10:26:09,584 - INFO - Processed 28000000 reads so far
2011-05-20 10:26:20,707 - INFO - Processed 28100000 reads so far
2011-05-20 10:26:32,494 - INFO - Processed 28200000 reads so far
2011-05-20 10:26:43,524 - INFO - Processed 28300000 reads so far
2011-05-20 10:26:55,829 - INFO - Processed 28400000 reads so far
2011-05-20 10:27:06,179 - INFO - Processed 28500000 reads so far
2011-05-20 10:27:17,571 - INFO - Processed 28600000 reads so far
2011-05-20 10:27:28,284 - INFO - Processed 28700000 reads so far
2011-05-20 10:27:39,043 - INFO - Processed 28800000 reads so far
2011-05-20 10:27:41,429 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:122990125-143010125
2011-05-20 10:27:47,036 - INFO - Processed 28900000 reads so far
2011-05-20 10:27:50,434 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:2990005-23010005
2011-05-20 10:27:58,360 - INFO - Processed 29000000 reads so far
2011-05-20 10:28:09,431 - INFO - Processed 29100000 reads so far
2011-05-20 10:28:20,560 - INFO - Processed 29200000 reads so far
2011-05-20 10:28:32,994 - INFO - Processed 29300000 reads so far
2011-05-20 10:28:43,930 - INFO - Processed 29400000 reads so far
2011-05-20 10:28:58,762 - INFO - Processed 29500000 reads so far
2011-05-20 10:29:10,760 - INFO - Processed 29600000 reads so far
2011-05-20 10:29:21,490 - INFO - Processed 29700000 reads so far
2011-05-20 10:29:33,006 - INFO - Processed 29800000 reads so far
2011-05-20 10:29:37,821 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:22990034-43010034
2011-05-20 10:29:44,772 - INFO - Processed 29900000 reads so far
2011-05-20 10:29:56,176 - INFO - Processed 30000000 reads so far
2011-05-20 10:30:08,855 - INFO - Processed 30100000 reads so far
2011-05-20 10:30:19,309 - INFO - Processed 30200000 reads so far
2011-05-20 10:30:28,051 - INFO - Processed 30300000 reads so far
2011-05-20 10:30:36,527 - INFO - Processed 30400000 reads so far
2011-05-20 10:30:45,665 - INFO - Processed 30500000 reads so far
2011-05-20 10:30:55,708 - INFO - Processed 30600000 reads so far
2011-05-20 10:31:07,310 - INFO - Processed 30700000 reads so far
2011-05-20 10:31:14,793 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:42990051-63010051
2011-05-20 10:31:15,463 - INFO - Processed 30800000 reads so far
2011-05-20 10:31:30,182 - INFO - Processed 30900000 reads so far
2011-05-20 10:31:43,515 - INFO - Processed 31000000 reads so far
2011-05-20 10:32:00,575 - INFO - Processed 31100000 reads so far
2011-05-20 10:32:11,813 - INFO - Processed 31200000 reads so far
2011-05-20 10:32:23,292 - INFO - Processed 31300000 reads so far
2011-05-20 10:32:33,084 - INFO - Processed 31400000 reads so far
2011-05-20 10:32:43,189 - INFO - Processed 31500000 reads so far
2011-05-20 10:32:52,629 - INFO - Processed 31600000 reads so far
2011-05-20 10:33:01,299 - INFO - Processed 31700000 reads so far
2011-05-20 10:33:02,554 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:62990059-83010059
2011-05-20 10:33:09,864 - INFO - Processed 31800000 reads so far
2011-05-20 10:33:18,500 - INFO - Processed 31900000 reads so far
2011-05-20 10:33:28,236 - INFO - Processed 32000000 reads so far
2011-05-20 10:33:36,642 - INFO - Processed 32100000 reads so far
2011-05-20 10:33:46,805 - INFO - Processed 32200000 reads so far
2011-05-20 10:33:55,343 - INFO - Processed 32300000 reads so far
2011-05-20 10:34:03,570 - INFO - Processed 32400000 reads so far
2011-05-20 10:34:11,970 - INFO - Processed 32500000 reads so far
2011-05-20 10:34:20,900 - INFO - Processed 32600000 reads so far
2011-05-20 10:34:28,727 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:82990065-103010065
2011-05-20 10:34:30,040 - INFO - Processed 32700000 reads so far
2011-05-20 10:34:38,953 - INFO - Processed 32800000 reads so far
2011-05-20 10:34:47,146 - INFO - Processed 32900000 reads so far
2011-05-20 10:34:55,571 - INFO - Processed 33000000 reads so far
2011-05-20 10:35:06,363 - INFO - Processed 33100000 reads so far
2011-05-20 10:35:14,700 - INFO - Processed 33200000 reads so far
2011-05-20 10:35:22,869 - INFO - Processed 33300000 reads so far
2011-05-20 10:35:30,869 - INFO - Processed 33400000 reads so far
2011-05-20 10:35:39,455 - INFO - Processed 33500000 reads so far
2011-05-20 10:35:49,409 - INFO - Processed 33600000 reads so far
2011-05-20 10:35:52,962 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:102990105-123010105
2011-05-20 10:35:54,785 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:2990015-23010015
2011-05-20 10:35:56,674 - INFO - Processed 33700000 reads so far
2011-05-20 10:36:05,693 - INFO - Processed 33800000 reads so far
2011-05-20 10:36:14,040 - INFO - Processed 33900000 reads so far
2011-05-20 10:36:21,661 - INFO - Processed 34000000 reads so far
2011-05-20 10:36:29,039 - INFO - Processed 34100000 reads so far
2011-05-20 10:36:40,588 - INFO - Processed 34200000 reads so far
2011-05-20 10:36:52,002 - INFO - Processed 34300000 reads so far
2011-05-20 10:37:03,112 - INFO - Processed 34400000 reads so far
2011-05-20 10:37:13,002 - INFO - Processed 34500000 reads so far
2011-05-20 10:37:23,029 - INFO - Processed 34600000 reads so far
2011-05-20 10:37:31,142 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:22990071-43010071
2011-05-20 10:37:32,766 - INFO - Processed 34700000 reads so far
2011-05-20 10:37:42,539 - INFO - Processed 34800000 reads so far
2011-05-20 10:37:50,866 - INFO - Processed 34900000 reads so far
2011-05-20 10:37:59,359 - INFO - Processed 35000000 reads so far
2011-05-20 10:38:07,570 - INFO - Processed 35100000 reads so far
2011-05-20 10:38:16,592 - INFO - Processed 35200000 reads so far
2011-05-20 10:38:26,847 - INFO - Processed 35300000 reads so far
2011-05-20 10:38:38,516 - INFO - Processed 35400000 reads so far
2011-05-20 10:38:49,508 - INFO - Processed 35500000 reads so far
2011-05-20 10:39:00,136 - INFO - Processed 35600000 reads so far
2011-05-20 10:39:03,086 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:42990073-63010073
2011-05-20 10:39:08,636 - INFO - Processed 35700000 reads so far
2011-05-20 10:39:18,051 - INFO - Processed 35800000 reads so far
2011-05-20 10:39:28,562 - INFO - Processed 35900000 reads so far
2011-05-20 10:39:40,497 - INFO - Processed 36000000 reads so far
2011-05-20 10:39:52,831 - INFO - Processed 36100000 reads so far
2011-05-20 10:40:03,198 - INFO - Processed 36200000 reads so far
2011-05-20 10:40:12,983 - INFO - Processed 36300000 reads so far
2011-05-20 10:40:28,584 - INFO - Processed 36400000 reads so far
2011-05-20 10:40:40,589 - INFO - Processed 36500000 reads so far
2011-05-20 10:40:46,967 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:62990085-83010085
2011-05-20 10:40:51,391 - INFO - Processed 36600000 reads so far
2011-05-20 10:41:03,159 - INFO - Processed 36700000 reads so far
2011-05-20 10:41:11,076 - INFO - Processed 36800000 reads so far
2011-05-20 10:41:20,735 - INFO - Processed 36900000 reads so far
2011-05-20 10:41:30,709 - INFO - Processed 37000000 reads so far
2011-05-20 10:41:38,732 - INFO - Processed 37100000 reads so far
2011-05-20 10:41:47,233 - INFO - Processed 37200000 reads so far
2011-05-20 10:41:59,448 - INFO - Processed 37300000 reads so far
2011-05-20 10:42:10,665 - INFO - Processed 37400000 reads so far
2011-05-20 10:42:15,803 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:82990101-103010101
2011-05-20 10:42:22,396 - INFO - Processed 37500000 reads so far
2011-05-20 10:42:31,533 - INFO - Processed 37600000 reads so far
2011-05-20 10:42:40,550 - INFO - Processed 37700000 reads so far
2011-05-20 10:42:51,412 - INFO - Processed 37800000 reads so far
2011-05-20 10:42:59,615 - INFO - Processed 37900000 reads so far
2011-05-20 10:43:07,323 - INFO - Processed 38000000 reads so far
2011-05-20 10:43:15,447 - INFO - Processed 38100000 reads so far
2011-05-20 10:43:21,974 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16_random:0-20010059
2011-05-20 10:43:22,008 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:2989994-23009994
2011-05-20 10:43:24,463 - INFO - Processed 38200000 reads so far
2011-05-20 10:43:33,435 - INFO - Processed 38300000 reads so far
2011-05-20 10:43:42,156 - INFO - Processed 38400000 reads so far
2011-05-20 10:43:52,909 - INFO - Processed 38500000 reads so far
2011-05-20 10:44:02,743 - INFO - Processed 38600000 reads so far
2011-05-20 10:44:10,762 - INFO - Processed 38700000 reads so far
2011-05-20 10:44:19,535 - INFO - Processed 38800000 reads so far
2011-05-20 10:44:28,762 - INFO - Processed 38900000 reads so far
2011-05-20 10:44:38,254 - INFO - Processed 39000000 reads so far
2011-05-20 10:44:51,121 - INFO - Processed 39100000 reads so far
2011-05-20 10:44:54,660 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:22990027-43010027
2011-05-20 10:44:59,777 - INFO - Processed 39200000 reads so far
2011-05-20 10:45:09,926 - INFO - Processed 39300000 reads so far
2011-05-20 10:45:20,277 - INFO - Processed 39400000 reads so far
2011-05-20 10:45:29,740 - INFO - Processed 39500000 reads so far
2011-05-20 10:45:38,356 - INFO - Processed 39600000 reads so far
2011-05-20 10:45:47,911 - INFO - Processed 39700000 reads so far
2011-05-20 10:45:56,674 - INFO - Processed 39800000 reads so far
2011-05-20 10:46:07,354 - INFO - Processed 39900000 reads so far
2011-05-20 10:46:16,640 - INFO - Processed 40000000 reads so far
2011-05-20 10:46:25,667 - INFO - Processed 40100000 reads so far
2011-05-20 10:46:28,540 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:42990056-63010056
2011-05-20 10:46:37,070 - INFO - Processed 40200000 reads so far
2011-05-20 10:46:52,389 - INFO - Processed 40300000 reads so far
2011-05-20 10:47:05,153 - INFO - Processed 40400000 reads so far
2011-05-20 10:47:12,841 - INFO - Processed 40500000 reads so far
2011-05-20 10:47:21,001 - INFO - Processed 40600000 reads so far
2011-05-20 10:47:32,129 - INFO - Processed 40700000 reads so far
2011-05-20 10:47:43,687 - INFO - Processed 40800000 reads so far
2011-05-20 10:47:56,517 - INFO - Processed 40900000 reads so far
2011-05-20 10:48:08,378 - INFO - Processed 41000000 reads so far
2011-05-20 10:48:13,880 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:62990068-83010068
2011-05-20 10:48:18,253 - INFO - Processed 41100000 reads so far
2011-05-20 10:48:26,748 - INFO - Processed 41200000 reads so far
2011-05-20 10:48:35,252 - INFO - Processed 41300000 reads so far
2011-05-20 10:48:44,455 - INFO - Processed 41400000 reads so far
2011-05-20 10:48:53,706 - INFO - Processed 41500000 reads so far
2011-05-20 10:49:03,556 - INFO - Processed 41600000 reads so far
2011-05-20 10:49:15,556 - INFO - Processed 41700000 reads so far
2011-05-20 10:49:24,890 - INFO - Processed 41800000 reads so far
2011-05-20 10:49:33,601 - INFO - Processed 41900000 reads so far
2011-05-20 10:49:42,909 - INFO - Processed 42000000 reads so far
2011-05-20 10:49:44,088 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:82990164-103010164
2011-05-20 10:49:53,507 - INFO - Processed 42100000 reads so far
2011-05-20 10:50:02,329 - INFO - Processed 42200000 reads so far
2011-05-20 10:50:10,110 - INFO - Processed 42300000 reads so far
2011-05-20 10:50:18,236 - INFO - Processed 42400000 reads so far
2011-05-20 10:50:27,112 - INFO - Processed 42500000 reads so far
2011-05-20 10:50:35,384 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17_random:0-20010044
2011-05-20 10:50:36,383 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:2990004-23010004
2011-05-20 10:50:36,654 - INFO - Processed 42600000 reads so far
2011-05-20 10:50:44,305 - INFO - Processed 42700000 reads so far
2011-05-20 10:50:53,972 - INFO - Processed 42800000 reads so far
2011-05-20 10:51:01,902 - INFO - Processed 42900000 reads so far
2011-05-20 10:51:11,875 - INFO - Processed 43000000 reads so far
2011-05-20 10:51:20,733 - INFO - Processed 43100000 reads so far
2011-05-20 10:51:29,702 - INFO - Processed 43200000 reads so far
2011-05-20 10:51:37,123 - INFO - Processed 43300000 reads so far
2011-05-20 10:51:45,624 - INFO - Processed 43400000 reads so far
2011-05-20 10:51:53,669 - INFO - Processed 43500000 reads so far
2011-05-20 10:52:00,640 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:22990057-43010057
2011-05-20 10:52:01,757 - INFO - Processed 43600000 reads so far
2011-05-20 10:52:09,380 - INFO - Processed 43700000 reads so far
2011-05-20 10:52:17,867 - INFO - Processed 43800000 reads so far
2011-05-20 10:52:30,061 - INFO - Processed 43900000 reads so far
2011-05-20 10:52:38,923 - INFO - Processed 44000000 reads so far
2011-05-20 10:52:47,736 - INFO - Processed 44100000 reads so far
2011-05-20 10:52:56,665 - INFO - Processed 44200000 reads so far
2011-05-20 10:53:05,759 - INFO - Processed 44300000 reads so far
2011-05-20 10:53:14,027 - INFO - Processed 44400000 reads so far
2011-05-20 10:53:21,491 - INFO - Processed 44500000 reads so far
2011-05-20 10:53:25,499 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:42990106-63010106
2011-05-20 10:53:31,204 - INFO - Processed 44600000 reads so far
2011-05-20 10:53:39,191 - INFO - Processed 44700000 reads so far
2011-05-20 10:53:47,412 - INFO - Processed 44800000 reads so far
2011-05-20 10:53:56,593 - INFO - Processed 44900000 reads so far
2011-05-20 10:54:04,984 - INFO - Processed 45000000 reads so far
2011-05-20 10:54:13,324 - INFO - Processed 45100000 reads so far
2011-05-20 10:54:23,594 - INFO - Processed 45200000 reads so far
2011-05-20 10:54:31,990 - INFO - Processed 45300000 reads so far
2011-05-20 10:54:41,545 - INFO - Processed 45400000 reads so far
2011-05-20 10:54:48,574 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:62990137-83010137
2011-05-20 10:54:49,481 - INFO - Processed 45500000 reads so far
2011-05-20 10:54:59,931 - INFO - Processed 45600000 reads so far
2011-05-20 10:55:07,865 - INFO - Processed 45700000 reads so far
2011-05-20 10:55:15,605 - INFO - Processed 45800000 reads so far
2011-05-20 10:55:26,591 - INFO - Processed 45900000 reads so far
2011-05-20 10:55:34,841 - INFO - Processed 46000000 reads so far
2011-05-20 10:55:46,101 - INFO - Processed 46100000 reads so far
2011-05-20 10:55:57,496 - INFO - Processed 46200000 reads so far
2011-05-20 10:56:08,449 - INFO - Processed 46300000 reads so far
2011-05-20 10:56:19,800 - INFO - Processed 46400000 reads so far
2011-05-20 10:56:26,493 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:82990147-103010147
2011-05-20 10:56:31,799 - INFO - Processed 46500000 reads so far
2011-05-20 10:56:42,868 - INFO - Processed 46600000 reads so far
2011-05-20 10:56:54,940 - INFO - Processed 46700000 reads so far
2011-05-20 10:57:07,640 - INFO - Processed 46800000 reads so far
2011-05-20 10:57:08,814 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:2990103-23010103
2011-05-20 10:57:20,066 - INFO - Processed 46900000 reads so far
2011-05-20 10:57:31,545 - INFO - Processed 47000000 reads so far
2011-05-20 10:57:44,545 - INFO - Processed 47100000 reads so far
2011-05-20 10:57:56,519 - INFO - Processed 47200000 reads so far
2011-05-20 10:58:08,110 - INFO - Processed 47300000 reads so far
2011-05-20 10:58:19,189 - INFO - Processed 47400000 reads so far
2011-05-20 10:58:30,234 - INFO - Processed 47500000 reads so far
2011-05-20 10:58:41,995 - INFO - Processed 47600000 reads so far
2011-05-20 10:58:53,069 - INFO - Processed 47700000 reads so far
2011-05-20 10:58:58,165 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:22990125-43010125
2011-05-20 10:59:02,915 - INFO - Processed 47800000 reads so far
2011-05-20 10:59:09,964 - INFO - Processed 47900000 reads so far
2011-05-20 10:59:20,238 - INFO - Processed 48000000 reads so far
2011-05-20 10:59:31,431 - INFO - Processed 48100000 reads so far
2011-05-20 10:59:42,463 - INFO - Processed 48200000 reads so far
2011-05-20 10:59:53,753 - INFO - Processed 48300000 reads so far
2011-05-20 11:00:06,359 - INFO - Processed 48400000 reads so far
2011-05-20 11:00:17,556 - INFO - Processed 48500000 reads so far
2011-05-20 11:00:30,191 - INFO - Processed 48600000 reads so far
2011-05-20 11:00:41,390 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:42990184-63010184
2011-05-20 11:00:41,532 - INFO - Processed 48700000 reads so far
2011-05-20 11:00:50,588 - INFO - Processed 48800000 reads so far
2011-05-20 11:01:02,122 - INFO - Processed 48900000 reads so far
2011-05-20 11:01:13,120 - INFO - Processed 49000000 reads so far
2011-05-20 11:01:24,465 - INFO - Processed 49100000 reads so far
2011-05-20 11:01:38,457 - INFO - Processed 49200000 reads so far
2011-05-20 11:01:49,703 - INFO - Processed 49300000 reads so far
2011-05-20 11:01:58,336 - INFO - Processed 49400000 reads so far
2011-05-20 11:02:09,663 - INFO - Processed 49500000 reads so far
2011-05-20 11:02:19,911 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:2989972-23009972
2011-05-20 11:02:21,935 - INFO - Processed 49600000 reads so far
2011-05-20 11:02:33,240 - INFO - Processed 49700000 reads so far
2011-05-20 11:02:46,325 - INFO - Processed 49800000 reads so far
2011-05-20 11:02:57,657 - INFO - Processed 49900000 reads so far
2011-05-20 11:03:09,033 - INFO - Processed 50000000 reads so far
2011-05-20 11:03:21,007 - INFO - Processed 50100000 reads so far
2011-05-20 11:03:32,240 - INFO - Processed 50200000 reads so far
2011-05-20 11:03:44,620 - INFO - Processed 50300000 reads so far
2011-05-20 11:03:55,989 - INFO - Processed 50400000 reads so far
2011-05-20 11:04:05,524 - INFO - Processed 50500000 reads so far
2011-05-20 11:04:06,847 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:22989981-43009981
2011-05-20 11:04:14,137 - INFO - Processed 50600000 reads so far
2011-05-20 11:04:22,439 - INFO - Processed 50700000 reads so far
2011-05-20 11:04:32,786 - INFO - Processed 50800000 reads so far
2011-05-20 11:04:43,872 - INFO - Processed 50900000 reads so far
2011-05-20 11:04:52,282 - INFO - Processed 51000000 reads so far
2011-05-20 11:05:00,260 - INFO - Processed 51100000 reads so far
2011-05-20 11:05:10,494 - INFO - Processed 51200000 reads so far
2011-05-20 11:05:19,506 - INFO - Processed 51300000 reads so far
2011-05-20 11:05:30,643 - INFO - Processed 51400000 reads so far
2011-05-20 11:05:36,199 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:42990047-63010047
2011-05-20 11:05:39,612 - INFO - Processed 51500000 reads so far
2011-05-20 11:05:49,655 - INFO - Processed 51600000 reads so far
2011-05-20 11:06:00,035 - INFO - Processed 51700000 reads so far
2011-05-20 11:06:09,692 - INFO - Processed 51800000 reads so far
2011-05-20 11:06:20,404 - INFO - Processed 51900000 reads so far
2011-05-20 11:06:28,420 - INFO - Processed 52000000 reads so far
2011-05-20 11:06:38,072 - INFO - Processed 52100000 reads so far
2011-05-20 11:06:48,085 - INFO - Processed 52200000 reads so far
2011-05-20 11:06:56,665 - INFO - Processed 52300000 reads so far
2011-05-20 11:07:07,365 - INFO - Processed 52400000 reads so far
2011-05-20 11:07:07,985 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:62990058-83010058
2011-05-20 11:07:17,008 - INFO - Processed 52500000 reads so far
2011-05-20 11:07:27,499 - INFO - Processed 52600000 reads so far
2011-05-20 11:07:37,781 - INFO - Processed 52700000 reads so far
2011-05-20 11:07:46,163 - INFO - Processed 52800000 reads so far
2011-05-20 11:07:56,092 - INFO - Processed 52900000 reads so far
2011-05-20 11:08:05,466 - INFO - Processed 53000000 reads so far
2011-05-20 11:08:15,818 - INFO - Processed 53100000 reads so far
2011-05-20 11:08:24,855 - INFO - Processed 53200000 reads so far
2011-05-20 11:08:32,528 - INFO - Processed 53300000 reads so far
2011-05-20 11:08:38,033 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:82990067-103010067
2011-05-20 11:08:44,093 - INFO - Processed 53400000 reads so far
2011-05-20 11:08:51,437 - INFO - Processed 53500000 reads so far
2011-05-20 11:08:59,966 - INFO - Processed 53600000 reads so far
2011-05-20 11:09:09,873 - INFO - Processed 53700000 reads so far
2011-05-20 11:09:20,557 - INFO - Processed 53800000 reads so far
2011-05-20 11:09:36,961 - INFO - Processed 53900000 reads so far
2011-05-20 11:09:57,723 - INFO - Processed 54000000 reads so far
2011-05-20 11:10:12,919 - INFO - Processed 54100000 reads so far
2011-05-20 11:10:34,788 - INFO - Processed 54200000 reads so far
2011-05-20 11:10:47,437 - INFO - Processed 54300000 reads so far
2011-05-20 11:10:47,511 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:102990082-123010082
2011-05-20 11:11:14,514 - INFO - Processed 54400000 reads so far
2011-05-20 11:11:27,915 - INFO - Processed 54500000 reads so far
2011-05-20 11:11:49,776 - INFO - Processed 54600000 reads so far
2011-05-20 11:11:59,928 - INFO - Processed 54700000 reads so far
2011-05-20 11:12:09,005 - INFO - Processed 54800000 reads so far
2011-05-20 11:12:18,301 - INFO - Processed 54900000 reads so far
2011-05-20 11:12:29,434 - INFO - Processed 55000000 reads so far
2011-05-20 11:12:41,169 - INFO - Processed 55100000 reads so far
2011-05-20 11:12:49,019 - INFO - Processed 55200000 reads so far
2011-05-20 11:12:50,148 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:122990104-143010104
2011-05-20 11:12:59,076 - INFO - Processed 55300000 reads so far
2011-05-20 11:13:08,918 - INFO - Processed 55400000 reads so far
2011-05-20 11:13:19,473 - INFO - Processed 55500000 reads so far
2011-05-20 11:13:31,649 - INFO - Processed 55600000 reads so far
2011-05-20 11:13:43,929 - INFO - Processed 55700000 reads so far
2011-05-20 11:13:54,978 - INFO - Processed 55800000 reads so far
2011-05-20 11:14:06,159 - INFO - Processed 55900000 reads so far
2011-05-20 11:14:18,729 - INFO - Processed 56000000 reads so far
2011-05-20 11:14:29,652 - INFO - Processed 56100000 reads so far
2011-05-20 11:14:38,105 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:142990110-163010110
2011-05-20 11:14:41,295 - INFO - Processed 56200000 reads so far
2011-05-20 11:14:52,454 - INFO - Processed 56300000 reads so far
2011-05-20 11:15:02,252 - INFO - Processed 56400000 reads so far
2011-05-20 11:15:14,552 - INFO - Processed 56500000 reads so far
2011-05-20 11:15:25,546 - INFO - Processed 56600000 reads so far
2011-05-20 11:15:36,554 - INFO - Processed 56700000 reads so far
2011-05-20 11:15:49,145 - INFO - Processed 56800000 reads so far
2011-05-20 11:15:59,280 - INFO - Processed 56900000 reads so far
2011-05-20 11:16:10,353 - INFO - Processed 57000000 reads so far
2011-05-20 11:16:20,236 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:162990117-183010117
2011-05-20 11:16:22,170 - INFO - Processed 57100000 reads so far
2011-05-20 11:16:34,056 - INFO - Processed 57200000 reads so far
2011-05-20 11:16:45,193 - INFO - Processed 57300000 reads so far
2011-05-20 11:16:57,279 - INFO - Processed 57400000 reads so far
2011-05-20 11:17:08,065 - INFO - Processed 57500000 reads so far
2011-05-20 11:17:18,797 - INFO - Processed 57600000 reads so far
2011-05-20 11:17:27,824 - INFO - Processed 57700000 reads so far
2011-05-20 11:17:35,170 - INFO - Processed 57800000 reads so far
2011-05-20 11:17:44,100 - INFO - Processed 57900000 reads so far
2011-05-20 11:17:51,130 - INFO - Processed 58000000 reads so far
2011-05-20 11:17:57,695 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:182990145-203010145
2011-05-20 11:18:02,494 - INFO - Processed 58100000 reads so far
2011-05-20 11:18:10,170 - INFO - Processed 58200000 reads so far
2011-05-20 11:18:18,522 - INFO - Processed 58300000 reads so far
2011-05-20 11:18:28,414 - INFO - Processed 58400000 reads so far
2011-05-20 11:18:37,228 - INFO - Processed 58500000 reads so far
2011-05-20 11:19:34,879 - INFO - Processed 58600000 reads so far
2011-05-20 11:19:46,041 - INFO - Processed 58700000 reads so far
2011-05-20 11:19:52,273 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1_random:0-20010000
2011-05-20 11:19:58,295 - INFO - Processed 58800000 reads so far
2011-05-20 11:20:03,067 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:2990109-23010109
2011-05-20 11:20:07,116 - INFO - Processed 58900000 reads so far
2011-05-20 11:20:17,300 - INFO - Processed 59000000 reads so far
2011-05-20 11:20:27,872 - INFO - Processed 59100000 reads so far
2011-05-20 11:20:39,497 - INFO - Processed 59200000 reads so far
2011-05-20 11:20:51,835 - INFO - Processed 59300000 reads so far
2011-05-20 11:21:04,379 - INFO - Processed 59400000 reads so far
2011-05-20 11:21:15,408 - INFO - Processed 59500000 reads so far
2011-05-20 11:21:26,705 - INFO - Processed 59600000 reads so far
2011-05-20 11:21:38,872 - INFO - Processed 59700000 reads so far
2011-05-20 11:21:50,896 - INFO - Processed 59800000 reads so far
2011-05-20 11:21:53,818 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:22990119-43010119
2011-05-20 11:22:01,584 - INFO - Processed 59900000 reads so far
2011-05-20 11:22:10,985 - INFO - Processed 60000000 reads so far
2011-05-20 11:22:23,283 - INFO - Processed 60100000 reads so far
2011-05-20 11:22:35,379 - INFO - Processed 60200000 reads so far
2011-05-20 11:22:46,411 - INFO - Processed 60300000 reads so far
2011-05-20 11:22:57,862 - INFO - Processed 60400000 reads so far
2011-05-20 11:23:10,471 - INFO - Processed 60500000 reads so far
2011-05-20 11:23:21,311 - INFO - Processed 60600000 reads so far
2011-05-20 11:23:32,610 - INFO - Processed 60700000 reads so far
2011-05-20 11:23:39,228 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:42990139-63010139
2011-05-20 11:23:42,232 - INFO - Processed 60800000 reads so far
2011-05-20 11:23:52,969 - INFO - Processed 60900000 reads so far
2011-05-20 11:24:04,256 - INFO - Processed 61000000 reads so far
2011-05-20 11:24:14,464 - INFO - Processed 61100000 reads so far
2011-05-20 11:24:26,835 - INFO - Processed 61200000 reads so far
2011-05-20 11:24:40,232 - INFO - Processed 61300000 reads so far
2011-05-20 11:24:51,494 - INFO - Processed 61400000 reads so far
2011-05-20 11:25:03,318 - INFO - Processed 61500000 reads so far
2011-05-20 11:25:17,018 - INFO - Processed 61600000 reads so far
2011-05-20 11:25:25,948 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:62990152-83010152
2011-05-20 11:25:27,994 - INFO - Processed 61700000 reads so far
2011-05-20 11:25:45,958 - INFO - Processed 61800000 reads so far
2011-05-20 11:25:57,335 - INFO - Processed 61900000 reads so far
2011-05-20 11:26:06,751 - INFO - Processed 62000000 reads so far
2011-05-20 11:26:18,774 - INFO - Processed 62100000 reads so far
2011-05-20 11:26:30,241 - INFO - Processed 62200000 reads so far
2011-05-20 11:26:41,646 - INFO - Processed 62300000 reads so far
2011-05-20 11:26:53,131 - INFO - Processed 62400000 reads so far
2011-05-20 11:27:01,067 - INFO - Processed 62500000 reads so far
2011-05-20 11:27:10,688 - INFO - Processed 62600000 reads so far
2011-05-20 11:27:20,657 - INFO - Processed 62700000 reads so far
2011-05-20 11:27:25,760 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:82990188-103010188
2011-05-20 11:27:30,298 - INFO - Processed 62800000 reads so far
2011-05-20 11:27:40,398 - INFO - Processed 62900000 reads so far
2011-05-20 11:27:52,205 - INFO - Processed 63000000 reads so far
2011-05-20 11:28:03,551 - INFO - Processed 63100000 reads so far
2011-05-20 11:28:14,300 - INFO - Processed 63200000 reads so far
2011-05-20 11:28:26,075 - INFO - Processed 63300000 reads so far
2011-05-20 11:28:37,306 - INFO - Processed 63400000 reads so far
2011-05-20 11:28:47,773 - INFO - Processed 63500000 reads so far
2011-05-20 11:28:56,946 - INFO - Processed 63600000 reads so far
2011-05-20 11:29:07,182 - INFO - Processed 63700000 reads so far
2011-05-20 11:29:15,339 - INFO - Processed 63800000 reads so far
2011-05-20 11:29:23,814 - INFO - Processed 63900000 reads so far
2011-05-20 11:29:30,854 - INFO - Processed 64000000 reads so far
2011-05-20 11:29:38,206 - INFO - Processed 64100000 reads so far
2011-05-20 11:29:45,592 - INFO - Processed 64200000 reads so far
2011-05-20 11:29:53,107 - INFO - Processed 64300000 reads so far
2011-05-20 11:30:03,697 - INFO - Processed 64400000 reads so far
2011-05-20 11:30:14,225 - INFO - Processed 64500000 reads so far
2011-05-20 11:30:22,711 - INFO - Processed 64600000 reads so far
2011-05-20 11:30:31,206 - INFO - Processed 64700000 reads so far
2011-05-20 11:30:39,690 - INFO - Processed 64800000 reads so far
2011-05-20 11:30:48,697 - INFO - Processed 64900000 reads so far
2011-05-20 11:30:58,017 - INFO - Processed 65000000 reads so far
2011-05-20 11:31:07,368 - INFO - Processed 65100000 reads so far
2011-05-20 11:31:16,223 - INFO - Processed 65200000 reads so far
2011-05-20 11:31:24,553 - INFO - Processed 65300000 reads so far
2011-05-20 11:31:34,864 - INFO - Processed 65400000 reads so far
2011-05-20 11:31:44,621 - INFO - Processed 65500000 reads so far
2011-05-20 11:31:55,357 - INFO - Processed 65600000 reads so far
2011-05-20 11:32:04,305 - INFO - Processed 65700000 reads so far
2011-05-20 11:32:13,997 - INFO - Processed 65800000 reads so far
2011-05-20 11:32:23,006 - INFO - Processed 65900000 reads so far
2011-05-20 11:32:32,343 - INFO - Processed 66000000 reads so far
2011-05-20 11:32:41,527 - INFO - Processed 66100000 reads so far
2011-05-20 11:32:50,140 - INFO - Processed 66200000 reads so far
2011-05-20 11:32:57,002 - INFO - Processed 66300000 reads so far
2011-05-20 11:33:03,666 - INFO - Processed 66400000 reads so far
2011-05-20 11:33:10,744 - INFO - Processed 66500000 reads so far
2011-05-20 11:33:18,591 - INFO - Processed 66600000 reads so far
2011-05-20 11:33:27,292 - INFO - Processed 66700000 reads so far
2011-05-20 11:33:38,054 - INFO - Processed 66800000 reads so far
2011-05-20 11:33:46,547 - INFO - Processed 66900000 reads so far
2011-05-20 11:33:55,399 - INFO - Processed 67000000 reads so far
2011-05-20 11:34:06,049 - INFO - Processed 67100000 reads so far
2011-05-20 11:34:29,217 - INFO - Processed 67200000 reads so far
2011-05-20 11:34:38,459 - INFO - Processed 67300000 reads so far
2011-05-20 11:34:49,301 - INFO - Processed 67400000 reads so far
2011-05-20 11:34:58,761 - INFO - Processed 67500000 reads so far
2011-05-20 11:35:08,340 - INFO - Processed 67600000 reads so far
2011-05-20 11:35:17,678 - INFO - Processed 67700000 reads so far
2011-05-20 11:35:27,105 - INFO - Processed 67800000 reads so far
2011-05-20 11:35:36,385 - INFO - Processed 67900000 reads so far
2011-05-20 11:35:46,607 - INFO - Processed 68000000 reads so far
2011-05-20 11:36:01,627 - INFO - Processed 68100000 reads so far
2011-05-20 11:36:13,479 - INFO - Processed 68200000 reads so far
2011-05-20 11:36:22,742 - INFO - Processed 68300000 reads so far
2011-05-20 11:36:31,493 - INFO - Processed 68400000 reads so far
2011-05-20 11:36:40,024 - INFO - Processed 68500000 reads so far
2011-05-20 11:36:49,063 - INFO - Processed 68600000 reads so far
2011-05-20 11:36:58,906 - INFO - Processed 68700000 reads so far
2011-05-20 11:37:08,853 - INFO - Processed 68800000 reads so far
2011-05-20 11:37:17,661 - INFO - Processed 68900000 reads so far
2011-05-20 11:37:26,302 - INFO - Processed 69000000 reads so far
2011-05-20 11:37:36,638 - INFO - Processed 69100000 reads so far
2011-05-20 11:37:47,139 - INFO - Processed 69200000 reads so far
2011-05-20 11:37:55,574 - INFO - Processed 69300000 reads so far
2011-05-20 11:38:04,163 - INFO - Processed 69400000 reads so far
2011-05-20 11:38:14,118 - INFO - Processed 69500000 reads so far
2011-05-20 11:38:23,045 - INFO - Processed 69600000 reads so far
2011-05-20 11:38:32,100 - INFO - Processed 69700000 reads so far
2011-05-20 11:38:39,622 - INFO - Processed 69800000 reads so far
2011-05-20 11:38:47,396 - INFO - Processed 69900000 reads so far
2011-05-20 11:38:56,424 - INFO - Processed 70000000 reads so far
2011-05-20 11:39:05,999 - INFO - Processed 70100000 reads so far
2011-05-20 11:39:17,690 - INFO - Processed 70200000 reads so far
2011-05-20 11:39:28,400 - INFO - Processed 70300000 reads so far
2011-05-20 11:39:37,566 - INFO - Processed 70400000 reads so far
2011-05-20 11:39:47,178 - INFO - Processed 70500000 reads so far
2011-05-20 11:39:56,198 - INFO - Processed 70600000 reads so far
2011-05-20 11:40:05,672 - INFO - Processed 70700000 reads so far
2011-05-20 11:40:16,222 - INFO - Processed 70800000 reads so far
2011-05-20 11:40:25,584 - INFO - Processed 70900000 reads so far
2011-05-20 11:40:38,544 - INFO - Processed 71000000 reads so far
2011-05-20 11:40:52,139 - INFO - Processed 71100000 reads so far
2011-05-20 11:41:01,910 - INFO - Processed 71200000 reads so far
2011-05-20 11:41:11,588 - INFO - Processed 71300000 reads so far
2011-05-20 11:41:20,915 - INFO - Processed 71400000 reads so far
2011-05-20 11:41:30,616 - INFO - Processed 71500000 reads so far
2011-05-20 11:41:40,350 - INFO - Processed 71600000 reads so far
2011-05-20 11:41:50,334 - INFO - Processed 71700000 reads so far
2011-05-20 11:42:02,406 - INFO - Processed 71800000 reads so far
2011-05-20 11:42:13,809 - INFO - Processed 71900000 reads so far
2011-05-20 11:42:16,841 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:102990194-123010194
2011-05-20 11:42:25,878 - INFO - Processed 72000000 reads so far
2011-05-20 11:42:36,927 - INFO - Processed 72100000 reads so far
2011-05-20 11:42:47,796 - INFO - Processed 72200000 reads so far
2011-05-20 11:42:58,719 - INFO - Processed 72300000 reads so far
2011-05-20 11:43:10,260 - INFO - Processed 72400000 reads so far
2011-05-20 11:43:21,148 - INFO - Processed 72500000 reads so far
2011-05-20 11:43:32,157 - INFO - Processed 72600000 reads so far
2011-05-20 11:43:43,787 - INFO - Processed 72700000 reads so far
2011-05-20 11:43:55,668 - INFO - Processed 72800000 reads so far
2011-05-20 11:44:02,292 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:122990221-143010221
2011-05-20 11:44:06,701 - INFO - Processed 72900000 reads so far
2011-05-20 11:44:17,766 - INFO - Processed 73000000 reads so far
2011-05-20 11:44:30,239 - INFO - Processed 73100000 reads so far
2011-05-20 11:44:43,699 - INFO - Processed 73200000 reads so far
2011-05-20 11:44:55,473 - INFO - Processed 73300000 reads so far
2011-05-20 11:45:07,398 - INFO - Processed 73400000 reads so far
2011-05-20 11:45:18,674 - INFO - Processed 73500000 reads so far
2011-05-20 11:45:31,252 - INFO - Processed 73600000 reads so far
2011-05-20 11:45:42,968 - INFO - Processed 73700000 reads so far
2011-05-20 11:45:54,646 - INFO - Processed 73800000 reads so far
2011-05-20 11:45:57,491 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:142990248-163010248
2011-05-20 11:46:05,506 - INFO - Processed 73900000 reads so far
2011-05-20 11:46:16,071 - INFO - Processed 74000000 reads so far
2011-05-20 11:46:30,493 - INFO - Processed 74100000 reads so far
2011-05-20 11:46:39,555 - INFO - Processed 74200000 reads so far
2011-05-20 11:46:51,917 - INFO - Processed 74300000 reads so far
2011-05-20 11:47:06,723 - INFO - Processed 74400000 reads so far
2011-05-20 11:47:18,342 - INFO - Processed 74500000 reads so far
2011-05-20 11:47:29,758 - INFO - Processed 74600000 reads so far
2011-05-20 11:47:42,991 - INFO - Processed 74700000 reads so far
2011-05-20 11:47:55,327 - INFO - Processed 74800000 reads so far
2011-05-20 11:47:58,017 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:162990274-183010274
2011-05-20 11:48:09,754 - INFO - Processed 74900000 reads so far
2011-05-20 11:48:22,816 - INFO - Processed 75000000 reads so far
2011-05-20 11:48:34,014 - INFO - Processed 75100000 reads so far
2011-05-20 11:48:45,484 - INFO - Processed 75200000 reads so far
2011-05-20 11:48:56,678 - INFO - Processed 75300000 reads so far
2011-05-20 11:49:08,876 - INFO - Processed 75400000 reads so far
2011-05-20 11:49:20,222 - INFO - Processed 75500000 reads so far
2011-05-20 11:49:31,121 - INFO - Processed 75600000 reads so far
2011-05-20 11:49:41,626 - INFO - Processed 75700000 reads so far
2011-05-20 11:49:51,545 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:2989994-23009994
2011-05-20 11:49:54,115 - INFO - Processed 75800000 reads so far
2011-05-20 11:50:06,599 - INFO - Processed 75900000 reads so far
2011-05-20 11:50:17,448 - INFO - Processed 76000000 reads so far
2011-05-20 11:50:27,600 - INFO - Processed 76100000 reads so far
2011-05-20 11:50:37,709 - INFO - Processed 76200000 reads so far
2011-05-20 11:50:49,440 - INFO - Processed 76300000 reads so far
2011-05-20 11:50:59,655 - INFO - Processed 76400000 reads so far
2011-05-20 11:51:09,896 - INFO - Processed 76500000 reads so far
2011-05-20 11:51:23,798 - INFO - Processed 76600000 reads so far
2011-05-20 11:51:36,329 - INFO - Processed 76700000 reads so far
2011-05-20 11:51:37,752 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:22990051-43010051
2011-05-20 11:51:49,756 - INFO - Processed 76800000 reads so far
2011-05-20 11:52:02,474 - INFO - Processed 76900000 reads so far
2011-05-20 11:52:14,987 - INFO - Processed 77000000 reads so far
2011-05-20 11:52:26,704 - INFO - Processed 77100000 reads so far
2011-05-20 11:52:40,180 - INFO - Processed 77200000 reads so far
2011-05-20 11:52:53,428 - INFO - Processed 77300000 reads so far
2011-05-20 11:53:07,514 - INFO - Processed 77400000 reads so far
2011-05-20 11:53:20,219 - INFO - Processed 77500000 reads so far
2011-05-20 11:53:33,571 - INFO - Processed 77600000 reads so far
2011-05-20 11:53:41,642 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:42990069-63010069
2011-05-20 11:53:46,069 - INFO - Processed 77700000 reads so far
2011-05-20 11:53:58,914 - INFO - Processed 77800000 reads so far
2011-05-20 11:54:12,300 - INFO - Processed 77900000 reads so far
2011-05-20 11:54:24,609 - INFO - Processed 78000000 reads so far
2011-05-20 11:54:37,301 - INFO - Processed 78100000 reads so far
2011-05-20 11:54:49,854 - INFO - Processed 78200000 reads so far
2011-05-20 11:55:01,309 - INFO - Processed 78300000 reads so far
2011-05-20 11:55:12,298 - INFO - Processed 78400000 reads so far
2011-05-20 11:55:24,624 - INFO - Processed 78500000 reads so far
2011-05-20 11:55:33,130 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:62990113-83010113
2011-05-20 11:55:35,882 - INFO - Processed 78600000 reads so far
2011-05-20 11:55:47,472 - INFO - Processed 78700000 reads so far
2011-05-20 11:55:59,473 - INFO - Processed 78800000 reads so far
2011-05-20 11:56:12,514 - INFO - Processed 78900000 reads so far
2011-05-20 11:56:24,340 - INFO - Processed 79000000 reads so far
2011-05-20 11:56:36,929 - INFO - Processed 79100000 reads so far
2011-05-20 11:56:48,596 - INFO - Processed 79200000 reads so far
2011-05-20 11:57:03,466 - INFO - Processed 79300000 reads so far
2011-05-20 11:57:15,224 - INFO - Processed 79400000 reads so far
2011-05-20 11:57:28,794 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:82990114-103010114
2011-05-20 11:57:30,104 - INFO - Processed 79500000 reads so far
2011-05-20 11:57:42,365 - INFO - Processed 79600000 reads so far
2011-05-20 11:57:54,517 - INFO - Processed 79700000 reads so far
2011-05-20 11:58:07,522 - INFO - Processed 79800000 reads so far
2011-05-20 11:58:20,041 - INFO - Processed 79900000 reads so far
2011-05-20 11:58:31,824 - INFO - Processed 80000000 reads so far
2011-05-20 11:58:45,710 - INFO - Processed 80100000 reads so far
2011-05-20 11:58:58,325 - INFO - Processed 80200000 reads so far
2011-05-20 11:59:11,985 - INFO - Processed 80300000 reads so far
2011-05-20 11:59:24,056 - INFO - Processed 80400000 reads so far
2011-05-20 11:59:30,445 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:102990151-123010151
2011-05-20 11:59:37,349 - INFO - Processed 80500000 reads so far
2011-05-20 11:59:49,655 - INFO - Processed 80600000 reads so far
2011-05-20 12:00:02,716 - INFO - Processed 80700000 reads so far
2011-05-20 12:00:15,673 - INFO - Processed 80800000 reads so far
2011-05-20 12:00:27,135 - INFO - Processed 80900000 reads so far
2011-05-20 12:00:40,297 - INFO - Processed 81000000 reads so far
2011-05-20 12:00:52,842 - INFO - Processed 81100000 reads so far
2011-05-20 12:01:05,364 - INFO - Processed 81200000 reads so far
2011-05-20 12:01:17,495 - INFO - Processed 81300000 reads so far
2011-05-20 12:01:28,621 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:122990156-143010156
2011-05-20 12:01:30,835 - INFO - Processed 81400000 reads so far
2011-05-20 12:01:43,505 - INFO - Processed 81500000 reads so far
2011-05-20 12:01:58,715 - INFO - Processed 81600000 reads so far
2011-05-20 12:02:11,056 - INFO - Processed 81700000 reads so far
2011-05-20 12:02:24,490 - INFO - Processed 81800000 reads so far
2011-05-20 12:02:36,054 - INFO - Processed 81900000 reads so far
2011-05-20 12:02:49,040 - INFO - Processed 82000000 reads so far
2011-05-20 12:03:04,488 - INFO - Processed 82100000 reads so far
2011-05-20 12:03:16,468 - INFO - Processed 82200000 reads so far
2011-05-20 12:03:28,851 - INFO - Processed 82300000 reads so far
2011-05-20 12:03:32,688 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:142990162-163010162
2011-05-20 12:03:41,488 - INFO - Processed 82400000 reads so far
2011-05-20 12:03:54,449 - INFO - Processed 82500000 reads so far
2011-05-20 12:04:10,108 - INFO - Processed 82600000 reads so far
2011-05-20 12:04:21,885 - INFO - Processed 82700000 reads so far
2011-05-20 12:04:33,628 - INFO - Processed 82800000 reads so far
2011-05-20 12:04:45,523 - INFO - Processed 82900000 reads so far
2011-05-20 12:04:58,047 - INFO - Processed 83000000 reads so far
2011-05-20 12:05:10,026 - INFO - Processed 83100000 reads so far
2011-05-20 12:05:14,619 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3_random:0-20010010
2011-05-20 12:05:14,751 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:2989978-23009978
2011-05-20 12:05:22,794 - INFO - Processed 83200000 reads so far
2011-05-20 12:05:35,102 - INFO - Processed 83300000 reads so far
2011-05-20 12:05:47,667 - INFO - Processed 83400000 reads so far
2011-05-20 12:05:59,796 - INFO - Processed 83500000 reads so far
2011-05-20 12:06:12,231 - INFO - Processed 83600000 reads so far
2011-05-20 12:06:25,959 - INFO - Processed 83700000 reads so far
2011-05-20 12:06:38,055 - INFO - Processed 83800000 reads so far
2011-05-20 12:06:50,087 - INFO - Processed 83900000 reads so far
2011-05-20 12:07:02,966 - INFO - Processed 84000000 reads so far
2011-05-20 12:07:15,219 - INFO - Processed 84100000 reads so far
2011-05-20 12:07:15,289 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:22989980-43009980
2011-05-20 12:07:31,422 - INFO - Processed 84200000 reads so far
2011-05-20 12:07:44,297 - INFO - Processed 84300000 reads so far
2011-05-20 12:07:57,684 - INFO - Processed 84400000 reads so far
2011-05-20 12:08:09,223 - INFO - Processed 84500000 reads so far
2011-05-20 12:08:21,279 - INFO - Processed 84600000 reads so far
2011-05-20 12:08:33,745 - INFO - Processed 84700000 reads so far
2011-05-20 12:08:45,758 - INFO - Processed 84800000 reads so far
2011-05-20 12:08:57,714 - INFO - Processed 84900000 reads so far
2011-05-20 12:09:09,543 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:42990016-63010016
2011-05-20 12:09:11,759 - INFO - Processed 85000000 reads so far
2011-05-20 12:09:23,888 - INFO - Processed 85100000 reads so far
2011-05-20 12:09:36,804 - INFO - Processed 85200000 reads so far
2011-05-20 12:09:49,213 - INFO - Processed 85300000 reads so far
2011-05-20 12:10:01,198 - INFO - Processed 85400000 reads so far
2011-05-20 12:10:13,222 - INFO - Processed 85500000 reads so far
2011-05-20 12:10:26,102 - INFO - Processed 85600000 reads so far
2011-05-20 12:10:39,097 - INFO - Processed 85700000 reads so far
2011-05-20 12:10:56,506 - INFO - Processed 85800000 reads so far
2011-05-20 12:11:17,295 - INFO - Processed 85900000 reads so far
2011-05-20 12:11:21,787 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:62990029-83010029
2011-05-20 12:11:30,479 - INFO - Processed 86000000 reads so far
2011-05-20 12:11:53,749 - INFO - Processed 86100000 reads so far
2011-05-20 12:12:07,777 - INFO - Processed 86200000 reads so far
2011-05-20 12:12:26,630 - INFO - Processed 86300000 reads so far
2011-05-20 12:12:39,790 - INFO - Processed 86400000 reads so far
2011-05-20 12:12:52,497 - INFO - Processed 86500000 reads so far
2011-05-20 12:13:07,259 - INFO - Processed 86600000 reads so far
2011-05-20 12:13:23,474 - INFO - Processed 86700000 reads so far
2011-05-20 12:13:37,423 - INFO - Processed 86800000 reads so far
2011-05-20 12:13:53,477 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:82990046-103010046
2011-05-20 12:13:56,875 - INFO - Processed 86900000 reads so far
2011-05-20 12:14:08,356 - INFO - Processed 87000000 reads so far
2011-05-20 12:14:20,035 - INFO - Processed 87100000 reads so far
2011-05-20 12:14:35,939 - INFO - Processed 87200000 reads so far
2011-05-20 12:14:50,087 - INFO - Processed 87300000 reads so far
2011-05-20 12:15:10,168 - INFO - Processed 87400000 reads so far
2011-05-20 12:15:23,106 - INFO - Processed 87500000 reads so far
2011-05-20 12:15:35,825 - INFO - Processed 87600000 reads so far
2011-05-20 12:15:50,659 - INFO - Processed 87700000 reads so far
2011-05-20 12:16:02,155 - INFO - Processed 87800000 reads so far
2011-05-20 12:16:05,094 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:102990049-123010049
2011-05-20 12:16:13,935 - INFO - Processed 87900000 reads so far
2011-05-20 12:16:26,396 - INFO - Processed 88000000 reads so far
2011-05-20 12:16:39,045 - INFO - Processed 88100000 reads so far
2011-05-20 12:16:52,986 - INFO - Processed 88200000 reads so far
2011-05-20 12:17:04,520 - INFO - Processed 88300000 reads so far
2011-05-20 12:17:16,379 - INFO - Processed 88400000 reads so far
2011-05-20 12:17:25,236 - INFO - Processed 88500000 reads so far
2011-05-20 12:17:35,561 - INFO - Processed 88600000 reads so far
2011-05-20 12:17:44,952 - INFO - Processed 88700000 reads so far
2011-05-20 12:17:49,247 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:122990071-143010071
2011-05-20 12:17:59,457 - INFO - Processed 88800000 reads so far
2011-05-20 12:18:11,515 - INFO - Processed 88900000 reads so far
2011-05-20 12:18:24,785 - INFO - Processed 89000000 reads so far
2011-05-20 12:18:38,095 - INFO - Processed 89100000 reads so far
2011-05-20 12:18:50,373 - INFO - Processed 89200000 reads so far
2011-05-20 12:19:02,637 - INFO - Processed 89300000 reads so far
2011-05-20 12:19:14,821 - INFO - Processed 89400000 reads so far
2011-05-20 12:19:27,192 - INFO - Processed 89500000 reads so far
2011-05-20 12:19:39,437 - INFO - Processed 89600000 reads so far
2011-05-20 12:19:47,072 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:142990148-163010148
2011-05-20 12:19:51,949 - INFO - Processed 89700000 reads so far
2011-05-20 12:20:04,314 - INFO - Processed 89800000 reads so far
2011-05-20 12:20:17,763 - INFO - Processed 89900000 reads so far
2011-05-20 12:20:30,852 - INFO - Processed 90000000 reads so far
2011-05-20 12:20:44,040 - INFO - Processed 90100000 reads so far
2011-05-20 12:20:55,849 - INFO - Processed 90200000 reads so far
2011-05-20 12:21:09,438 - INFO - Processed 90300000 reads so far
2011-05-20 12:21:14,240 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4_random:0-20010035
2011-05-20 12:21:14,928 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:2990023-23010023
2011-05-20 12:21:22,225 - INFO - Processed 90400000 reads so far
2011-05-20 12:21:34,472 - INFO - Processed 90500000 reads so far
2011-05-20 12:21:48,268 - INFO - Processed 90600000 reads so far
2011-05-20 12:22:00,878 - INFO - Processed 90700000 reads so far
2011-05-20 12:22:13,535 - INFO - Processed 90800000 reads so far
2011-05-20 12:22:25,690 - INFO - Processed 90900000 reads so far
2011-05-20 12:22:37,592 - INFO - Processed 91000000 reads so far
2011-05-20 12:22:50,747 - INFO - Processed 91100000 reads so far
2011-05-20 12:23:02,632 - INFO - Processed 91200000 reads so far
2011-05-20 12:23:11,736 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:22990513-43010513
2011-05-20 12:23:14,865 - INFO - Processed 91300000 reads so far
2011-05-20 12:23:29,545 - INFO - Processed 91400000 reads so far
2011-05-20 12:23:42,976 - INFO - Processed 91500000 reads so far
2011-05-20 12:23:56,031 - INFO - Processed 91600000 reads so far
2011-05-20 12:24:08,813 - INFO - Processed 91700000 reads so far
2011-05-20 12:24:20,644 - INFO - Processed 91800000 reads so far
2011-05-20 12:24:34,449 - INFO - Processed 91900000 reads so far
2011-05-20 12:24:46,468 - INFO - Processed 92000000 reads so far
2011-05-20 12:24:58,266 - INFO - Processed 92100000 reads so far
2011-05-20 12:25:09,756 - INFO - Processed 92200000 reads so far
2011-05-20 12:25:15,233 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:42990519-63010519
2011-05-20 12:25:22,897 - INFO - Processed 92300000 reads so far
2011-05-20 12:25:35,954 - INFO - Processed 92400000 reads so far
2011-05-20 12:25:48,043 - INFO - Processed 92500000 reads so far
2011-05-20 12:26:00,297 - INFO - Processed 92600000 reads so far
2011-05-20 12:26:11,955 - INFO - Processed 92700000 reads so far
2011-05-20 12:26:22,125 - INFO - Processed 92800000 reads so far
2011-05-20 12:26:32,953 - INFO - Processed 92900000 reads so far
2011-05-20 12:26:48,188 - INFO - Processed 93000000 reads so far
2011-05-20 12:27:00,212 - INFO - Processed 93100000 reads so far
2011-05-20 12:27:07,408 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:62990552-83010552
2011-05-20 12:27:13,338 - INFO - Processed 93200000 reads so far
2011-05-20 12:27:24,754 - INFO - Processed 93300000 reads so far
2011-05-20 12:27:35,987 - INFO - Processed 93400000 reads so far
2011-05-20 12:27:47,825 - INFO - Processed 93500000 reads so far
2011-05-20 12:28:02,615 - INFO - Processed 93600000 reads so far
2011-05-20 12:28:14,958 - INFO - Processed 93700000 reads so far
2011-05-20 12:28:27,367 - INFO - Processed 93800000 reads so far
2011-05-20 12:28:39,410 - INFO - Processed 93900000 reads so far
2011-05-20 12:28:51,033 - INFO - Processed 94000000 reads so far
2011-05-20 12:29:00,355 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:82990604-103010604
2011-05-20 12:29:02,954 - INFO - Processed 94100000 reads so far
2011-05-20 12:29:16,949 - INFO - Processed 94200000 reads so far
2011-05-20 12:29:29,270 - INFO - Processed 94300000 reads so far
2011-05-20 12:29:41,641 - INFO - Processed 94400000 reads so far
2011-05-20 12:29:53,357 - INFO - Processed 94500000 reads so far
2011-05-20 12:30:05,223 - INFO - Processed 94600000 reads so far
2011-05-20 12:30:17,086 - INFO - Processed 94700000 reads so far
2011-05-20 12:30:27,751 - INFO - Processed 94800000 reads so far
2011-05-20 12:30:39,724 - INFO - Processed 94900000 reads so far
2011-05-20 12:30:47,986 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:102990611-123010611
2011-05-20 12:30:51,697 - INFO - Processed 95000000 reads so far
2011-05-20 12:31:04,660 - INFO - Processed 95100000 reads so far
2011-05-20 12:31:15,840 - INFO - Processed 95200000 reads so far
2011-05-20 12:31:29,462 - INFO - Processed 95300000 reads so far
2011-05-20 12:31:42,815 - INFO - Processed 95400000 reads so far
2011-05-20 12:31:58,815 - INFO - Processed 95500000 reads so far
2011-05-20 12:32:10,846 - INFO - Processed 95600000 reads so far
2011-05-20 12:32:25,794 - INFO - Processed 95700000 reads so far
2011-05-20 12:32:38,481 - INFO - Processed 95800000 reads so far
2011-05-20 12:32:51,799 - INFO - Processed 95900000 reads so far
2011-05-20 12:32:55,643 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:122990614-143010614
2011-05-20 12:33:04,185 - INFO - Processed 96000000 reads so far
2011-05-20 12:33:16,898 - INFO - Processed 96100000 reads so far
2011-05-20 12:33:29,561 - INFO - Processed 96200000 reads so far
2011-05-20 12:33:41,784 - INFO - Processed 96300000 reads so far
2011-05-20 12:33:54,378 - INFO - Processed 96400000 reads so far
2011-05-20 12:34:05,701 - INFO - Processed 96500000 reads so far
2011-05-20 12:34:16,482 - INFO - Processed 96600000 reads so far
2011-05-20 12:34:30,707 - INFO - Processed 96700000 reads so far
2011-05-20 12:34:47,851 - INFO - Processed 96800000 reads so far
2011-05-20 12:34:58,323 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:142990631-163010631
2011-05-20 12:35:00,671 - INFO - Processed 96900000 reads so far
2011-05-20 12:35:12,434 - INFO - Processed 97000000 reads so far
2011-05-20 12:35:24,031 - INFO - Processed 97100000 reads so far
2011-05-20 12:35:36,554 - INFO - Processed 97200000 reads so far
2011-05-20 12:35:49,930 - INFO - Processed 97300000 reads so far
2011-05-20 12:35:54,518 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5_random:0-20010305
2011-05-20 12:35:55,071 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:2990010-23010010
2011-05-20 12:36:02,217 - INFO - Processed 97400000 reads so far
2011-05-20 12:36:16,001 - INFO - Processed 97500000 reads so far
2011-05-20 12:36:28,710 - INFO - Processed 97600000 reads so far
2011-05-20 12:36:41,395 - INFO - Processed 97700000 reads so far
2011-05-20 12:36:53,599 - INFO - Processed 97800000 reads so far
2011-05-20 12:37:05,732 - INFO - Processed 97900000 reads so far
2011-05-20 12:37:17,299 - INFO - Processed 98000000 reads so far
2011-05-20 12:37:30,462 - INFO - Processed 98100000 reads so far
2011-05-20 12:37:43,118 - INFO - Processed 98200000 reads so far
2011-05-20 12:37:51,019 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:22990024-43010024
2011-05-20 12:37:55,681 - INFO - Processed 98300000 reads so far
2011-05-20 12:38:08,730 - INFO - Processed 98400000 reads so far
2011-05-20 12:38:20,423 - INFO - Processed 98500000 reads so far
2011-05-20 12:38:33,111 - INFO - Processed 98600000 reads so far
2011-05-20 12:38:46,719 - INFO - Processed 98700000 reads so far
2011-05-20 12:38:59,230 - INFO - Processed 98800000 reads so far
2011-05-20 12:39:11,544 - INFO - Processed 98900000 reads so far
2011-05-20 12:39:22,565 - INFO - Processed 99000000 reads so far
2011-05-20 12:39:34,793 - INFO - Processed 99100000 reads so far
2011-05-20 12:39:47,962 - INFO - Processed 99200000 reads so far
2011-05-20 12:39:50,006 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:42990037-63010037
2011-05-20 12:40:00,440 - INFO - Processed 99300000 reads so far
2011-05-20 12:40:14,171 - INFO - Processed 99400000 reads so far
2011-05-20 12:40:27,999 - INFO - Processed 99500000 reads so far
2011-05-20 12:40:40,566 - INFO - Processed 99600000 reads so far
2011-05-20 12:40:52,360 - INFO - Processed 99700000 reads so far
2011-05-20 12:41:06,342 - INFO - Processed 99800000 reads so far
2011-05-20 12:41:19,853 - INFO - Processed 99900000 reads so far
2011-05-20 12:41:32,094 - INFO - Processed 100000000 reads so far
2011-05-20 12:41:44,318 - INFO - Processed 100100000 reads so far
2011-05-20 12:41:56,606 - INFO - Processed 100200000 reads so far
2011-05-20 12:41:58,173 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:62990081-83010081
2011-05-20 12:42:08,907 - INFO - Processed 100300000 reads so far
2011-05-20 12:42:20,937 - INFO - Processed 100400000 reads so far
2011-05-20 12:42:34,523 - INFO - Processed 100500000 reads so far
2011-05-20 12:42:46,382 - INFO - Processed 100600000 reads so far
2011-05-20 12:42:58,020 - INFO - Processed 100700000 reads so far
2011-05-20 12:43:09,224 - INFO - Processed 100800000 reads so far
2011-05-20 12:43:21,131 - INFO - Processed 100900000 reads so far
2011-05-20 12:43:32,545 - INFO - Processed 101000000 reads so far
2011-05-20 12:43:43,718 - INFO - Processed 101100000 reads so far
2011-05-20 12:43:44,687 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:82990085-103010085
2011-05-20 12:43:57,290 - INFO - Processed 101200000 reads so far
2011-05-20 12:44:07,579 - INFO - Processed 101300000 reads so far
2011-05-20 12:44:19,658 - INFO - Processed 101400000 reads so far
2011-05-20 12:44:31,138 - INFO - Processed 101500000 reads so far
2011-05-20 12:44:43,071 - INFO - Processed 101600000 reads so far
2011-05-20 12:44:54,506 - INFO - Processed 101700000 reads so far
2011-05-20 12:45:02,692 - INFO - Processed 101800000 reads so far
2011-05-20 12:45:11,383 - INFO - Processed 101900000 reads so far
2011-05-20 12:45:24,578 - INFO - Processed 102000000 reads so far
2011-05-20 12:45:34,330 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:102990117-123010117
2011-05-20 12:45:36,323 - INFO - Processed 102100000 reads so far
2011-05-20 12:45:45,342 - INFO - Processed 102200000 reads so far
2011-05-20 12:45:52,019 - INFO - Processed 102300000 reads so far
2011-05-20 12:46:01,817 - INFO - Processed 102400000 reads so far
2011-05-20 12:46:10,682 - INFO - Processed 102500000 reads so far
2011-05-20 12:46:19,645 - INFO - Processed 102600000 reads so far
2011-05-20 12:46:26,846 - INFO - Processed 102700000 reads so far
2011-05-20 12:46:35,772 - INFO - Processed 102800000 reads so far
2011-05-20 12:46:46,428 - INFO - Processed 102900000 reads so far
2011-05-20 12:46:58,923 - INFO - Processed 103000000 reads so far
2011-05-20 12:47:09,932 - INFO - Processed 103100000 reads so far
2011-05-20 12:47:20,781 - INFO - Processed 103200000 reads so far
2011-05-20 12:47:32,168 - INFO - Processed 103300000 reads so far
2011-05-20 12:47:44,105 - INFO - Processed 103400000 reads so far
2011-05-20 12:47:54,971 - INFO - Processed 103500000 reads so far
2011-05-20 12:48:04,674 - INFO - Processed 103600000 reads so far
2011-05-20 12:48:16,732 - INFO - Processed 103700000 reads so far
2011-05-20 12:48:28,649 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:122990136-143010136
2011-05-20 12:48:30,152 - INFO - Processed 103800000 reads so far
2011-05-20 12:48:38,251 - INFO - Processed 103900000 reads so far
2011-05-20 12:48:45,232 - INFO - Processed 104000000 reads so far
2011-05-20 12:48:52,039 - INFO - Processed 104100000 reads so far
2011-05-20 12:49:00,829 - INFO - Processed 104200000 reads so far
2011-05-20 12:49:12,240 - INFO - Processed 104300000 reads so far
2011-05-20 12:49:23,748 - INFO - Processed 104400000 reads so far
2011-05-20 12:49:36,694 - INFO - Processed 104500000 reads so far
2011-05-20 12:49:50,005 - INFO - Processed 104600000 reads so far
2011-05-20 12:50:01,423 - INFO - Processed 104700000 reads so far
2011-05-20 12:50:08,700 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:142990170-163010170
2011-05-20 12:50:14,078 - INFO - Processed 104800000 reads so far
2011-05-20 12:50:25,765 - INFO - Processed 104900000 reads so far
2011-05-20 12:50:37,176 - INFO - Processed 105000000 reads so far
2011-05-20 12:50:45,360 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:2990031-23010031
2011-05-20 12:50:48,719 - INFO - Processed 105100000 reads so far
2011-05-20 12:51:01,906 - INFO - Processed 105200000 reads so far
2011-05-20 12:51:13,615 - INFO - Processed 105300000 reads so far
2011-05-20 12:51:25,198 - INFO - Processed 105400000 reads so far
2011-05-20 12:51:36,674 - INFO - Processed 105500000 reads so far
2011-05-20 12:51:48,650 - INFO - Processed 105600000 reads so far
2011-05-20 12:52:00,112 - INFO - Processed 105700000 reads so far
2011-05-20 12:52:11,644 - INFO - Processed 105800000 reads so far
2011-05-20 12:52:18,225 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:22990678-43010678
2011-05-20 12:52:23,647 - INFO - Processed 105900000 reads so far
2011-05-20 12:52:35,544 - INFO - Processed 106000000 reads so far
2011-05-20 12:52:46,934 - INFO - Processed 106100000 reads so far
2011-05-20 12:52:59,336 - INFO - Processed 106200000 reads so far
2011-05-20 12:53:10,853 - INFO - Processed 106300000 reads so far
2011-05-20 12:53:23,043 - INFO - Processed 106400000 reads so far
2011-05-20 12:53:34,468 - INFO - Processed 106500000 reads so far
2011-05-20 12:53:45,492 - INFO - Processed 106600000 reads so far
2011-05-20 12:53:47,050 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:46346433-66366433
2011-05-20 12:53:54,648 - INFO - Processed 106700000 reads so far
2011-05-20 12:54:01,416 - INFO - Processed 106800000 reads so far
2011-05-20 12:54:08,387 - INFO - Processed 106900000 reads so far
2011-05-20 12:54:15,658 - INFO - Processed 107000000 reads so far
2011-05-20 12:54:23,592 - INFO - Processed 107100000 reads so far
2011-05-20 12:54:35,057 - INFO - Processed 107200000 reads so far
2011-05-20 12:54:43,309 - INFO - Processed 107300000 reads so far
2011-05-20 12:54:51,818 - INFO - Processed 107400000 reads so far
2011-05-20 12:55:02,510 - INFO - Processed 107500000 reads so far
2011-05-20 12:55:11,576 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:66346434-86366434
2011-05-20 12:55:12,428 - INFO - Processed 107600000 reads so far
2011-05-20 12:55:20,473 - INFO - Processed 107700000 reads so far
2011-05-20 12:55:28,006 - INFO - Processed 107800000 reads so far
2011-05-20 12:55:35,517 - INFO - Processed 107900000 reads so far
2011-05-20 12:55:43,750 - INFO - Processed 108000000 reads so far
2011-05-20 12:55:53,487 - INFO - Processed 108100000 reads so far
2011-05-20 12:56:00,560 - INFO - Processed 108200000 reads so far
2011-05-20 12:56:10,247 - INFO - Processed 108300000 reads so far
2011-05-20 12:56:20,821 - INFO - Processed 108400000 reads so far
2011-05-20 12:56:31,369 - INFO - Processed 108500000 reads so far
2011-05-20 12:56:36,312 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:86346502-106366502
2011-05-20 12:56:39,002 - INFO - Processed 108600000 reads so far
2011-05-20 12:56:46,428 - INFO - Processed 108700000 reads so far
2011-05-20 12:56:53,764 - INFO - Processed 108800000 reads so far
2011-05-20 12:57:02,026 - INFO - Processed 108900000 reads so far
2011-05-20 12:57:13,252 - INFO - Processed 109000000 reads so far
2011-05-20 12:57:23,372 - INFO - Processed 109100000 reads so far
2011-05-20 12:57:30,450 - INFO - Processed 109200000 reads so far
2011-05-20 12:57:39,588 - INFO - Processed 109300000 reads so far
2011-05-20 12:57:47,023 - INFO - Processed 109400000 reads so far
2011-05-20 12:57:56,661 - INFO - Processed 109500000 reads so far
2011-05-20 12:57:57,601 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:106346513-126366513
2011-05-20 12:58:08,151 - INFO - Processed 109600000 reads so far
2011-05-20 12:58:29,196 - INFO - Processed 109700000 reads so far
2011-05-20 12:58:36,358 - INFO - Processed 109800000 reads so far
2011-05-20 12:58:44,425 - INFO - Processed 109900000 reads so far
2011-05-20 12:58:53,018 - INFO - Processed 110000000 reads so far
2011-05-20 12:59:01,600 - INFO - Processed 110100000 reads so far
2011-05-20 12:59:11,657 - INFO - Processed 110200000 reads so far
2011-05-20 12:59:22,045 - INFO - Processed 110300000 reads so far
2011-05-20 12:59:32,455 - INFO - Processed 110400000 reads so far
2011-05-20 12:59:37,058 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:126346530-146366530
2011-05-20 12:59:39,807 - INFO - Processed 110500000 reads so far
2011-05-20 12:59:47,141 - INFO - Processed 110600000 reads so far
2011-05-20 12:59:54,400 - INFO - Processed 110700000 reads so far
2011-05-20 13:00:05,514 - INFO - Processed 110800000 reads so far
2011-05-20 13:00:15,553 - INFO - Processed 110900000 reads so far
2011-05-20 13:00:22,779 - INFO - Processed 111000000 reads so far
2011-05-20 13:00:30,003 - INFO - Processed 111100000 reads so far
2011-05-20 13:00:39,599 - INFO - Processed 111200000 reads so far
2011-05-20 13:00:47,236 - INFO - Processed 111300000 reads so far
2011-05-20 13:00:54,601 - INFO - Processed 111400000 reads so far
2011-05-20 13:00:58,585 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:146346540-166366540
2011-05-20 13:01:01,878 - INFO - Processed 111500000 reads so far
2011-05-20 13:01:09,263 - INFO - Processed 111600000 reads so far
2011-05-20 13:01:18,850 - INFO - Processed 111700000 reads so far
2011-05-20 13:01:24,593 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7_random:0-20010006
2011-05-20 13:01:25,769 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:2990072-23010072
2011-05-20 13:01:29,760 - INFO - Processed 111800000 reads so far
2011-05-20 13:01:37,465 - INFO - Processed 111900000 reads so far
2011-05-20 13:01:46,316 - INFO - Processed 112000000 reads so far
2011-05-20 13:01:56,341 - INFO - Processed 112100000 reads so far
2011-05-20 13:02:04,920 - INFO - Processed 112200000 reads so far
2011-05-20 13:02:12,259 - INFO - Processed 112300000 reads so far
2011-05-20 13:02:20,110 - INFO - Processed 112400000 reads so far
2011-05-20 13:02:27,595 - INFO - Processed 112500000 reads so far
2011-05-20 13:02:34,774 - INFO - Processed 112600000 reads so far
2011-05-20 13:02:40,804 - INFO - Processed 112700000 reads so far
2011-05-20 13:02:47,492 - INFO - Processed 112800000 reads so far
2011-05-20 13:02:52,098 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:22990113-43010113
2011-05-20 13:02:57,783 - INFO - Processed 112900000 reads so far
2011-05-20 13:03:06,390 - INFO - Processed 113000000 reads so far
2011-05-20 13:03:14,571 - INFO - Processed 113100000 reads so far
2011-05-20 13:03:24,098 - INFO - Processed 113200000 reads so far
2011-05-20 13:03:32,801 - INFO - Processed 113300000 reads so far
2011-05-20 13:03:41,672 - INFO - Processed 113400000 reads so far
2011-05-20 13:03:48,916 - INFO - Processed 113500000 reads so far
2011-05-20 13:03:56,197 - INFO - Processed 113600000 reads so far
2011-05-20 13:04:03,604 - INFO - Processed 113700000 reads so far
2011-05-20 13:04:11,806 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:42990121-63010121
2011-05-20 13:04:14,258 - INFO - Processed 113800000 reads so far
2011-05-20 13:04:24,398 - INFO - Processed 113900000 reads so far
2011-05-20 13:04:31,838 - INFO - Processed 114000000 reads so far
2011-05-20 13:04:43,229 - INFO - Processed 114100000 reads so far
2011-05-20 13:04:54,549 - INFO - Processed 114200000 reads so far
2011-05-20 13:05:04,332 - INFO - Processed 114300000 reads so far
2011-05-20 13:05:13,448 - INFO - Processed 114400000 reads so far
2011-05-20 13:05:23,823 - INFO - Processed 114500000 reads so far
2011-05-20 13:05:32,005 - INFO - Processed 114600000 reads so far
2011-05-20 13:05:33,029 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:62990137-83010137
2011-05-20 13:05:41,694 - INFO - Processed 114700000 reads so far
2011-05-20 13:05:52,779 - INFO - Processed 114800000 reads so far
2011-05-20 13:06:04,022 - INFO - Processed 114900000 reads so far
2011-05-20 13:06:15,573 - INFO - Processed 115000000 reads so far
2011-05-20 13:06:26,167 - INFO - Processed 115100000 reads so far
2011-05-20 13:06:36,162 - INFO - Processed 115200000 reads so far
2011-05-20 13:06:47,444 - INFO - Processed 115300000 reads so far
2011-05-20 13:06:58,776 - INFO - Processed 115400000 reads so far
2011-05-20 13:07:10,163 - INFO - Processed 115500000 reads so far
2011-05-20 13:07:17,590 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:82990168-103010168
2011-05-20 13:07:21,529 - INFO - Processed 115600000 reads so far
2011-05-20 13:07:32,812 - INFO - Processed 115700000 reads so far
2011-05-20 13:07:45,476 - INFO - Processed 115800000 reads so far
2011-05-20 13:07:56,034 - INFO - Processed 115900000 reads so far
2011-05-20 13:08:06,723 - INFO - Processed 116000000 reads so far
2011-05-20 13:08:20,193 - INFO - Processed 116100000 reads so far
2011-05-20 13:08:27,090 - INFO - Processed 116200000 reads so far
2011-05-20 13:08:35,903 - INFO - Processed 116300000 reads so far
2011-05-20 13:08:47,712 - INFO - Processed 116400000 reads so far
2011-05-20 13:08:57,855 - INFO - Processed 116500000 reads so far
2011-05-20 13:08:59,014 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:102990184-123010184
2011-05-20 13:09:09,319 - INFO - Processed 116600000 reads so far
2011-05-20 13:09:20,655 - INFO - Processed 116700000 reads so far
2011-05-20 13:09:32,417 - INFO - Processed 116800000 reads so far
2011-05-20 13:09:58,384 - INFO - Processed 116900000 reads so far
2011-05-20 13:10:13,597 - INFO - Processed 117000000 reads so far
2011-05-20 13:10:22,972 - INFO - Processed 117100000 reads so far
2011-05-20 13:10:40,933 - INFO - Processed 117200000 reads so far
2011-05-20 13:10:54,467 - INFO - Processed 117300000 reads so far
2011-05-20 13:11:20,690 - INFO - Processed 117400000 reads so far
2011-05-20 13:11:27,258 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:122990273-143010273
2011-05-20 13:11:30,268 - INFO - Processed 117500000 reads so far
2011-05-20 13:11:48,972 - INFO - Processed 117600000 reads so far
2011-05-20 13:12:01,087 - INFO - Processed 117700000 reads so far
2011-05-20 13:12:09,461 - INFO - Processed 117800000 reads so far
2011-05-20 13:12:16,352 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8_random:0-20010012
2011-05-20 13:12:17,461 - INFO - Processed 117900000 reads so far
2011-05-20 13:12:27,485 - INFO - Processed 118000000 reads so far
2011-05-20 13:12:29,970 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:2989996-23009996
2011-05-20 13:12:42,357 - INFO - Processed 118100000 reads so far
2011-05-20 13:12:55,484 - INFO - Processed 118200000 reads so far
2011-05-20 13:13:03,725 - INFO - Processed 118300000 reads so far
2011-05-20 13:13:11,845 - INFO - Processed 118400000 reads so far
2011-05-20 13:13:32,493 - INFO - Processed 118500000 reads so far
2011-05-20 13:13:39,402 - INFO - Processed 118600000 reads so far
2011-05-20 13:13:49,183 - INFO - Processed 118700000 reads so far
2011-05-20 13:14:08,109 - INFO - Processed 118800000 reads so far
2011-05-20 13:14:17,294 - INFO - Processed 118900000 reads so far
2011-05-20 13:14:26,516 - INFO - Processed 119000000 reads so far
2011-05-20 13:14:47,922 - INFO - Processed 119100000 reads so far
2011-05-20 13:14:54,420 - INFO - Processed 119200000 reads so far
2011-05-20 13:15:04,421 - INFO - Processed 119300000 reads so far
2011-05-20 13:15:21,290 - INFO - Processed 119400000 reads so far
2011-05-20 13:15:31,914 - INFO - Processed 119500000 reads so far
2011-05-20 13:15:41,533 - INFO - Processed 119600000 reads so far
2011-05-20 13:15:51,268 - INFO - Processed 119700000 reads so far
2011-05-20 13:16:02,049 - INFO - Processed 119800000 reads so far
2011-05-20 13:16:10,755 - INFO - Processed 119900000 reads so far
2011-05-20 13:16:19,720 - INFO - Processed 120000000 reads so far
2011-05-20 13:16:29,671 - INFO - Processed 120100000 reads so far
2011-05-20 13:16:40,749 - INFO - Processed 120200000 reads so far
2011-05-20 13:16:50,367 - INFO - Processed 120300000 reads so far
2011-05-20 13:16:58,994 - INFO - Processed 120400000 reads so far
2011-05-20 13:17:04,828 - INFO - Processed 120500000 reads so far
2011-05-20 13:17:11,923 - INFO - Processed 120600000 reads so far
2011-05-20 13:17:18,943 - INFO - Processed 120700000 reads so far
2011-05-20 13:17:30,602 - INFO - Processed 120800000 reads so far
2011-05-20 13:17:39,137 - INFO - Processed 120900000 reads so far
2011-05-20 13:17:47,631 - INFO - Processed 121000000 reads so far
2011-05-20 13:17:55,987 - INFO - Processed 121100000 reads so far
2011-05-20 13:18:05,060 - INFO - Processed 121200000 reads so far
2011-05-20 13:18:14,576 - INFO - Processed 121300000 reads so far
2011-05-20 13:18:20,893 - INFO - Processed 121400000 reads so far
2011-05-20 13:18:28,325 - INFO - Processed 121500000 reads so far
2011-05-20 13:18:34,708 - INFO - Processed 121600000 reads so far
2011-05-20 13:18:42,298 - INFO - Processed 121700000 reads so far
2011-05-20 13:18:52,503 - INFO - Processed 121800000 reads so far
2011-05-20 13:18:59,022 - INFO - Processed 121900000 reads so far
2011-05-20 13:19:05,988 - INFO - Processed 122000000 reads so far
2011-05-20 13:19:16,083 - INFO - Processed 122100000 reads so far
2011-05-20 13:19:25,849 - INFO - Processed 122200000 reads so far
2011-05-20 13:19:34,869 - INFO - Processed 122300000 reads so far
2011-05-20 13:19:42,376 - INFO - Processed 122400000 reads so far
2011-05-20 13:19:50,268 - INFO - Processed 122500000 reads so far
2011-05-20 13:20:01,261 - INFO - Processed 122600000 reads so far
2011-05-20 13:20:08,009 - INFO - Processed 122700000 reads so far
2011-05-20 13:20:14,530 - INFO - Processed 122800000 reads so far
2011-05-20 13:20:23,943 - INFO - Processed 122900000 reads so far
2011-05-20 13:20:31,573 - INFO - Processed 123000000 reads so far
2011-05-20 13:20:37,922 - INFO - Processed 123100000 reads so far
2011-05-20 13:20:47,287 - INFO - Processed 123200000 reads so far
2011-05-20 13:20:55,908 - INFO - Processed 123300000 reads so far
2011-05-20 13:21:03,210 - INFO - Processed 123400000 reads so far
2011-05-20 13:21:10,421 - INFO - Processed 123500000 reads so far
2011-05-20 13:21:17,118 - INFO - Processed 123600000 reads so far
2011-05-20 13:21:24,528 - INFO - Processed 123700000 reads so far
2011-05-20 13:21:33,394 - INFO - Processed 123800000 reads so far
2011-05-20 13:21:42,133 - INFO - Processed 123900000 reads so far
2011-05-20 13:21:51,760 - INFO - Processed 124000000 reads so far
2011-05-20 13:22:02,426 - INFO - Processed 124100000 reads so far
2011-05-20 13:22:13,384 - INFO - Processed 124200000 reads so far
2011-05-20 13:22:22,009 - INFO - Processed 124300000 reads so far
2011-05-20 13:22:34,193 - INFO - Processed 124400000 reads so far
2011-05-20 13:22:48,679 - INFO - Processed 124500000 reads so far
2011-05-20 13:23:00,559 - INFO - Processed 124600000 reads so far
2011-05-20 13:23:11,977 - INFO - Processed 124700000 reads so far
2011-05-20 13:23:12,618 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:22990028-43010028
2011-05-20 13:23:22,987 - INFO - Processed 124800000 reads so far
2011-05-20 13:23:34,139 - INFO - Processed 124900000 reads so far
2011-05-20 13:23:46,149 - INFO - Processed 125000000 reads so far
2011-05-20 13:23:57,208 - INFO - Processed 125100000 reads so far
2011-05-20 13:24:09,729 - INFO - Processed 125200000 reads so far
2011-05-20 13:24:21,686 - INFO - Processed 125300000 reads so far
2011-05-20 13:24:32,249 - INFO - Processed 125400000 reads so far
2011-05-20 13:24:43,077 - INFO - Processed 125500000 reads so far
2011-05-20 13:24:54,476 - INFO - Processed 125600000 reads so far
2011-05-20 13:25:07,262 - INFO - Processed 125700000 reads so far
2011-05-20 13:25:18,382 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:42990033-63010033
2011-05-20 13:25:18,593 - INFO - Processed 125800000 reads so far
2011-05-20 13:25:31,164 - INFO - Processed 125900000 reads so far
2011-05-20 13:25:42,278 - INFO - Processed 126000000 reads so far
2011-05-20 13:25:53,700 - INFO - Processed 126100000 reads so far
2011-05-20 13:26:03,489 - INFO - Processed 126200000 reads so far
2011-05-20 13:26:14,185 - INFO - Processed 126300000 reads so far
2011-05-20 13:26:24,548 - INFO - Processed 126400000 reads so far
2011-05-20 13:26:34,098 - INFO - Processed 126500000 reads so far
2011-05-20 13:26:45,385 - INFO - Processed 126600000 reads so far
2011-05-20 13:26:56,386 - INFO - Processed 126700000 reads so far
2011-05-20 13:27:03,616 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:62990035-83010035
2011-05-20 13:27:08,262 - INFO - Processed 126800000 reads so far
2011-05-20 13:27:19,133 - INFO - Processed 126900000 reads so far
2011-05-20 13:27:29,429 - INFO - Processed 127000000 reads so far
2011-05-20 13:27:39,721 - INFO - Processed 127100000 reads so far
2011-05-20 13:27:51,030 - INFO - Processed 127200000 reads so far
2011-05-20 13:28:01,501 - INFO - Processed 127300000 reads so far
2011-05-20 13:28:13,763 - INFO - Processed 127400000 reads so far
2011-05-20 13:28:23,033 - INFO - Processed 127500000 reads so far
2011-05-20 13:28:33,459 - INFO - Processed 127600000 reads so far
2011-05-20 13:28:42,063 - INFO - Processed 127700000 reads so far
2011-05-20 13:28:43,529 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:82990161-103010161
2011-05-20 13:28:51,167 - INFO - Processed 127800000 reads so far
2011-05-20 13:29:02,224 - INFO - Processed 127900000 reads so far
2011-05-20 13:29:11,635 - INFO - Processed 128000000 reads so far
2011-05-20 13:29:21,320 - INFO - Processed 128100000 reads so far
2011-05-20 13:29:33,683 - INFO - Processed 128200000 reads so far
2011-05-20 13:29:44,473 - INFO - Processed 128300000 reads so far
2011-05-20 13:29:55,367 - INFO - Processed 128400000 reads so far
2011-05-20 13:30:06,540 - INFO - Processed 128500000 reads so far
2011-05-20 13:30:17,121 - INFO - Processed 128600000 reads so far
2011-05-20 13:30:23,905 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:102990171-123010171
2011-05-20 13:30:28,298 - INFO - Processed 128700000 reads so far
2011-05-20 13:30:40,328 - INFO - Processed 128800000 reads so far
2011-05-20 13:30:53,045 - INFO - Processed 128900000 reads so far
2011-05-20 13:31:05,476 - INFO - Processed 129000000 reads so far
2011-05-20 13:31:14,920 - INFO - Processed 129100000 reads so far
2011-05-20 13:31:25,729 - INFO - Processed 129200000 reads so far
2011-05-20 13:31:37,857 - INFO - Processed 129300000 reads so far
2011-05-20 13:31:48,191 - INFO - Processed 129400000 reads so far
2011-05-20 13:31:57,573 - INFO - Processed 129500000 reads so far
2011-05-20 13:32:09,081 - INFO - Processed 129600000 reads so far
2011-05-20 13:32:12,787 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:122990186-143010186
2011-05-20 13:32:16,810 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9_random:0-20010005
2011-05-20 13:32:17,537 - INFO - Processed 129700000 reads so far
2011-05-20 13:32:18,599 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrM:0-20010000
2011-05-20 13:32:24,373 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrUn_random:0-20010000
2011-05-20 13:32:25,297 - INFO - Processed 129800000 reads so far
2011-05-20 13:32:37,746 - INFO - Processed 129900000 reads so far
2011-05-20 13:32:46,364 - INFO - Processed 130000000 reads so far
2011-05-20 13:32:55,753 - INFO - Processed 130100000 reads so far
2011-05-20 13:33:00,166 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:2990057-23010057
2011-05-20 13:33:04,553 - INFO - Processed 130200000 reads so far
2011-05-20 13:33:13,446 - INFO - Processed 130300000 reads so far
2011-05-20 13:33:23,476 - INFO - Processed 130400000 reads so far
2011-05-20 13:33:34,476 - INFO - Processed 130500000 reads so far
2011-05-20 13:33:43,555 - INFO - Processed 130600000 reads so far
2011-05-20 13:33:54,507 - INFO - Processed 130700000 reads so far
2011-05-20 13:33:54,761 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:22990107-43010107
2011-05-20 13:34:04,315 - INFO - Processed 130800000 reads so far
2011-05-20 13:34:14,336 - INFO - Processed 130900000 reads so far
2011-05-20 13:34:21,792 - INFO - Processed 131000000 reads so far
2011-05-20 13:34:33,073 - INFO - Processed 131100000 reads so far
2011-05-20 13:34:44,453 - INFO - Processed 131200000 reads so far
2011-05-20 13:34:49,073 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:42990110-63010110
2011-05-20 13:34:55,115 - INFO - Processed 131300000 reads so far
2011-05-20 13:35:05,463 - INFO - Processed 131400000 reads so far
2011-05-20 13:35:16,448 - INFO - Processed 131500000 reads so far
2011-05-20 13:35:28,648 - INFO - Processed 131600000 reads so far
2011-05-20 13:35:40,614 - INFO - Processed 131700000 reads so far
2011-05-20 13:35:47,104 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:62990133-83010133
2011-05-20 13:35:53,702 - INFO - Processed 131800000 reads so far
2011-05-20 13:36:05,899 - INFO - Processed 131900000 reads so far
2011-05-20 13:36:18,616 - INFO - Processed 132000000 reads so far
2011-05-20 13:36:30,512 - INFO - Processed 132100000 reads so far
2011-05-20 13:36:44,139 - INFO - Processed 132200000 reads so far
2011-05-20 13:36:50,079 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:82990168-103010168
2011-05-20 13:36:58,074 - INFO - Processed 132300000 reads so far
2011-05-20 13:37:09,845 - INFO - Processed 132400000 reads so far
2011-05-20 13:37:21,706 - INFO - Processed 132500000 reads so far
2011-05-20 13:37:36,196 - INFO - Processed 132600000 reads so far
2011-05-20 13:37:48,867 - INFO - Processed 132700000 reads so far
2011-05-20 13:37:51,435 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:102990181-123010181
2011-05-20 13:38:02,286 - INFO - Processed 132800000 reads so far
2011-05-20 13:38:13,437 - INFO - Processed 132900000 reads so far
2011-05-20 13:38:24,434 - INFO - Processed 133000000 reads so far
2011-05-20 13:38:35,091 - INFO - Processed 133100000 reads so far
2011-05-20 13:38:47,091 - INFO - Processed 133200000 reads so far
2011-05-20 13:38:58,682 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:122990236-143010236
2011-05-20 13:38:59,618 - INFO - Processed 133300000 reads so far
2011-05-20 13:39:11,100 - INFO - Processed 133400000 reads so far
2011-05-20 13:39:20,917 - INFO - Processed 133500000 reads so far
2011-05-20 13:39:30,126 - INFO - Processed 133600000 reads so far
2011-05-20 13:39:39,577 - INFO - Processed 133700000 reads so far
2011-05-20 13:39:48,488 - INFO - Processed 133800000 reads so far
2011-05-20 13:39:52,985 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:142990240-163010240
2011-05-20 13:40:00,159 - INFO - Processed 133900000 reads so far
2011-05-20 13:40:12,092 - INFO - Processed 134000000 reads so far
2011-05-20 13:40:25,444 - INFO - Processed 134100000 reads so far
2011-05-20 13:40:36,591 - INFO - Processed 134200000 reads so far
2011-05-20 13:40:46,418 - INFO - Processed 134300000 reads so far
2011-05-20 13:40:46,761 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:162990380-183010380
2011-05-20 13:40:56,842 - INFO - Processed 134400000 reads so far
2011-05-20 13:41:02,163 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX_random:0-20010000
2011-05-20 13:41:04,657 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY:0-20010000
2011-05-20 13:41:07,488 - INFO - Processed 134500000 reads so far
2011-05-20 13:41:14,588 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:0-20010275
2011-05-20 13:41:18,248 - INFO - Processed 134600000 reads so far
2011-05-20 13:41:27,025 - INFO - Processed 134700000 reads so far
2011-05-20 13:41:36,297 - INFO - Processed 134800000 reads so far
2011-05-20 13:41:45,432 - INFO - Processed 134900000 reads so far
2011-05-20 13:41:53,781 - INFO - Processed 135000000 reads so far
2011-05-20 13:42:03,555 - INFO - Processed 135100000 reads so far
2011-05-20 13:42:13,273 - INFO - Processed 135200000 reads so far
2011-05-20 13:42:22,846 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:19990580-40010580
2011-05-20 13:42:24,125 - INFO - Processed 135300000 reads so far
2011-05-20 13:42:34,797 - INFO - Processed 135400000 reads so far
2011-05-20 13:42:47,376 - INFO - Processed 135500000 reads so far
2011-05-20 13:42:59,312 - INFO - Processed 135600000 reads so far
2011-05-20 13:43:08,645 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:39990585-60010585
2011-05-20 13:43:10,054 - INFO - Processed 135700000 reads so far
2011-05-20 13:43:20,738 - INFO - Processed 135800000 reads so far
2011-05-20 13:43:32,657 - INFO - Processed 135900000 reads so far
2011-05-20 13:43:43,746 - INFO - Processed 136000000 reads so far
2011-05-20 13:43:52,381 - INFO - Processed 136100000 reads so far
2011-05-20 13:44:03,684 - INFO - Processed 136200000 reads so far
2011-05-20 13:44:10,710 - INFO - Processed 136300000 reads so far
2011-05-20 13:44:14,529 - INFO - Processed 136400000 reads so far
2011-05-20 13:44:18,644 - INFO - Processed 136500000 reads so far
2011-05-20 13:44:21,211 - INFO - Processed 136600000 reads so far
2011-05-20 13:44:24,181 - INFO - Processed 136700000 reads so far
2011-05-20 13:44:26,903 - INFO - Processed 136800000 reads so far
2011-05-20 13:44:31,924 - INFO - Processed 136900000 reads so far
2011-05-20 13:44:35,912 - INFO - Processed 137000000 reads so far
2011-05-20 13:44:39,922 - INFO - Processed 137100000 reads so far
2011-05-20 13:44:43,934 - INFO - Processed 137200000 reads so far
2011-05-20 13:44:48,169 - INFO - Processed 137300000 reads so far
2011-05-20 13:44:52,351 - INFO - Processed 137400000 reads so far
2011-05-20 13:44:56,443 - INFO - Processed 137500000 reads so far
2011-05-20 13:45:00,476 - INFO - Processed 137600000 reads so far
2011-05-20 13:45:04,556 - INFO - Processed 137700000 reads so far
2011-05-20 13:45:09,390 - INFO - Processed 137800000 reads so far
2011-05-20 13:45:13,312 - INFO - Processed 137900000 reads so far
2011-05-20 13:45:17,335 - INFO - Processed 138000000 reads so far
2011-05-20 13:45:21,326 - INFO - Processed 138100000 reads so far
2011-05-20 13:45:25,394 - INFO - Processed 138200000 reads so far
2011-05-20 13:45:28,652 - INFO - Finished loading data. Outputting QC metrics
2011-05-20 13:45:49,556 - INFO - Finished outputting QC metrics
2011-05-20 13:45:49,662 - INFO - Finished generating QC metrics