2011-05-19 20:54:11,260 - INFO - Generating QC metrics for BAM File ['WTCHG_12345.bam']
2011-05-19 20:54:11,260 - INFO - Output will go to WTCHG_12345.qc.txt.tmp
2011-05-19 20:54:11,261 - INFO - Reading GC Map from file /data/Genomes/gcMap/Mouse37.gcMap.gz
2011-05-19 20:57:16,156 - INFO - Finished reading GC Map
2011-05-19 20:57:16,156 - INFO - Reading CDS from exon definition file /data/Genomes/annotation/Mouse37.refGene.txt.gz
2011-05-19 20:57:19,028 - INFO - Read 382138 exons (33804740 nucleotides) for 32 chromosomes
2011-05-19 20:57:19,029 - INFO - Computing coverage cut-off
2011-05-19 20:57:19,029 - INFO - Retrieving BAM file coverage info from samtools pileup
2011-05-19 20:57:24,235 - INFO - Processed 1000000 pile-up sites
2011-05-19 20:57:28,453 - INFO - Processed 2000000 pile-up sites
2011-05-19 20:57:32,890 - INFO - Processed 3000000 pile-up sites
2011-05-19 20:57:37,217 - INFO - Processed 4000000 pile-up sites
2011-05-19 20:57:42,115 - INFO - Processed 5000000 pile-up sites
2011-05-19 20:57:47,785 - INFO - Processed 6000000 pile-up sites
2011-05-19 20:57:52,486 - INFO - Processed 7000000 pile-up sites
2011-05-19 20:57:57,218 - INFO - Processed 8000000 pile-up sites
2011-05-19 20:58:01,569 - INFO - Processed 9000000 pile-up sites
2011-05-19 20:58:06,585 - INFO - Processed 10000000 pile-up sites
2011-05-19 20:58:11,335 - INFO - Processed 11000000 pile-up sites
2011-05-19 20:58:15,950 - INFO - Processed 12000000 pile-up sites
2011-05-19 20:58:19,695 - INFO - Processed 13000000 pile-up sites
2011-05-19 20:58:22,388 - INFO - Processed 14000000 pile-up sites
2011-05-19 20:58:24,918 - INFO - Processed 15000000 pile-up sites
2011-05-19 20:58:27,400 - INFO - Processed 16000000 pile-up sites
2011-05-19 20:58:30,518 - INFO - Processed 17000000 pile-up sites
2011-05-19 20:58:34,151 - INFO - Processed 18000000 pile-up sites
2011-05-19 20:58:37,937 - INFO - Processed 19000000 pile-up sites
2011-05-19 20:58:42,345 - INFO - Processed 20000000 pile-up sites
2011-05-19 20:58:46,702 - INFO - Processed 21000000 pile-up sites
2011-05-19 20:58:50,617 - INFO - Processed 22000000 pile-up sites
2011-05-19 20:58:54,382 - INFO - Processed 23000000 pile-up sites
2011-05-19 20:58:59,032 - INFO - Processed 24000000 pile-up sites
2011-05-19 20:59:03,748 - INFO - Processed 25000000 pile-up sites
2011-05-19 20:59:09,470 - INFO - Processed 26000000 pile-up sites
2011-05-19 20:59:14,258 - INFO - Processed 27000000 pile-up sites
2011-05-19 20:59:19,604 - INFO - Processed 28000000 pile-up sites
2011-05-19 20:59:23,955 - INFO - Processed 29000000 pile-up sites
2011-05-19 20:59:28,184 - INFO - Processed 30000000 pile-up sites
2011-05-19 20:59:33,342 - INFO - Processed 31000000 pile-up sites
2011-05-19 20:59:37,318 - INFO - Processed 32000000 pile-up sites
2011-05-19 20:59:41,304 - INFO - Processed 33000000 pile-up sites
2011-05-19 20:59:45,396 - INFO - Processed 34000000 pile-up sites
2011-05-19 20:59:49,453 - INFO - Finished processing pile-up on 34995264 sites (200000002 nucleotides)
2011-05-19 20:59:49,453 - INFO - Coverage cut-off value is 45
2011-05-19 20:59:49,454 - INFO - Loading data into QC data manager
2011-05-19 20:59:49,613 - WARNING - Found RG tag 'SM' (value: 330) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,613 - WARNING - Found RG tag 'ID' (value: WTCHG_12345) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,614 - WARNING - Found RG tag 'SM' (value: 330) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,614 - WARNING - Found RG tag 'ID' (value: WTCHG_12345) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,614 - WARNING - Found RG tag 'SM' (value: 330) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,614 - WARNING - Found RG tag 'ID' (value: WTCHG_12345) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,614 - WARNING - Found RG tag 'SM' (value: 330) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,614 - WARNING - Found RG tag 'ID' (value: WTCHG_12345) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,668 - WARNING - Found RG tag 'SM' (value: 330) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,668 - WARNING - Found RG tag 'ID' (value: WTCHG_12345) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,669 - WARNING - Found RG tag 'SM' (value: 330) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,669 - WARNING - Found RG tag 'ID' (value: WTCHG_12345) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,669 - WARNING - Found RG tag 'SM' (value: 330) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,669 - WARNING - Found RG tag 'ID' (value: WTCHG_12345) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,669 - WARNING - Found RG tag 'SM' (value: 330) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,669 - WARNING - Found RG tag 'ID' (value: WTCHG_12345) duplicated in CO field (value: 4635/10) -- ignoring CO value
2011-05-19 20:59:49,679 - INFO - Reading data from BAM file WTCHG_12345.bam. All reads in file will be read
2011-05-19 20:59:49,722 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:2990039-23010039
2011-05-19 21:00:00,663 - INFO - Processed 100000 reads so far
2011-05-19 21:00:11,086 - INFO - Processed 200000 reads so far
2011-05-19 21:00:24,421 - INFO - Processed 300000 reads so far
2011-05-19 21:00:34,175 - INFO - Processed 400000 reads so far
2011-05-19 21:00:43,169 - INFO - Processed 500000 reads so far
2011-05-19 21:00:53,777 - INFO - Processed 600000 reads so far
2011-05-19 21:01:02,334 - INFO - Processed 700000 reads so far
2011-05-19 21:01:12,587 - INFO - Processed 800000 reads so far
2011-05-19 21:01:21,309 - INFO - Processed 900000 reads so far
2011-05-19 21:01:30,927 - INFO - Processed 1000000 reads so far
2011-05-19 21:01:39,426 - INFO - Processed 1100000 reads so far
2011-05-19 21:01:43,786 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:22990044-43010044
2011-05-19 21:01:48,036 - INFO - Processed 1200000 reads so far
2011-05-19 21:01:56,876 - INFO - Processed 1300000 reads so far
2011-05-19 21:02:08,021 - INFO - Processed 1400000 reads so far
2011-05-19 21:02:19,325 - INFO - Processed 1500000 reads so far
2011-05-19 21:02:30,144 - INFO - Processed 1600000 reads so far
2011-05-19 21:02:40,678 - INFO - Processed 1700000 reads so far
2011-05-19 21:02:49,843 - INFO - Processed 1800000 reads so far
2011-05-19 21:02:59,767 - INFO - Processed 1900000 reads so far
2011-05-19 21:03:09,894 - INFO - Processed 2000000 reads so far
2011-05-19 21:03:21,834 - INFO - Processed 2100000 reads so far
2011-05-19 21:03:32,559 - INFO - Processed 2200000 reads so far
2011-05-19 21:03:34,467 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:42990105-63010105
2011-05-19 21:03:42,732 - INFO - Processed 2300000 reads so far
2011-05-19 21:03:52,594 - INFO - Processed 2400000 reads so far
2011-05-19 21:04:00,027 - INFO - Processed 2500000 reads so far
2011-05-19 21:04:08,244 - INFO - Processed 2600000 reads so far
2011-05-19 21:04:17,287 - INFO - Processed 2700000 reads so far
2011-05-19 21:04:29,362 - INFO - Processed 2800000 reads so far
2011-05-19 21:04:39,981 - INFO - Processed 2900000 reads so far
2011-05-19 21:04:52,240 - INFO - Processed 3000000 reads so far
2011-05-19 21:05:03,954 - INFO - Processed 3100000 reads so far
2011-05-19 21:05:16,957 - INFO - Processed 3200000 reads so far
2011-05-19 21:05:25,314 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:62990110-83010110
2011-05-19 21:05:28,386 - INFO - Processed 3300000 reads so far
2011-05-19 21:05:40,539 - INFO - Processed 3400000 reads so far
2011-05-19 21:05:51,690 - INFO - Processed 3500000 reads so far
2011-05-19 21:06:02,103 - INFO - Processed 3600000 reads so far
2011-05-19 21:06:13,973 - INFO - Processed 3700000 reads so far
2011-05-19 21:06:25,985 - INFO - Processed 3800000 reads so far
2011-05-19 21:06:36,958 - INFO - Processed 3900000 reads so far
2011-05-19 21:06:50,323 - INFO - Processed 4000000 reads so far
2011-05-19 21:07:02,947 - INFO - Processed 4100000 reads so far
2011-05-19 21:07:14,505 - INFO - Processed 4200000 reads so far
2011-05-19 21:07:26,603 - INFO - Processed 4300000 reads so far
2011-05-19 21:07:30,896 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:82990125-103010125
2011-05-19 21:07:39,362 - INFO - Processed 4400000 reads so far
2011-05-19 21:07:50,564 - INFO - Processed 4500000 reads so far
2011-05-19 21:08:02,633 - INFO - Processed 4600000 reads so far
2011-05-19 21:08:13,942 - INFO - Processed 4700000 reads so far
2011-05-19 21:08:24,131 - INFO - Processed 4800000 reads so far
2011-05-19 21:08:35,447 - INFO - Processed 4900000 reads so far
2011-05-19 21:08:46,759 - INFO - Processed 5000000 reads so far
2011-05-19 21:08:58,278 - INFO - Processed 5100000 reads so far
2011-05-19 21:09:09,526 - INFO - Processed 5200000 reads so far
2011-05-19 21:09:20,867 - INFO - Processed 5300000 reads so far
2011-05-19 21:09:30,826 - INFO - Processed 5400000 reads so far
2011-05-19 21:09:33,263 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:102990150-123010150
2011-05-19 21:09:45,310 - INFO - Processed 5500000 reads so far
2011-05-19 21:10:13,734 - INFO - Processed 5600000 reads so far
2011-05-19 21:10:41,008 - INFO - Processed 5700000 reads so far
2011-05-19 21:10:55,586 - INFO - Processed 5800000 reads so far
2011-05-19 21:11:12,224 - INFO - Processed 5900000 reads so far
2011-05-19 21:11:20,578 - INFO - Processed 6000000 reads so far
2011-05-19 21:11:29,892 - INFO - Processed 6100000 reads so far
2011-05-19 21:11:40,612 - INFO - Processed 6200000 reads so far
2011-05-19 21:11:51,233 - INFO - Processed 6300000 reads so far
2011-05-19 21:12:03,568 - INFO - Processed 6400000 reads so far
2011-05-19 21:12:12,943 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:122990183-143010183
2011-05-19 21:12:14,896 - INFO - Processed 6500000 reads so far
2011-05-19 21:12:26,378 - INFO - Processed 6600000 reads so far
2011-05-19 21:12:38,687 - INFO - Processed 6700000 reads so far
2011-05-19 21:12:50,540 - INFO - Processed 6800000 reads so far
2011-05-19 21:12:57,315 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:2990002-23010002
2011-05-19 21:13:04,529 - INFO - Processed 6900000 reads so far
2011-05-19 21:13:13,871 - INFO - Processed 7000000 reads so far
2011-05-19 21:13:25,691 - INFO - Processed 7100000 reads so far
2011-05-19 21:13:36,509 - INFO - Processed 7200000 reads so far
2011-05-19 21:13:47,112 - INFO - Processed 7300000 reads so far
2011-05-19 21:13:58,525 - INFO - Processed 7400000 reads so far
2011-05-19 21:14:08,402 - INFO - Processed 7500000 reads so far
2011-05-19 21:14:21,349 - INFO - Processed 7600000 reads so far
2011-05-19 21:14:33,089 - INFO - Processed 7700000 reads so far
2011-05-19 21:14:43,089 - INFO - Processed 7800000 reads so far
2011-05-19 21:14:51,960 - INFO - Processed 7900000 reads so far
2011-05-19 21:15:03,579 - INFO - Processed 8000000 reads so far
2011-05-19 21:15:12,563 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:22990003-43010003
2011-05-19 21:15:14,383 - INFO - Processed 8100000 reads so far
2011-05-19 21:15:24,674 - INFO - Processed 8200000 reads so far
2011-05-19 21:15:34,460 - INFO - Processed 8300000 reads so far
2011-05-19 21:15:44,921 - INFO - Processed 8400000 reads so far
2011-05-19 21:15:57,039 - INFO - Processed 8500000 reads so far
2011-05-19 21:16:07,049 - INFO - Processed 8600000 reads so far
2011-05-19 21:16:17,767 - INFO - Processed 8700000 reads so far
2011-05-19 21:16:30,918 - INFO - Processed 8800000 reads so far
2011-05-19 21:16:44,984 - INFO - Processed 8900000 reads so far
2011-05-19 21:16:56,495 - INFO - Processed 9000000 reads so far
2011-05-19 21:17:10,129 - INFO - Processed 9100000 reads so far
2011-05-19 21:17:15,524 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:42990010-63010010
2011-05-19 21:17:21,083 - INFO - Processed 9200000 reads so far
2011-05-19 21:17:34,010 - INFO - Processed 9300000 reads so far
2011-05-19 21:17:45,500 - INFO - Processed 9400000 reads so far
2011-05-19 21:17:57,000 - INFO - Processed 9500000 reads so far
2011-05-19 21:18:09,206 - INFO - Processed 9600000 reads so far
2011-05-19 21:18:21,596 - INFO - Processed 9700000 reads so far
2011-05-19 21:18:33,342 - INFO - Processed 9800000 reads so far
2011-05-19 21:18:45,064 - INFO - Processed 9900000 reads so far
2011-05-19 21:18:56,844 - INFO - Processed 10000000 reads so far
2011-05-19 21:19:09,777 - INFO - Processed 10100000 reads so far
2011-05-19 21:19:21,325 - INFO - Processed 10200000 reads so far
2011-05-19 21:19:25,620 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:62990052-83010052
2011-05-19 21:19:32,615 - INFO - Processed 10300000 reads so far
2011-05-19 21:19:44,098 - INFO - Processed 10400000 reads so far
2011-05-19 21:19:58,855 - INFO - Processed 10500000 reads so far
2011-05-19 21:20:11,014 - INFO - Processed 10600000 reads so far
2011-05-19 21:20:21,859 - INFO - Processed 10700000 reads so far
2011-05-19 21:20:36,773 - INFO - Processed 10800000 reads so far
2011-05-19 21:20:48,677 - INFO - Processed 10900000 reads so far
2011-05-19 21:21:00,380 - INFO - Processed 11000000 reads so far
2011-05-19 21:21:11,850 - INFO - Processed 11100000 reads so far
2011-05-19 21:21:24,567 - INFO - Processed 11200000 reads so far
2011-05-19 21:21:36,429 - INFO - Processed 11300000 reads so far
2011-05-19 21:21:39,330 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:82990064-103010064
2011-05-19 21:21:48,191 - INFO - Processed 11400000 reads so far
2011-05-19 21:22:01,453 - INFO - Processed 11500000 reads so far
2011-05-19 21:22:12,089 - INFO - Processed 11600000 reads so far
2011-05-19 21:22:23,317 - INFO - Processed 11700000 reads so far
2011-05-19 21:22:35,488 - INFO - Processed 11800000 reads so far
2011-05-19 21:22:47,173 - INFO - Processed 11900000 reads so far
2011-05-19 21:22:59,015 - INFO - Processed 12000000 reads so far
2011-05-19 21:23:11,042 - INFO - Processed 12100000 reads so far
2011-05-19 21:23:24,119 - INFO - Processed 12200000 reads so far
2011-05-19 21:23:34,237 - INFO - Processed 12300000 reads so far
2011-05-19 21:23:42,403 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:102990083-123010083
2011-05-19 21:23:46,081 - INFO - Processed 12400000 reads so far
2011-05-19 21:23:56,263 - INFO - Processed 12500000 reads so far
2011-05-19 21:24:07,005 - INFO - Processed 12600000 reads so far
2011-05-19 21:24:17,603 - INFO - Processed 12700000 reads so far
2011-05-19 21:24:27,750 - INFO - Processed 12800000 reads so far
2011-05-19 21:24:38,107 - INFO - Processed 12900000 reads so far
2011-05-19 21:24:48,459 - INFO - Processed 13000000 reads so far
2011-05-19 21:25:00,799 - INFO - Processed 13100000 reads so far
2011-05-19 21:25:12,808 - INFO - Processed 13200000 reads so far
2011-05-19 21:25:23,337 - INFO - Processed 13300000 reads so far
2011-05-19 21:25:32,515 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:2990044-23010044
2011-05-19 21:25:34,392 - INFO - Processed 13400000 reads so far
2011-05-19 21:25:43,731 - INFO - Processed 13500000 reads so far
2011-05-19 21:25:52,423 - INFO - Processed 13600000 reads so far
2011-05-19 21:26:06,915 - INFO - Processed 13700000 reads so far
2011-05-19 21:26:17,762 - INFO - Processed 13800000 reads so far
2011-05-19 21:26:28,232 - INFO - Processed 13900000 reads so far
2011-05-19 21:26:39,072 - INFO - Processed 14000000 reads so far
2011-05-19 21:26:50,473 - INFO - Processed 14100000 reads so far
2011-05-19 21:27:01,237 - INFO - Processed 14200000 reads so far
2011-05-19 21:27:10,976 - INFO - Processed 14300000 reads so far
2011-05-19 21:27:22,205 - INFO - Processed 14400000 reads so far
2011-05-19 21:27:32,366 - INFO - Processed 14500000 reads so far
2011-05-19 21:27:43,573 - INFO - Processed 14600000 reads so far
2011-05-19 21:27:44,955 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:22990212-43010212
2011-05-19 21:27:53,852 - INFO - Processed 14700000 reads so far
2011-05-19 21:28:05,159 - INFO - Processed 14800000 reads so far
2011-05-19 21:28:17,024 - INFO - Processed 14900000 reads so far
2011-05-19 21:28:27,968 - INFO - Processed 15000000 reads so far
2011-05-19 21:28:37,228 - INFO - Processed 15100000 reads so far
2011-05-19 21:28:48,410 - INFO - Processed 15200000 reads so far
2011-05-19 21:29:00,998 - INFO - Processed 15300000 reads so far
2011-05-19 21:29:12,108 - INFO - Processed 15400000 reads so far
2011-05-19 21:29:25,155 - INFO - Processed 15500000 reads so far
2011-05-19 21:29:36,617 - INFO - Processed 15600000 reads so far
2011-05-19 21:29:38,319 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:42990216-63010216
2011-05-19 21:29:47,868 - INFO - Processed 15700000 reads so far
2011-05-19 21:30:00,347 - INFO - Processed 15800000 reads so far
2011-05-19 21:30:10,717 - INFO - Processed 15900000 reads so far
2011-05-19 21:30:21,847 - INFO - Processed 16000000 reads so far
2011-05-19 21:30:33,348 - INFO - Processed 16100000 reads so far
2011-05-19 21:30:44,552 - INFO - Processed 16200000 reads so far
2011-05-19 21:30:55,867 - INFO - Processed 16300000 reads so far
2011-05-19 21:31:09,062 - INFO - Processed 16400000 reads so far
2011-05-19 21:31:21,986 - INFO - Processed 16500000 reads so far
2011-05-19 21:31:33,848 - INFO - Processed 16600000 reads so far
2011-05-19 21:31:40,439 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:62990249-83010249
2011-05-19 21:31:47,121 - INFO - Processed 16700000 reads so far
2011-05-19 21:31:58,336 - INFO - Processed 16800000 reads so far
2011-05-19 21:32:11,521 - INFO - Processed 16900000 reads so far
2011-05-19 21:32:26,645 - INFO - Processed 17000000 reads so far
2011-05-19 21:32:38,164 - INFO - Processed 17100000 reads so far
2011-05-19 21:32:47,388 - INFO - Processed 17200000 reads so far
2011-05-19 21:32:58,282 - INFO - Processed 17300000 reads so far
2011-05-19 21:33:08,367 - INFO - Processed 17400000 reads so far
2011-05-19 21:33:19,528 - INFO - Processed 17500000 reads so far
2011-05-19 21:33:32,792 - INFO - Processed 17600000 reads so far
2011-05-19 21:33:43,568 - INFO - Processed 17700000 reads so far
2011-05-19 21:33:46,620 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:82990318-103010318
2011-05-19 21:33:54,437 - INFO - Processed 17800000 reads so far
2011-05-19 21:34:07,967 - INFO - Processed 17900000 reads so far
2011-05-19 21:34:19,346 - INFO - Processed 18000000 reads so far
2011-05-19 21:34:35,665 - INFO - Processed 18100000 reads so far
2011-05-19 21:34:51,572 - INFO - Processed 18200000 reads so far
2011-05-19 21:35:01,421 - INFO - Processed 18300000 reads so far
2011-05-19 21:35:10,540 - INFO - Processed 18400000 reads so far
2011-05-19 21:35:21,465 - INFO - Processed 18500000 reads so far
2011-05-19 21:35:33,657 - INFO - Processed 18600000 reads so far
2011-05-19 21:35:46,008 - INFO - Processed 18700000 reads so far
2011-05-19 21:35:57,289 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:102990323-123010323
2011-05-19 21:36:00,594 - INFO - Processed 18800000 reads so far
2011-05-19 21:36:12,997 - INFO - Processed 18900000 reads so far
2011-05-19 21:36:24,258 - INFO - Processed 19000000 reads so far
2011-05-19 21:36:35,888 - INFO - Processed 19100000 reads so far
2011-05-19 21:36:47,134 - INFO - Processed 19200000 reads so far
2011-05-19 21:36:59,848 - INFO - Processed 19300000 reads so far
2011-05-19 21:37:11,927 - INFO - Processed 19400000 reads so far
2011-05-19 21:37:22,151 - INFO - Processed 19500000 reads so far
2011-05-19 21:37:34,056 - INFO - Processed 19600000 reads so far
2011-05-19 21:37:45,552 - INFO - Processed 19700000 reads so far
2011-05-19 21:37:56,441 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:2990031-23010031
2011-05-19 21:37:58,564 - INFO - Processed 19800000 reads so far
2011-05-19 21:38:09,503 - INFO - Processed 19900000 reads so far
2011-05-19 21:38:20,800 - INFO - Processed 20000000 reads so far
2011-05-19 21:38:30,947 - INFO - Processed 20100000 reads so far
2011-05-19 21:38:41,981 - INFO - Processed 20200000 reads so far
2011-05-19 21:38:53,918 - INFO - Processed 20300000 reads so far
2011-05-19 21:39:05,134 - INFO - Processed 20400000 reads so far
2011-05-19 21:39:18,395 - INFO - Processed 20500000 reads so far
2011-05-19 21:39:30,164 - INFO - Processed 20600000 reads so far
2011-05-19 21:39:41,884 - INFO - Processed 20700000 reads so far
2011-05-19 21:39:53,088 - INFO - Processed 20800000 reads so far
2011-05-19 21:39:58,028 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:22990079-43010079
2011-05-19 21:40:05,185 - INFO - Processed 20900000 reads so far
2011-05-19 21:40:16,999 - INFO - Processed 21000000 reads so far
2011-05-19 21:40:28,847 - INFO - Processed 21100000 reads so far
2011-05-19 21:40:40,738 - INFO - Processed 21200000 reads so far
2011-05-19 21:40:52,529 - INFO - Processed 21300000 reads so far
2011-05-19 21:41:04,813 - INFO - Processed 21400000 reads so far
2011-05-19 21:41:17,080 - INFO - Processed 21500000 reads so far
2011-05-19 21:41:30,344 - INFO - Processed 21600000 reads so far
2011-05-19 21:41:41,908 - INFO - Processed 21700000 reads so far
2011-05-19 21:41:52,886 - INFO - Processed 21800000 reads so far
2011-05-19 21:42:03,999 - INFO - Processed 21900000 reads so far
2011-05-19 21:42:09,227 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:42990080-63010080
2011-05-19 21:42:15,340 - INFO - Processed 22000000 reads so far
2011-05-19 21:42:27,701 - INFO - Processed 22100000 reads so far
2011-05-19 21:42:38,831 - INFO - Processed 22200000 reads so far
2011-05-19 21:42:48,212 - INFO - Processed 22300000 reads so far
2011-05-19 21:42:59,071 - INFO - Processed 22400000 reads so far
2011-05-19 21:43:09,064 - INFO - Processed 22500000 reads so far
2011-05-19 21:43:20,084 - INFO - Processed 22600000 reads so far
2011-05-19 21:43:30,221 - INFO - Processed 22700000 reads so far
2011-05-19 21:43:40,859 - INFO - Processed 22800000 reads so far
2011-05-19 21:43:52,811 - INFO - Processed 22900000 reads so far
2011-05-19 21:44:01,864 - INFO - Processed 23000000 reads so far
2011-05-19 21:44:06,140 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:62990087-83010087
2011-05-19 21:44:11,253 - INFO - Processed 23100000 reads so far
2011-05-19 21:44:22,497 - INFO - Processed 23200000 reads so far
2011-05-19 21:44:33,566 - INFO - Processed 23300000 reads so far
2011-05-19 21:44:45,550 - INFO - Processed 23400000 reads so far
2011-05-19 21:44:56,214 - INFO - Processed 23500000 reads so far
2011-05-19 21:45:03,562 - INFO - Processed 23600000 reads so far
2011-05-19 21:45:16,563 - INFO - Processed 23700000 reads so far
2011-05-19 21:45:27,736 - INFO - Processed 23800000 reads so far
2011-05-19 21:45:36,283 - INFO - Processed 23900000 reads so far
2011-05-19 21:45:45,153 - INFO - Processed 24000000 reads so far
2011-05-19 21:45:54,433 - INFO - Processed 24100000 reads so far
2011-05-19 21:46:00,990 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:82990151-103010151
2011-05-19 21:46:03,623 - INFO - Processed 24200000 reads so far
2011-05-19 21:46:10,574 - INFO - Processed 24300000 reads so far
2011-05-19 21:46:19,443 - INFO - Processed 24400000 reads so far
2011-05-19 21:46:28,506 - INFO - Processed 24500000 reads so far
2011-05-19 21:46:36,872 - INFO - Processed 24600000 reads so far
2011-05-19 21:46:45,556 - INFO - Processed 24700000 reads so far
2011-05-19 21:46:55,367 - INFO - Processed 24800000 reads so far
2011-05-19 21:47:04,936 - INFO - Processed 24900000 reads so far
2011-05-19 21:47:12,182 - INFO - Processed 25000000 reads so far
2011-05-19 21:47:20,936 - INFO - Processed 25100000 reads so far
2011-05-19 21:47:28,996 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:102990153-123010153
2011-05-19 21:47:29,812 - INFO - Processed 25200000 reads so far
2011-05-19 21:47:40,768 - INFO - Processed 25300000 reads so far
2011-05-19 21:47:48,686 - INFO - Processed 25400000 reads so far
2011-05-19 21:47:58,093 - INFO - Processed 25500000 reads so far
2011-05-19 21:48:07,685 - INFO - Processed 25600000 reads so far
2011-05-19 21:48:18,174 - INFO - Processed 25700000 reads so far
2011-05-19 21:48:30,464 - INFO - Processed 25800000 reads so far
2011-05-19 21:48:38,928 - INFO - Processed 25900000 reads so far
2011-05-19 21:48:47,575 - INFO - Processed 26000000 reads so far
2011-05-19 21:48:55,709 - INFO - Processed 26100000 reads so far
2011-05-19 21:48:57,617 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13_random:0-20010000
2011-05-19 21:48:58,406 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:2990030-23010030
2011-05-19 21:49:04,549 - INFO - Processed 26200000 reads so far
2011-05-19 21:49:14,161 - INFO - Processed 26300000 reads so far
2011-05-19 21:49:22,361 - INFO - Processed 26400000 reads so far
2011-05-19 21:49:31,208 - INFO - Processed 26500000 reads so far
2011-05-19 21:49:40,079 - INFO - Processed 26600000 reads so far
2011-05-19 21:49:48,009 - INFO - Processed 26700000 reads so far
2011-05-19 21:49:58,084 - INFO - Processed 26800000 reads so far
2011-05-19 21:50:07,964 - INFO - Processed 26900000 reads so far
2011-05-19 21:50:18,392 - INFO - Processed 27000000 reads so far
2011-05-19 21:50:27,638 - INFO - Processed 27100000 reads so far
2011-05-19 21:50:36,944 - INFO - Processed 27200000 reads so far
2011-05-19 21:50:46,128 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:22990058-43010058
2011-05-19 21:50:49,501 - INFO - Processed 27300000 reads so far
2011-05-19 21:51:00,567 - INFO - Processed 27400000 reads so far
2011-05-19 21:51:11,954 - INFO - Processed 27500000 reads so far
2011-05-19 21:51:23,127 - INFO - Processed 27600000 reads so far
2011-05-19 21:51:34,539 - INFO - Processed 27700000 reads so far
2011-05-19 21:51:44,834 - INFO - Processed 27800000 reads so far
2011-05-19 21:51:55,839 - INFO - Processed 27900000 reads so far
2011-05-19 21:52:06,710 - INFO - Processed 28000000 reads so far
2011-05-19 21:52:17,848 - INFO - Processed 28100000 reads so far
2011-05-19 21:52:28,836 - INFO - Processed 28200000 reads so far
2011-05-19 21:52:42,563 - INFO - Processed 28300000 reads so far
2011-05-19 21:52:52,614 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:42990088-63010088
2011-05-19 21:52:53,065 - INFO - Processed 28400000 reads so far
2011-05-19 21:53:02,899 - INFO - Processed 28500000 reads so far
2011-05-19 21:53:12,976 - INFO - Processed 28600000 reads so far
2011-05-19 21:53:22,166 - INFO - Processed 28700000 reads so far
2011-05-19 21:53:32,907 - INFO - Processed 28800000 reads so far
2011-05-19 21:53:41,887 - INFO - Processed 28900000 reads so far
2011-05-19 21:53:53,449 - INFO - Processed 29000000 reads so far
2011-05-19 21:54:01,410 - INFO - Processed 29100000 reads so far
2011-05-19 21:54:09,178 - INFO - Processed 29200000 reads so far
2011-05-19 21:54:17,176 - INFO - Processed 29300000 reads so far
2011-05-19 21:54:24,821 - INFO - Processed 29400000 reads so far
2011-05-19 21:54:33,242 - INFO - Processed 29500000 reads so far
2011-05-19 21:54:40,410 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:62990089-83010089
2011-05-19 21:54:41,598 - INFO - Processed 29600000 reads so far
2011-05-19 21:54:49,400 - INFO - Processed 29700000 reads so far
2011-05-19 21:55:00,847 - INFO - Processed 29800000 reads so far
2011-05-19 21:55:08,440 - INFO - Processed 29900000 reads so far
2011-05-19 21:55:16,008 - INFO - Processed 30000000 reads so far
2011-05-19 21:55:23,754 - INFO - Processed 30100000 reads so far
2011-05-19 21:55:31,564 - INFO - Processed 30200000 reads so far
2011-05-19 21:55:39,644 - INFO - Processed 30300000 reads so far
2011-05-19 21:55:47,120 - INFO - Processed 30400000 reads so far
2011-05-19 21:55:55,252 - INFO - Processed 30500000 reads so far
2011-05-19 21:56:03,048 - INFO - Processed 30600000 reads so far
2011-05-19 21:56:11,957 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:82990101-103010101
2011-05-19 21:56:13,400 - INFO - Processed 30700000 reads so far
2011-05-19 21:56:23,319 - INFO - Processed 30800000 reads so far
2011-05-19 21:56:33,689 - INFO - Processed 30900000 reads so far
2011-05-19 21:56:41,777 - INFO - Processed 31000000 reads so far
2011-05-19 21:56:51,940 - INFO - Processed 31100000 reads so far
2011-05-19 21:56:58,853 - INFO - Processed 31200000 reads so far
2011-05-19 21:57:07,585 - INFO - Processed 31300000 reads so far
2011-05-19 21:57:14,333 - INFO - Processed 31400000 reads so far
2011-05-19 21:57:23,284 - INFO - Processed 31500000 reads so far
2011-05-19 21:57:33,048 - INFO - Processed 31600000 reads so far
2011-05-19 21:57:42,404 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:102990111-123010111
2011-05-19 21:57:43,030 - INFO - Processed 31700000 reads so far
2011-05-19 21:57:58,160 - INFO - Processed 31800000 reads so far
2011-05-19 21:58:09,642 - INFO - Processed 31900000 reads so far
2011-05-19 21:58:21,263 - INFO - Processed 32000000 reads so far
2011-05-19 21:58:32,943 - INFO - Processed 32100000 reads so far
2011-05-19 21:58:41,814 - INFO - Processed 32200000 reads so far
2011-05-19 21:58:50,661 - INFO - Processed 32300000 reads so far
2011-05-19 21:58:59,476 - INFO - Processed 32400000 reads so far
2011-05-19 21:59:07,904 - INFO - Processed 32500000 reads so far
2011-05-19 21:59:17,072 - INFO - Processed 32600000 reads so far
2011-05-19 21:59:27,998 - INFO - Processed 32700000 reads so far
2011-05-19 21:59:31,061 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:122990130-143010130
2011-05-19 21:59:37,457 - INFO - Processed 32800000 reads so far
2011-05-19 21:59:42,934 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:2990016-23010016
2011-05-19 21:59:48,575 - INFO - Processed 32900000 reads so far
2011-05-19 21:59:59,936 - INFO - Processed 33000000 reads so far
2011-05-19 22:00:13,338 - INFO - Processed 33100000 reads so far
2011-05-19 22:00:24,990 - INFO - Processed 33200000 reads so far
2011-05-19 22:00:35,273 - INFO - Processed 33300000 reads so far
2011-05-19 22:00:45,110 - INFO - Processed 33400000 reads so far
2011-05-19 22:00:55,830 - INFO - Processed 33500000 reads so far
2011-05-19 22:01:04,928 - INFO - Processed 33600000 reads so far
2011-05-19 22:01:14,734 - INFO - Processed 33700000 reads so far
2011-05-19 22:01:25,621 - INFO - Processed 33800000 reads so far
2011-05-19 22:01:33,461 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:22990029-43010029
2011-05-19 22:01:34,291 - INFO - Processed 33900000 reads so far
2011-05-19 22:01:44,258 - INFO - Processed 34000000 reads so far
2011-05-19 22:01:55,812 - INFO - Processed 34100000 reads so far
2011-05-19 22:02:06,859 - INFO - Processed 34200000 reads so far
2011-05-19 22:02:18,237 - INFO - Processed 34300000 reads so far
2011-05-19 22:02:29,181 - INFO - Processed 34400000 reads so far
2011-05-19 22:02:38,835 - INFO - Processed 34500000 reads so far
2011-05-19 22:02:50,363 - INFO - Processed 34600000 reads so far
2011-05-19 22:03:00,759 - INFO - Processed 34700000 reads so far
2011-05-19 22:03:09,064 - INFO - Processed 34800000 reads so far
2011-05-19 22:03:17,472 - INFO - Processed 34900000 reads so far
2011-05-19 22:03:23,688 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:42990046-63010046
2011-05-19 22:03:26,643 - INFO - Processed 35000000 reads so far
2011-05-19 22:03:39,360 - INFO - Processed 35100000 reads so far
2011-05-19 22:03:49,968 - INFO - Processed 35200000 reads so far
2011-05-19 22:04:00,488 - INFO - Processed 35300000 reads so far
2011-05-19 22:04:08,519 - INFO - Processed 35400000 reads so far
2011-05-19 22:04:18,559 - INFO - Processed 35500000 reads so far
2011-05-19 22:04:29,679 - INFO - Processed 35600000 reads so far
2011-05-19 22:04:41,505 - INFO - Processed 35700000 reads so far
2011-05-19 22:04:50,168 - INFO - Processed 35800000 reads so far
2011-05-19 22:04:58,835 - INFO - Processed 35900000 reads so far
2011-05-19 22:05:08,327 - INFO - Processed 36000000 reads so far
2011-05-19 22:05:10,886 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:62990077-83010077
2011-05-19 22:05:17,087 - INFO - Processed 36100000 reads so far
2011-05-19 22:05:26,085 - INFO - Processed 36200000 reads so far
2011-05-19 22:05:34,711 - INFO - Processed 36300000 reads so far
2011-05-19 22:05:43,589 - INFO - Processed 36400000 reads so far
2011-05-19 22:05:51,975 - INFO - Processed 36500000 reads so far
2011-05-19 22:06:01,562 - INFO - Processed 36600000 reads so far
2011-05-19 22:06:10,597 - INFO - Processed 36700000 reads so far
2011-05-19 22:06:20,141 - INFO - Processed 36800000 reads so far
2011-05-19 22:06:31,586 - INFO - Processed 36900000 reads so far
2011-05-19 22:06:43,135 - INFO - Processed 37000000 reads so far
2011-05-19 22:06:54,098 - INFO - Processed 37100000 reads so far
2011-05-19 22:06:57,694 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:82990145-103010145
2011-05-19 22:07:04,409 - INFO - Processed 37200000 reads so far
2011-05-19 22:07:14,324 - INFO - Processed 37300000 reads so far
2011-05-19 22:07:22,618 - INFO - Processed 37400000 reads so far
2011-05-19 22:07:31,105 - INFO - Processed 37500000 reads so far
2011-05-19 22:07:40,720 - INFO - Processed 37600000 reads so far
2011-05-19 22:07:48,701 - INFO - Processed 37700000 reads so far
2011-05-19 22:07:56,825 - INFO - Processed 37800000 reads so far
2011-05-19 22:08:04,679 - INFO - Processed 37900000 reads so far
2011-05-19 22:08:13,758 - INFO - Processed 38000000 reads so far
2011-05-19 22:08:23,560 - INFO - Processed 38100000 reads so far
2011-05-19 22:08:33,837 - INFO - Processed 38200000 reads so far
2011-05-19 22:08:35,007 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:102990178-123010178
2011-05-19 22:08:36,877 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:2990031-23010031
2011-05-19 22:08:42,322 - INFO - Processed 38300000 reads so far
2011-05-19 22:08:52,375 - INFO - Processed 38400000 reads so far
2011-05-19 22:09:00,944 - INFO - Processed 38500000 reads so far
2011-05-19 22:09:09,256 - INFO - Processed 38600000 reads so far
2011-05-19 22:09:40,579 - INFO - Processed 38700000 reads so far
2011-05-19 22:09:50,933 - INFO - Processed 38800000 reads so far
2011-05-19 22:10:00,911 - INFO - Processed 38900000 reads so far
2011-05-19 22:10:10,342 - INFO - Processed 39000000 reads so far
2011-05-19 22:10:21,701 - INFO - Processed 39100000 reads so far
2011-05-19 22:10:31,593 - INFO - Processed 39200000 reads so far
2011-05-19 22:10:40,544 - INFO - Processed 39300000 reads so far
2011-05-19 22:10:48,637 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:22990044-43010044
2011-05-19 22:10:49,636 - INFO - Processed 39400000 reads so far
2011-05-19 22:10:59,483 - INFO - Processed 39500000 reads so far
2011-05-19 22:11:11,454 - INFO - Processed 39600000 reads so far
2011-05-19 22:11:22,811 - INFO - Processed 39700000 reads so far
2011-05-19 22:11:34,074 - INFO - Processed 39800000 reads so far
2011-05-19 22:11:46,294 - INFO - Processed 39900000 reads so far
2011-05-19 22:11:57,205 - INFO - Processed 40000000 reads so far
2011-05-19 22:12:08,627 - INFO - Processed 40100000 reads so far
2011-05-19 22:12:20,105 - INFO - Processed 40200000 reads so far
2011-05-19 22:12:33,010 - INFO - Processed 40300000 reads so far
2011-05-19 22:12:42,683 - INFO - Processed 40400000 reads so far
2011-05-19 22:12:50,497 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:42990082-63010082
2011-05-19 22:12:53,363 - INFO - Processed 40500000 reads so far
2011-05-19 22:13:04,788 - INFO - Processed 40600000 reads so far
2011-05-19 22:13:19,396 - INFO - Processed 40700000 reads so far
2011-05-19 22:13:31,101 - INFO - Processed 40800000 reads so far
2011-05-19 22:13:42,197 - INFO - Processed 40900000 reads so far
2011-05-19 22:13:53,854 - INFO - Processed 41000000 reads so far
2011-05-19 22:14:05,052 - INFO - Processed 41100000 reads so far
2011-05-19 22:14:16,099 - INFO - Processed 41200000 reads so far
2011-05-19 22:14:27,251 - INFO - Processed 41300000 reads so far
2011-05-19 22:14:38,499 - INFO - Processed 41400000 reads so far
2011-05-19 22:14:49,812 - INFO - Processed 41500000 reads so far
2011-05-19 22:14:52,540 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:62990087-83010087
2011-05-19 22:15:01,168 - INFO - Processed 41600000 reads so far
2011-05-19 22:15:12,168 - INFO - Processed 41700000 reads so far
2011-05-19 22:15:23,082 - INFO - Processed 41800000 reads so far
2011-05-19 22:15:34,121 - INFO - Processed 41900000 reads so far
2011-05-19 22:15:45,817 - INFO - Processed 42000000 reads so far
2011-05-19 22:15:55,157 - INFO - Processed 42100000 reads so far
2011-05-19 22:16:05,619 - INFO - Processed 42200000 reads so far
2011-05-19 22:16:15,772 - INFO - Processed 42300000 reads so far
2011-05-19 22:16:27,581 - INFO - Processed 42400000 reads so far
2011-05-19 22:16:36,901 - INFO - Processed 42500000 reads so far
2011-05-19 22:16:40,000 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:82990091-103010091
2011-05-19 22:16:47,427 - INFO - Processed 42600000 reads so far
2011-05-19 22:16:57,965 - INFO - Processed 42700000 reads so far
2011-05-19 22:17:09,012 - INFO - Processed 42800000 reads so far
2011-05-19 22:17:18,546 - INFO - Processed 42900000 reads so far
2011-05-19 22:17:28,752 - INFO - Processed 43000000 reads so far
2011-05-19 22:17:37,783 - INFO - Processed 43100000 reads so far
2011-05-19 22:17:46,049 - INFO - Processed 43200000 reads so far
2011-05-19 22:17:56,679 - INFO - Processed 43300000 reads so far
2011-05-19 22:18:05,113 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16_random:0-20010123
2011-05-19 22:18:05,153 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:2989983-23009983
2011-05-19 22:18:08,199 - INFO - Processed 43400000 reads so far
2011-05-19 22:18:19,407 - INFO - Processed 43500000 reads so far
2011-05-19 22:18:29,686 - INFO - Processed 43600000 reads so far
2011-05-19 22:18:42,527 - INFO - Processed 43700000 reads so far
2011-05-19 22:18:55,306 - INFO - Processed 43800000 reads so far
2011-05-19 22:19:04,700 - INFO - Processed 43900000 reads so far
2011-05-19 22:19:17,505 - INFO - Processed 44000000 reads so far
2011-05-19 22:19:27,812 - INFO - Processed 44100000 reads so far
2011-05-19 22:19:35,737 - INFO - Processed 44200000 reads so far
2011-05-19 22:19:48,378 - INFO - Processed 44300000 reads so far
2011-05-19 22:19:58,079 - INFO - Processed 44400000 reads so far
2011-05-19 22:20:03,368 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:22990022-43010022
2011-05-19 22:20:07,196 - INFO - Processed 44500000 reads so far
2011-05-19 22:20:19,174 - INFO - Processed 44600000 reads so far
2011-05-19 22:20:30,116 - INFO - Processed 44700000 reads so far
2011-05-19 22:20:39,719 - INFO - Processed 44800000 reads so far
2011-05-19 22:20:50,648 - INFO - Processed 44900000 reads so far
2011-05-19 22:20:59,762 - INFO - Processed 45000000 reads so far
2011-05-19 22:21:10,823 - INFO - Processed 45100000 reads so far
2011-05-19 22:21:20,131 - INFO - Processed 45200000 reads so far
2011-05-19 22:21:31,546 - INFO - Processed 45300000 reads so far
2011-05-19 22:21:42,637 - INFO - Processed 45400000 reads so far
2011-05-19 22:21:52,289 - INFO - Processed 45500000 reads so far
2011-05-19 22:22:02,953 - INFO - Processed 45600000 reads so far
2011-05-19 22:22:04,102 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:42990037-63010037
2011-05-19 22:22:13,571 - INFO - Processed 45700000 reads so far
2011-05-19 22:22:23,348 - INFO - Processed 45800000 reads so far
2011-05-19 22:22:33,832 - INFO - Processed 45900000 reads so far
2011-05-19 22:22:43,331 - INFO - Processed 46000000 reads so far
2011-05-19 22:22:54,471 - INFO - Processed 46100000 reads so far
2011-05-19 22:23:02,599 - INFO - Processed 46200000 reads so far
2011-05-19 22:23:11,387 - INFO - Processed 46300000 reads so far
2011-05-19 22:23:21,134 - INFO - Processed 46400000 reads so far
2011-05-19 22:23:30,280 - INFO - Processed 46500000 reads so far
2011-05-19 22:23:39,658 - INFO - Processed 46600000 reads so far
2011-05-19 22:23:44,929 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:62990050-83010050
2011-05-19 22:23:49,040 - INFO - Processed 46700000 reads so far
2011-05-19 22:24:04,938 - INFO - Processed 46800000 reads so far
2011-05-19 22:24:13,939 - INFO - Processed 46900000 reads so far
2011-05-19 22:24:22,303 - INFO - Processed 47000000 reads so far
2011-05-19 22:24:31,658 - INFO - Processed 47100000 reads so far
2011-05-19 22:24:42,425 - INFO - Processed 47200000 reads so far
2011-05-19 22:24:52,036 - INFO - Processed 47300000 reads so far
2011-05-19 22:25:01,782 - INFO - Processed 47400000 reads so far
2011-05-19 22:25:09,825 - INFO - Processed 47500000 reads so far
2011-05-19 22:25:19,384 - INFO - Processed 47600000 reads so far
2011-05-19 22:25:29,369 - INFO - Processed 47700000 reads so far
2011-05-19 22:25:33,720 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:82990166-103010166
2011-05-19 22:25:40,578 - INFO - Processed 47800000 reads so far
2011-05-19 22:25:50,374 - INFO - Processed 47900000 reads so far
2011-05-19 22:25:59,771 - INFO - Processed 48000000 reads so far
2011-05-19 22:26:08,549 - INFO - Processed 48100000 reads so far
2011-05-19 22:26:17,507 - INFO - Processed 48200000 reads so far
2011-05-19 22:26:27,485 - INFO - Processed 48300000 reads so far
2011-05-19 22:26:36,265 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17_random:0-20010086
2011-05-19 22:26:38,247 - INFO - Processed 48400000 reads so far
2011-05-19 22:26:39,231 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:2990000-23010000
2011-05-19 22:26:47,787 - INFO - Processed 48500000 reads so far
2011-05-19 22:26:57,452 - INFO - Processed 48600000 reads so far
2011-05-19 22:27:05,765 - INFO - Processed 48700000 reads so far
2011-05-19 22:27:16,325 - INFO - Processed 48800000 reads so far
2011-05-19 22:27:27,000 - INFO - Processed 48900000 reads so far
2011-05-19 22:27:38,096 - INFO - Processed 49000000 reads so far
2011-05-19 22:27:46,313 - INFO - Processed 49100000 reads so far
2011-05-19 22:27:57,232 - INFO - Processed 49200000 reads so far
2011-05-19 22:28:06,307 - INFO - Processed 49300000 reads so far
2011-05-19 22:28:16,226 - INFO - Processed 49400000 reads so far
2011-05-19 22:28:26,104 - INFO - Processed 49500000 reads so far
2011-05-19 22:28:29,336 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:22990003-43010003
2011-05-19 22:28:36,572 - INFO - Processed 49600000 reads so far
2011-05-19 22:28:45,810 - INFO - Processed 49700000 reads so far
2011-05-19 22:28:55,619 - INFO - Processed 49800000 reads so far
2011-05-19 22:29:09,282 - INFO - Processed 49900000 reads so far
2011-05-19 22:29:18,869 - INFO - Processed 50000000 reads so far
2011-05-19 22:29:28,234 - INFO - Processed 50100000 reads so far
2011-05-19 22:29:41,159 - INFO - Processed 50200000 reads so far
2011-05-19 22:29:51,788 - INFO - Processed 50300000 reads so far
2011-05-19 22:30:00,823 - INFO - Processed 50400000 reads so far
2011-05-19 22:30:12,884 - INFO - Processed 50500000 reads so far
2011-05-19 22:30:22,417 - INFO - Processed 50600000 reads so far
2011-05-19 22:30:26,180 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:42990010-63010010
2011-05-19 22:30:33,631 - INFO - Processed 50700000 reads so far
2011-05-19 22:30:44,297 - INFO - Processed 50800000 reads so far
2011-05-19 22:30:54,862 - INFO - Processed 50900000 reads so far
2011-05-19 22:31:08,769 - INFO - Processed 51000000 reads so far
2011-05-19 22:31:22,782 - INFO - Processed 51100000 reads so far
2011-05-19 22:31:33,021 - INFO - Processed 51200000 reads so far
2011-05-19 22:31:44,786 - INFO - Processed 51300000 reads so far
2011-05-19 22:31:56,645 - INFO - Processed 51400000 reads so far
2011-05-19 22:32:07,595 - INFO - Processed 51500000 reads so far
2011-05-19 22:32:16,680 - INFO - Processed 51600000 reads so far
2011-05-19 22:32:27,130 - INFO - Processed 51700000 reads so far
2011-05-19 22:32:27,396 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:62990036-83010036
2011-05-19 22:32:38,757 - INFO - Processed 51800000 reads so far
2011-05-19 22:32:47,791 - INFO - Processed 51900000 reads so far
2011-05-19 22:32:58,451 - INFO - Processed 52000000 reads so far
2011-05-19 22:33:08,006 - INFO - Processed 52100000 reads so far
2011-05-19 22:33:18,851 - INFO - Processed 52200000 reads so far
2011-05-19 22:33:29,852 - INFO - Processed 52300000 reads so far
2011-05-19 22:33:38,167 - INFO - Processed 52400000 reads so far
2011-05-19 22:33:51,583 - INFO - Processed 52500000 reads so far
2011-05-19 22:34:01,542 - INFO - Processed 52600000 reads so far
2011-05-19 22:34:13,001 - INFO - Processed 52700000 reads so far
2011-05-19 22:34:22,676 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:82990065-103010065
2011-05-19 22:34:23,950 - INFO - Processed 52800000 reads so far
2011-05-19 22:34:33,668 - INFO - Processed 52900000 reads so far
2011-05-19 22:34:44,107 - INFO - Processed 53000000 reads so far
2011-05-19 22:34:55,215 - INFO - Processed 53100000 reads so far
2011-05-19 22:35:06,635 - INFO - Processed 53200000 reads so far
2011-05-19 22:35:06,766 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:2990019-23010019
2011-05-19 22:35:18,493 - INFO - Processed 53300000 reads so far
2011-05-19 22:35:32,599 - INFO - Processed 53400000 reads so far
2011-05-19 22:35:44,092 - INFO - Processed 53500000 reads so far
2011-05-19 22:35:53,301 - INFO - Processed 53600000 reads so far
2011-05-19 22:36:05,944 - INFO - Processed 53700000 reads so far
2011-05-19 22:36:17,924 - INFO - Processed 53800000 reads so far
2011-05-19 22:36:29,072 - INFO - Processed 53900000 reads so far
2011-05-19 22:36:40,773 - INFO - Processed 54000000 reads so far
2011-05-19 22:36:50,598 - INFO - Processed 54100000 reads so far
2011-05-19 22:37:00,818 - INFO - Processed 54200000 reads so far
2011-05-19 22:37:05,139 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:22990043-43010043
2011-05-19 22:37:08,826 - INFO - Processed 54300000 reads so far
2011-05-19 22:37:19,777 - INFO - Processed 54400000 reads so far
2011-05-19 22:37:30,415 - INFO - Processed 54500000 reads so far
2011-05-19 22:37:40,602 - INFO - Processed 54600000 reads so far
2011-05-19 22:37:50,887 - INFO - Processed 54700000 reads so far
2011-05-19 22:38:02,253 - INFO - Processed 54800000 reads so far
2011-05-19 22:38:14,839 - INFO - Processed 54900000 reads so far
2011-05-19 22:38:22,065 - INFO - Processed 55000000 reads so far
2011-05-19 22:38:30,064 - INFO - Processed 55100000 reads so far
2011-05-19 22:38:37,474 - INFO - Processed 55200000 reads so far
2011-05-19 22:38:45,112 - INFO - Processed 55300000 reads so far
2011-05-19 22:38:50,121 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:42990089-63010089
2011-05-19 22:38:56,922 - INFO - Processed 55400000 reads so far
2011-05-19 22:39:07,503 - INFO - Processed 55500000 reads so far
2011-05-19 22:39:17,248 - INFO - Processed 55600000 reads so far
2011-05-19 22:39:29,580 - INFO - Processed 55700000 reads so far
2011-05-19 22:39:41,600 - INFO - Processed 55800000 reads so far
2011-05-19 22:39:52,691 - INFO - Processed 55900000 reads so far
2011-05-19 22:40:05,407 - INFO - Processed 56000000 reads so far
2011-05-19 22:40:17,828 - INFO - Processed 56100000 reads so far
2011-05-19 22:40:28,654 - INFO - Processed 56200000 reads so far
2011-05-19 22:40:39,392 - INFO - Processed 56300000 reads so far
2011-05-19 22:40:43,140 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:2989968-23009968
2011-05-19 22:40:50,916 - INFO - Processed 56400000 reads so far
2011-05-19 22:41:00,338 - INFO - Processed 56500000 reads so far
2011-05-19 22:41:09,939 - INFO - Processed 56600000 reads so far
2011-05-19 22:41:18,850 - INFO - Processed 56700000 reads so far
2011-05-19 22:41:29,376 - INFO - Processed 56800000 reads so far
2011-05-19 22:41:40,146 - INFO - Processed 56900000 reads so far
2011-05-19 22:41:52,083 - INFO - Processed 57000000 reads so far
2011-05-19 22:42:02,085 - INFO - Processed 57100000 reads so far
2011-05-19 22:42:10,439 - INFO - Processed 57200000 reads so far
2011-05-19 22:42:21,693 - INFO - Processed 57300000 reads so far
2011-05-19 22:42:30,483 - INFO - Processed 57400000 reads so far
2011-05-19 22:42:30,564 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:22990076-43010076
2011-05-19 22:42:38,199 - INFO - Processed 57500000 reads so far
2011-05-19 22:42:49,300 - INFO - Processed 57600000 reads so far
2011-05-19 22:42:57,485 - INFO - Processed 57700000 reads so far
2011-05-19 22:43:07,261 - INFO - Processed 57800000 reads so far
2011-05-19 22:43:15,913 - INFO - Processed 57900000 reads so far
2011-05-19 22:43:24,775 - INFO - Processed 58000000 reads so far
2011-05-19 22:43:32,666 - INFO - Processed 58100000 reads so far
2011-05-19 22:43:42,953 - INFO - Processed 58200000 reads so far
2011-05-19 22:43:52,510 - INFO - Processed 58300000 reads so far
2011-05-19 22:44:04,846 - INFO - Processed 58400000 reads so far
2011-05-19 22:44:12,346 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:42990079-63010079
2011-05-19 22:44:14,829 - INFO - Processed 58500000 reads so far
2011-05-19 22:44:23,813 - INFO - Processed 58600000 reads so far
2011-05-19 22:44:34,138 - INFO - Processed 58700000 reads so far
2011-05-19 22:44:43,325 - INFO - Processed 58800000 reads so far
2011-05-19 22:44:55,547 - INFO - Processed 58900000 reads so far
2011-05-19 22:45:14,477 - INFO - Processed 59000000 reads so far
2011-05-19 22:45:23,601 - INFO - Processed 59100000 reads so far
2011-05-19 22:45:34,130 - INFO - Processed 59200000 reads so far
2011-05-19 22:45:44,805 - INFO - Processed 59300000 reads so far
2011-05-19 22:45:55,338 - INFO - Processed 59400000 reads so far
2011-05-19 22:46:03,917 - INFO - Processed 59500000 reads so far
2011-05-19 22:46:11,223 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:62990091-83010091
2011-05-19 22:46:15,274 - INFO - Processed 59600000 reads so far
2011-05-19 22:46:26,092 - INFO - Processed 59700000 reads so far
2011-05-19 22:46:35,077 - INFO - Processed 59800000 reads so far
2011-05-19 22:46:45,082 - INFO - Processed 59900000 reads so far
2011-05-19 22:46:54,723 - INFO - Processed 60000000 reads so far
2011-05-19 22:47:04,371 - INFO - Processed 60100000 reads so far
2011-05-19 22:47:12,752 - INFO - Processed 60200000 reads so far
2011-05-19 22:47:20,935 - INFO - Processed 60300000 reads so far
2011-05-19 22:47:30,193 - INFO - Processed 60400000 reads so far
2011-05-19 22:47:37,594 - INFO - Processed 60500000 reads so far
2011-05-19 22:47:45,859 - INFO - Processed 60600000 reads so far
2011-05-19 22:47:48,177 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:82990143-103010143
2011-05-19 22:47:55,178 - INFO - Processed 60700000 reads so far
2011-05-19 22:48:07,605 - INFO - Processed 60800000 reads so far
2011-05-19 22:48:19,853 - INFO - Processed 60900000 reads so far
2011-05-19 22:48:29,941 - INFO - Processed 61000000 reads so far
2011-05-19 22:48:40,976 - INFO - Processed 61100000 reads so far
2011-05-19 22:48:51,729 - INFO - Processed 61200000 reads so far
2011-05-19 22:49:03,188 - INFO - Processed 61300000 reads so far
2011-05-19 22:49:14,620 - INFO - Processed 61400000 reads so far
2011-05-19 22:49:28,917 - INFO - Processed 61500000 reads so far
2011-05-19 22:49:40,264 - INFO - Processed 61600000 reads so far
2011-05-19 22:49:51,483 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:102990145-123010145
2011-05-19 22:49:54,315 - INFO - Processed 61700000 reads so far
2011-05-19 22:50:05,589 - INFO - Processed 61800000 reads so far
2011-05-19 22:50:16,794 - INFO - Processed 61900000 reads so far
2011-05-19 22:50:29,539 - INFO - Processed 62000000 reads so far
2011-05-19 22:50:40,728 - INFO - Processed 62100000 reads so far
2011-05-19 22:50:51,913 - INFO - Processed 62200000 reads so far
2011-05-19 22:51:03,677 - INFO - Processed 62300000 reads so far
2011-05-19 22:51:14,961 - INFO - Processed 62400000 reads so far
2011-05-19 22:51:26,118 - INFO - Processed 62500000 reads so far
2011-05-19 22:51:37,400 - INFO - Processed 62600000 reads so far
2011-05-19 22:51:49,356 - INFO - Processed 62700000 reads so far
2011-05-19 22:51:53,119 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:122990162-143010162
2011-05-19 22:52:00,460 - INFO - Processed 62800000 reads so far
2011-05-19 22:52:12,788 - INFO - Processed 62900000 reads so far
2011-05-19 22:52:23,869 - INFO - Processed 63000000 reads so far
2011-05-19 22:52:35,043 - INFO - Processed 63100000 reads so far
2011-05-19 22:52:46,121 - INFO - Processed 63200000 reads so far
2011-05-19 22:53:00,092 - INFO - Processed 63300000 reads so far
2011-05-19 22:53:12,583 - INFO - Processed 63400000 reads so far
2011-05-19 22:53:24,344 - INFO - Processed 63500000 reads so far
2011-05-19 22:53:35,899 - INFO - Processed 63600000 reads so far
2011-05-19 22:53:47,066 - INFO - Processed 63700000 reads so far
2011-05-19 22:53:58,805 - INFO - Processed 63800000 reads so far
2011-05-19 22:54:01,563 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:142990207-163010207
2011-05-19 22:54:09,643 - INFO - Processed 63900000 reads so far
2011-05-19 22:54:20,843 - INFO - Processed 64000000 reads so far
2011-05-19 22:54:31,603 - INFO - Processed 64100000 reads so far
2011-05-19 22:54:43,161 - INFO - Processed 64200000 reads so far
2011-05-19 22:54:53,111 - INFO - Processed 64300000 reads so far
2011-05-19 22:55:04,404 - INFO - Processed 64400000 reads so far
2011-05-19 22:55:13,607 - INFO - Processed 64500000 reads so far
2011-05-19 22:55:24,705 - INFO - Processed 64600000 reads so far
2011-05-19 22:55:36,052 - INFO - Processed 64700000 reads so far
2011-05-19 22:55:46,561 - INFO - Processed 64800000 reads so far
2011-05-19 22:55:54,581 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:162990227-183010227
2011-05-19 22:55:57,945 - INFO - Processed 64900000 reads so far
2011-05-19 22:56:08,032 - INFO - Processed 65000000 reads so far
2011-05-19 22:56:16,793 - INFO - Processed 65100000 reads so far
2011-05-19 22:56:26,225 - INFO - Processed 65200000 reads so far
2011-05-19 22:56:35,889 - INFO - Processed 65300000 reads so far
2011-05-19 22:56:44,671 - INFO - Processed 65400000 reads so far
2011-05-19 22:56:56,084 - INFO - Processed 65500000 reads so far
2011-05-19 22:57:09,091 - INFO - Processed 65600000 reads so far
2011-05-19 22:57:19,896 - INFO - Processed 65700000 reads so far
2011-05-19 22:57:31,443 - INFO - Processed 65800000 reads so far
2011-05-19 22:57:42,943 - INFO - Processed 65900000 reads so far
2011-05-19 22:57:54,100 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:182990245-203010245
2011-05-19 22:57:54,842 - INFO - Processed 66000000 reads so far
2011-05-19 22:58:07,350 - INFO - Processed 66100000 reads so far
2011-05-19 22:58:18,537 - INFO - Processed 66200000 reads so far
2011-05-19 22:58:29,883 - INFO - Processed 66300000 reads so far
2011-05-19 22:58:41,309 - INFO - Processed 66400000 reads so far
2011-05-19 22:58:52,461 - INFO - Processed 66500000 reads so far
2011-05-19 22:59:03,756 - INFO - Processed 66600000 reads so far
2011-05-19 22:59:16,024 - INFO - Processed 66700000 reads so far
2011-05-19 22:59:23,854 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1_random:0-20010000
2011-05-19 22:59:27,018 - INFO - Processed 66800000 reads so far
2011-05-19 22:59:33,759 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:2990005-23010005
2011-05-19 22:59:35,736 - INFO - Processed 66900000 reads so far
2011-05-19 22:59:45,542 - INFO - Processed 67000000 reads so far
2011-05-19 22:59:56,243 - INFO - Processed 67100000 reads so far
2011-05-19 23:00:05,357 - INFO - Processed 67200000 reads so far
2011-05-19 23:00:16,239 - INFO - Processed 67300000 reads so far
2011-05-19 23:00:24,559 - INFO - Processed 67400000 reads so far
2011-05-19 23:00:35,203 - INFO - Processed 67500000 reads so far
2011-05-19 23:00:44,601 - INFO - Processed 67600000 reads so far
2011-05-19 23:00:55,014 - INFO - Processed 67700000 reads so far
2011-05-19 23:01:02,930 - INFO - Processed 67800000 reads so far
2011-05-19 23:01:12,279 - INFO - Processed 67900000 reads so far
2011-05-19 23:01:20,012 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:22990015-43010015
2011-05-19 23:01:22,348 - INFO - Processed 68000000 reads so far
2011-05-19 23:01:36,403 - INFO - Processed 68100000 reads so far
2011-05-19 23:01:45,698 - INFO - Processed 68200000 reads so far
2011-05-19 23:01:54,379 - INFO - Processed 68300000 reads so far
2011-05-19 23:02:02,868 - INFO - Processed 68400000 reads so far
2011-05-19 23:02:13,823 - INFO - Processed 68500000 reads so far
2011-05-19 23:02:23,090 - INFO - Processed 68600000 reads so far
2011-05-19 23:02:34,367 - INFO - Processed 68700000 reads so far
2011-05-19 23:02:43,102 - INFO - Processed 68800000 reads so far
2011-05-19 23:02:53,680 - INFO - Processed 68900000 reads so far
2011-05-19 23:03:06,923 - INFO - Processed 69000000 reads so far
2011-05-19 23:03:10,839 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:42990055-63010055
2011-05-19 23:03:17,727 - INFO - Processed 69100000 reads so far
2011-05-19 23:03:29,633 - INFO - Processed 69200000 reads so far
2011-05-19 23:03:43,414 - INFO - Processed 69300000 reads so far
2011-05-19 23:03:55,279 - INFO - Processed 69400000 reads so far
2011-05-19 23:04:08,286 - INFO - Processed 69500000 reads so far
2011-05-19 23:04:20,045 - INFO - Processed 69600000 reads so far
2011-05-19 23:04:31,398 - INFO - Processed 69700000 reads so far
2011-05-19 23:04:41,092 - INFO - Processed 69800000 reads so far
2011-05-19 23:04:51,584 - INFO - Processed 69900000 reads so far
2011-05-19 23:05:00,975 - INFO - Processed 70000000 reads so far
2011-05-19 23:05:10,996 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:62990058-83010058
2011-05-19 23:05:12,282 - INFO - Processed 70100000 reads so far
2011-05-19 23:05:22,081 - INFO - Processed 70200000 reads so far
2011-05-19 23:05:32,798 - INFO - Processed 70300000 reads so far
2011-05-19 23:05:42,065 - INFO - Processed 70400000 reads so far
2011-05-19 23:05:50,474 - INFO - Processed 70500000 reads so far
2011-05-19 23:06:01,377 - INFO - Processed 70600000 reads so far
2011-05-19 23:06:11,334 - INFO - Processed 70700000 reads so far
2011-05-19 23:06:25,513 - INFO - Processed 70800000 reads so far
2011-05-19 23:06:37,434 - INFO - Processed 70900000 reads so far
2011-05-19 23:06:48,656 - INFO - Processed 71000000 reads so far
2011-05-19 23:07:00,366 - INFO - Processed 71100000 reads so far
2011-05-19 23:07:06,671 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:82990135-103010135
2011-05-19 23:07:11,838 - INFO - Processed 71200000 reads so far
2011-05-19 23:07:22,930 - INFO - Processed 71300000 reads so far
2011-05-19 23:07:32,985 - INFO - Processed 71400000 reads so far
2011-05-19 23:07:41,918 - INFO - Processed 71500000 reads so far
2011-05-19 23:07:50,868 - INFO - Processed 71600000 reads so far
2011-05-19 23:08:01,621 - INFO - Processed 71700000 reads so far
2011-05-19 23:08:12,654 - INFO - Processed 71800000 reads so far
2011-05-19 23:08:23,250 - INFO - Processed 71900000 reads so far
2011-05-19 23:08:33,424 - INFO - Processed 72000000 reads so far
2011-05-19 23:08:42,928 - INFO - Processed 72100000 reads so far
2011-05-19 23:08:50,734 - INFO - Processed 72200000 reads so far
2011-05-19 23:08:59,443 - INFO - Processed 72300000 reads so far
2011-05-19 23:09:07,045 - INFO - Processed 72400000 reads so far
2011-05-19 23:09:15,244 - INFO - Processed 72500000 reads so far
2011-05-19 23:09:24,711 - INFO - Processed 72600000 reads so far
2011-05-19 23:09:33,260 - INFO - Processed 72700000 reads so far
2011-05-19 23:09:40,874 - INFO - Processed 72800000 reads so far
2011-05-19 23:09:48,460 - INFO - Processed 72900000 reads so far
2011-05-19 23:09:59,487 - INFO - Processed 73000000 reads so far
2011-05-19 23:10:07,579 - INFO - Processed 73100000 reads so far
2011-05-19 23:10:16,593 - INFO - Processed 73200000 reads so far
2011-05-19 23:10:25,506 - INFO - Processed 73300000 reads so far
2011-05-19 23:10:34,627 - INFO - Processed 73400000 reads so far
2011-05-19 23:10:45,104 - INFO - Processed 73500000 reads so far
2011-05-19 23:10:53,706 - INFO - Processed 73600000 reads so far
2011-05-19 23:11:01,679 - INFO - Processed 73700000 reads so far
2011-05-19 23:11:08,563 - INFO - Processed 73800000 reads so far
2011-05-19 23:11:18,652 - INFO - Processed 73900000 reads so far
2011-05-19 23:11:26,595 - INFO - Processed 74000000 reads so far
2011-05-19 23:11:36,481 - INFO - Processed 74100000 reads so far
2011-05-19 23:11:45,806 - INFO - Processed 74200000 reads so far
2011-05-19 23:11:54,411 - INFO - Processed 74300000 reads so far
2011-05-19 23:12:02,618 - INFO - Processed 74400000 reads so far
2011-05-19 23:12:10,648 - INFO - Processed 74500000 reads so far
2011-05-19 23:12:18,576 - INFO - Processed 74600000 reads so far
2011-05-19 23:12:27,031 - INFO - Processed 74700000 reads so far
2011-05-19 23:12:35,688 - INFO - Processed 74800000 reads so far
2011-05-19 23:12:45,377 - INFO - Processed 74900000 reads so far
2011-05-19 23:12:53,807 - INFO - Processed 75000000 reads so far
2011-05-19 23:13:02,372 - INFO - Processed 75100000 reads so far
2011-05-19 23:13:09,954 - INFO - Processed 75200000 reads so far
2011-05-19 23:13:18,088 - INFO - Processed 75300000 reads so far
2011-05-19 23:13:25,241 - INFO - Processed 75400000 reads so far
2011-05-19 23:13:32,759 - INFO - Processed 75500000 reads so far
2011-05-19 23:13:41,037 - INFO - Processed 75600000 reads so far
2011-05-19 23:13:49,664 - INFO - Processed 75700000 reads so far
2011-05-19 23:13:58,130 - INFO - Processed 75800000 reads so far
2011-05-19 23:14:07,954 - INFO - Processed 75900000 reads so far
2011-05-19 23:14:17,238 - INFO - Processed 76000000 reads so far
2011-05-19 23:14:24,086 - INFO - Processed 76100000 reads so far
2011-05-19 23:14:31,966 - INFO - Processed 76200000 reads so far
2011-05-19 23:14:39,653 - INFO - Processed 76300000 reads so far
2011-05-19 23:14:47,629 - INFO - Processed 76400000 reads so far
2011-05-19 23:14:55,372 - INFO - Processed 76500000 reads so far
2011-05-19 23:15:02,742 - INFO - Processed 76600000 reads so far
2011-05-19 23:15:10,416 - INFO - Processed 76700000 reads so far
2011-05-19 23:15:18,299 - INFO - Processed 76800000 reads so far
2011-05-19 23:15:26,138 - INFO - Processed 76900000 reads so far
2011-05-19 23:15:32,766 - INFO - Processed 77000000 reads so far
2011-05-19 23:15:43,251 - INFO - Processed 77100000 reads so far
2011-05-19 23:15:51,263 - INFO - Processed 77200000 reads so far
2011-05-19 23:16:00,091 - INFO - Processed 77300000 reads so far
2011-05-19 23:16:08,580 - INFO - Processed 77400000 reads so far
2011-05-19 23:16:17,411 - INFO - Processed 77500000 reads so far
2011-05-19 23:16:31,894 - INFO - Processed 77600000 reads so far
2011-05-19 23:16:41,343 - INFO - Processed 77700000 reads so far
2011-05-19 23:16:52,235 - INFO - Processed 77800000 reads so far
2011-05-19 23:17:03,799 - INFO - Processed 77900000 reads so far
2011-05-19 23:17:14,590 - INFO - Processed 78000000 reads so far
2011-05-19 23:17:25,204 - INFO - Processed 78100000 reads so far
2011-05-19 23:17:36,849 - INFO - Processed 78200000 reads so far
2011-05-19 23:17:46,470 - INFO - Processed 78300000 reads so far
2011-05-19 23:17:57,125 - INFO - Processed 78400000 reads so far
2011-05-19 23:18:06,591 - INFO - Processed 78500000 reads so far
2011-05-19 23:18:16,915 - INFO - Processed 78600000 reads so far
2011-05-19 23:18:26,213 - INFO - Processed 78700000 reads so far
2011-05-19 23:18:35,525 - INFO - Processed 78800000 reads so far
2011-05-19 23:18:58,702 - INFO - Processed 78900000 reads so far
2011-05-19 23:19:08,707 - INFO - Processed 79000000 reads so far
2011-05-19 23:19:17,752 - INFO - Processed 79100000 reads so far
2011-05-19 23:19:26,778 - INFO - Processed 79200000 reads so far
2011-05-19 23:19:36,263 - INFO - Processed 79300000 reads so far
2011-05-19 23:19:45,881 - INFO - Processed 79400000 reads so far
2011-05-19 23:19:57,602 - INFO - Processed 79500000 reads so far
2011-05-19 23:20:06,887 - INFO - Processed 79600000 reads so far
2011-05-19 23:20:17,344 - INFO - Processed 79700000 reads so far
2011-05-19 23:20:26,546 - INFO - Processed 79800000 reads so far
2011-05-19 23:20:35,644 - INFO - Processed 79900000 reads so far
2011-05-19 23:20:44,657 - INFO - Processed 80000000 reads so far
2011-05-19 23:20:53,839 - INFO - Processed 80100000 reads so far
2011-05-19 23:21:05,054 - INFO - Processed 80200000 reads so far
2011-05-19 23:21:15,443 - INFO - Processed 80300000 reads so far
2011-05-19 23:21:23,155 - INFO - Processed 80400000 reads so far
2011-05-19 23:21:32,613 - INFO - Processed 80500000 reads so far
2011-05-19 23:21:41,934 - INFO - Processed 80600000 reads so far
2011-05-19 23:21:51,310 - INFO - Processed 80700000 reads so far
2011-05-19 23:22:00,599 - INFO - Processed 80800000 reads so far
2011-05-19 23:22:10,069 - INFO - Processed 80900000 reads so far
2011-05-19 23:22:20,343 - INFO - Processed 81000000 reads so far
2011-05-19 23:22:28,026 - INFO - Processed 81100000 reads so far
2011-05-19 23:22:33,937 - INFO - Processed 81200000 reads so far
2011-05-19 23:22:43,247 - INFO - Processed 81300000 reads so far
2011-05-19 23:22:52,692 - INFO - Processed 81400000 reads so far
2011-05-19 23:23:02,047 - INFO - Processed 81500000 reads so far
2011-05-19 23:23:12,457 - INFO - Processed 81600000 reads so far
2011-05-19 23:23:21,681 - INFO - Processed 81700000 reads so far
2011-05-19 23:23:31,362 - INFO - Processed 81800000 reads so far
2011-05-19 23:23:40,946 - INFO - Processed 81900000 reads so far
2011-05-19 23:23:50,549 - INFO - Processed 82000000 reads so far
2011-05-19 23:24:00,167 - INFO - Processed 82100000 reads so far
2011-05-19 23:24:09,709 - INFO - Processed 82200000 reads so far
2011-05-19 23:24:18,596 - INFO - Processed 82300000 reads so far
2011-05-19 23:24:29,594 - INFO - Processed 82400000 reads so far
2011-05-19 23:24:40,663 - INFO - Processed 82500000 reads so far
2011-05-19 23:24:45,123 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:102990153-123010153
2011-05-19 23:24:49,976 - INFO - Processed 82600000 reads so far
2011-05-19 23:25:00,929 - INFO - Processed 82700000 reads so far
2011-05-19 23:25:10,078 - INFO - Processed 82800000 reads so far
2011-05-19 23:25:28,693 - INFO - Processed 82900000 reads so far
2011-05-19 23:25:40,470 - INFO - Processed 83000000 reads so far
2011-05-19 23:25:49,510 - INFO - Processed 83100000 reads so far
2011-05-19 23:25:58,950 - INFO - Processed 83200000 reads so far
2011-05-19 23:26:07,905 - INFO - Processed 83300000 reads so far
2011-05-19 23:26:16,772 - INFO - Processed 83400000 reads so far
2011-05-19 23:26:27,884 - INFO - Processed 83500000 reads so far
2011-05-19 23:26:39,195 - INFO - Processed 83600000 reads so far
2011-05-19 23:26:41,074 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:122990205-143010205
2011-05-19 23:26:48,189 - INFO - Processed 83700000 reads so far
2011-05-19 23:26:58,076 - INFO - Processed 83800000 reads so far
2011-05-19 23:27:07,666 - INFO - Processed 83900000 reads so far
2011-05-19 23:27:18,085 - INFO - Processed 84000000 reads so far
2011-05-19 23:27:28,716 - INFO - Processed 84100000 reads so far
2011-05-19 23:27:37,082 - INFO - Processed 84200000 reads so far
2011-05-19 23:27:48,110 - INFO - Processed 84300000 reads so far
2011-05-19 23:27:59,674 - INFO - Processed 84400000 reads so far
2011-05-19 23:28:08,497 - INFO - Processed 84500000 reads so far
2011-05-19 23:28:17,968 - INFO - Processed 84600000 reads so far
2011-05-19 23:28:28,190 - INFO - Processed 84700000 reads so far
2011-05-19 23:28:29,925 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:142990206-163010206
2011-05-19 23:28:38,609 - INFO - Processed 84800000 reads so far
2011-05-19 23:28:49,247 - INFO - Processed 84900000 reads so far
2011-05-19 23:28:59,981 - INFO - Processed 85000000 reads so far
2011-05-19 23:29:10,411 - INFO - Processed 85100000 reads so far
2011-05-19 23:29:21,561 - INFO - Processed 85200000 reads so far
2011-05-19 23:29:32,919 - INFO - Processed 85300000 reads so far
2011-05-19 23:29:43,712 - INFO - Processed 85400000 reads so far
2011-05-19 23:29:54,762 - INFO - Processed 85500000 reads so far
2011-05-19 23:30:05,495 - INFO - Processed 85600000 reads so far
2011-05-19 23:30:14,937 - INFO - Processed 85700000 reads so far
2011-05-19 23:30:26,363 - INFO - Processed 85800000 reads so far
2011-05-19 23:30:27,752 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:162990209-183010209
2011-05-19 23:30:40,445 - INFO - Processed 85900000 reads so far
2011-05-19 23:30:51,811 - INFO - Processed 86000000 reads so far
2011-05-19 23:31:04,146 - INFO - Processed 86100000 reads so far
2011-05-19 23:31:14,034 - INFO - Processed 86200000 reads so far
2011-05-19 23:31:24,097 - INFO - Processed 86300000 reads so far
2011-05-19 23:31:35,205 - INFO - Processed 86400000 reads so far
2011-05-19 23:31:44,704 - INFO - Processed 86500000 reads so far
2011-05-19 23:31:57,240 - INFO - Processed 86600000 reads so far
2011-05-19 23:32:07,342 - INFO - Processed 86700000 reads so far
2011-05-19 23:32:17,878 - INFO - Processed 86800000 reads so far
2011-05-19 23:32:27,584 - INFO - Processed 86900000 reads so far
2011-05-19 23:32:33,312 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:2989994-23009994
2011-05-19 23:32:38,464 - INFO - Processed 87000000 reads so far
2011-05-19 23:32:49,476 - INFO - Processed 87100000 reads so far
2011-05-19 23:33:01,061 - INFO - Processed 87200000 reads so far
2011-05-19 23:33:11,493 - INFO - Processed 87300000 reads so far
2011-05-19 23:33:20,857 - INFO - Processed 87400000 reads so far
2011-05-19 23:33:34,046 - INFO - Processed 87500000 reads so far
2011-05-19 23:33:45,338 - INFO - Processed 87600000 reads so far
2011-05-19 23:33:55,327 - INFO - Processed 87700000 reads so far
2011-05-19 23:34:06,435 - INFO - Processed 87800000 reads so far
2011-05-19 23:34:16,596 - INFO - Processed 87900000 reads so far
2011-05-19 23:34:27,421 - INFO - Processed 88000000 reads so far
2011-05-19 23:34:28,423 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:22990001-43010001
2011-05-19 23:34:37,025 - INFO - Processed 88100000 reads so far
2011-05-19 23:34:48,078 - INFO - Processed 88200000 reads so far
2011-05-19 23:34:56,769 - INFO - Processed 88300000 reads so far
2011-05-19 23:35:06,145 - INFO - Processed 88400000 reads so far
2011-05-19 23:35:13,899 - INFO - Processed 88500000 reads so far
2011-05-19 23:35:22,904 - INFO - Processed 88600000 reads so far
2011-05-19 23:35:32,454 - INFO - Processed 88700000 reads so far
2011-05-19 23:35:41,840 - INFO - Processed 88800000 reads so far
2011-05-19 23:35:52,359 - INFO - Processed 88900000 reads so far
2011-05-19 23:36:02,282 - INFO - Processed 89000000 reads so far
2011-05-19 23:36:11,484 - INFO - Processed 89100000 reads so far
2011-05-19 23:36:11,698 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:42990006-63010006
2011-05-19 23:36:21,380 - INFO - Processed 89200000 reads so far
2011-05-19 23:36:32,527 - INFO - Processed 89300000 reads so far
2011-05-19 23:36:43,485 - INFO - Processed 89400000 reads so far
2011-05-19 23:36:55,702 - INFO - Processed 89500000 reads so far
2011-05-19 23:37:07,763 - INFO - Processed 89600000 reads so far
2011-05-19 23:37:19,162 - INFO - Processed 89700000 reads so far
2011-05-19 23:37:29,560 - INFO - Processed 89800000 reads so far
2011-05-19 23:37:40,896 - INFO - Processed 89900000 reads so far
2011-05-19 23:37:52,034 - INFO - Processed 90000000 reads so far
2011-05-19 23:38:00,741 - INFO - Processed 90100000 reads so far
2011-05-19 23:38:07,191 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:62990043-83010043
2011-05-19 23:38:16,139 - INFO - Processed 90200000 reads so far
2011-05-19 23:38:23,148 - INFO - Processed 90300000 reads so far
2011-05-19 23:38:31,973 - INFO - Processed 90400000 reads so far
2011-05-19 23:38:43,461 - INFO - Processed 90500000 reads so far
2011-05-19 23:39:13,255 - INFO - Processed 90600000 reads so far
2011-05-19 23:39:40,157 - INFO - Processed 90700000 reads so far
2011-05-19 23:39:48,887 - INFO - Processed 90800000 reads so far
2011-05-19 23:39:56,014 - INFO - Processed 90900000 reads so far
2011-05-19 23:40:04,949 - INFO - Processed 91000000 reads so far
2011-05-19 23:40:13,054 - INFO - Processed 91100000 reads so far
2011-05-19 23:40:20,250 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:82990045-103010045
2011-05-19 23:40:22,133 - INFO - Processed 91200000 reads so far
2011-05-19 23:40:31,493 - INFO - Processed 91300000 reads so far
2011-05-19 23:40:44,164 - INFO - Processed 91400000 reads so far
2011-05-19 23:40:56,613 - INFO - Processed 91500000 reads so far
2011-05-19 23:41:09,269 - INFO - Processed 91600000 reads so far
2011-05-19 23:41:21,900 - INFO - Processed 91700000 reads so far
2011-05-19 23:41:32,989 - INFO - Processed 91800000 reads so far
2011-05-19 23:41:44,357 - INFO - Processed 91900000 reads so far
2011-05-19 23:41:58,291 - INFO - Processed 92000000 reads so far
2011-05-19 23:42:09,542 - INFO - Processed 92100000 reads so far
2011-05-19 23:42:20,670 - INFO - Processed 92200000 reads so far
2011-05-19 23:42:29,714 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:102990092-123010092
2011-05-19 23:42:32,736 - INFO - Processed 92300000 reads so far
2011-05-19 23:42:44,101 - INFO - Processed 92400000 reads so far
2011-05-19 23:42:55,150 - INFO - Processed 92500000 reads so far
2011-05-19 23:43:07,725 - INFO - Processed 92600000 reads so far
2011-05-19 23:43:18,943 - INFO - Processed 92700000 reads so far
2011-05-19 23:43:30,153 - INFO - Processed 92800000 reads so far
2011-05-19 23:43:44,363 - INFO - Processed 92900000 reads so far
2011-05-19 23:43:51,549 - INFO - Processed 93000000 reads so far
2011-05-19 23:44:02,119 - INFO - Processed 93100000 reads so far
2011-05-19 23:44:15,352 - INFO - Processed 93200000 reads so far
2011-05-19 23:44:24,148 - INFO - Processed 93300000 reads so far
2011-05-19 23:44:28,386 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:122990102-143010102
2011-05-19 23:44:35,946 - INFO - Processed 93400000 reads so far
2011-05-19 23:44:49,565 - INFO - Processed 93500000 reads so far
2011-05-19 23:44:59,687 - INFO - Processed 93600000 reads so far
2011-05-19 23:45:10,279 - INFO - Processed 93700000 reads so far
2011-05-19 23:45:20,623 - INFO - Processed 93800000 reads so far
2011-05-19 23:45:31,664 - INFO - Processed 93900000 reads so far
2011-05-19 23:45:42,347 - INFO - Processed 94000000 reads so far
2011-05-19 23:45:53,598 - INFO - Processed 94100000 reads so far
2011-05-19 23:46:06,298 - INFO - Processed 94200000 reads so far
2011-05-19 23:46:17,861 - INFO - Processed 94300000 reads so far
2011-05-19 23:46:29,585 - INFO - Processed 94400000 reads so far
2011-05-19 23:46:31,619 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:142990125-163010125
2011-05-19 23:46:44,993 - INFO - Processed 94500000 reads so far
2011-05-19 23:46:57,378 - INFO - Processed 94600000 reads so far
2011-05-19 23:47:10,699 - INFO - Processed 94700000 reads so far
2011-05-19 23:47:21,884 - INFO - Processed 94800000 reads so far
2011-05-19 23:47:33,154 - INFO - Processed 94900000 reads so far
2011-05-19 23:47:44,879 - INFO - Processed 95000000 reads so far
2011-05-19 23:47:57,284 - INFO - Processed 95100000 reads so far
2011-05-19 23:48:08,725 - INFO - Processed 95200000 reads so far
2011-05-19 23:48:41,541 - INFO - Processed 95300000 reads so far
2011-05-19 23:48:45,575 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3_random:0-20010091
2011-05-19 23:48:45,784 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:2989983-23009983
2011-05-19 23:48:54,441 - INFO - Processed 95400000 reads so far
2011-05-19 23:49:05,366 - INFO - Processed 95500000 reads so far
2011-05-19 23:49:13,981 - INFO - Processed 95600000 reads so far
2011-05-19 23:49:26,446 - INFO - Processed 95700000 reads so far
2011-05-19 23:49:36,329 - INFO - Processed 95800000 reads so far
2011-05-19 23:49:46,306 - INFO - Processed 95900000 reads so far
2011-05-19 23:49:55,325 - INFO - Processed 96000000 reads so far
2011-05-19 23:50:07,006 - INFO - Processed 96100000 reads so far
2011-05-19 23:50:15,581 - INFO - Processed 96200000 reads so far
2011-05-19 23:50:25,424 - INFO - Processed 96300000 reads so far
2011-05-19 23:50:33,970 - INFO - Processed 96400000 reads so far
2011-05-19 23:50:37,735 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:22989991-43009991
2011-05-19 23:50:43,167 - INFO - Processed 96500000 reads so far
2011-05-19 23:50:54,910 - INFO - Processed 96600000 reads so far
2011-05-19 23:51:06,005 - INFO - Processed 96700000 reads so far
2011-05-19 23:51:18,792 - INFO - Processed 96800000 reads so far
2011-05-19 23:51:29,358 - INFO - Processed 96900000 reads so far
2011-05-19 23:51:39,335 - INFO - Processed 97000000 reads so far
2011-05-19 23:51:52,613 - INFO - Processed 97100000 reads so far
2011-05-19 23:52:05,306 - INFO - Processed 97200000 reads so far
2011-05-19 23:52:16,636 - INFO - Processed 97300000 reads so far
2011-05-19 23:52:27,854 - INFO - Processed 97400000 reads so far
2011-05-19 23:52:33,567 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:42989993-63009993
2011-05-19 23:52:37,960 - INFO - Processed 97500000 reads so far
2011-05-19 23:52:50,371 - INFO - Processed 97600000 reads so far
2011-05-19 23:53:02,077 - INFO - Processed 97700000 reads so far
2011-05-19 23:53:11,804 - INFO - Processed 97800000 reads so far
2011-05-19 23:53:22,788 - INFO - Processed 97900000 reads so far
2011-05-19 23:53:32,866 - INFO - Processed 98000000 reads so far
2011-05-19 23:53:42,931 - INFO - Processed 98100000 reads so far
2011-05-19 23:53:55,106 - INFO - Processed 98200000 reads so far
2011-05-19 23:54:04,253 - INFO - Processed 98300000 reads so far
2011-05-19 23:54:12,479 - INFO - Processed 98400000 reads so far
2011-05-19 23:54:21,557 - INFO - Processed 98500000 reads so far
2011-05-19 23:54:27,992 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:62989999-83009999
2011-05-19 23:54:33,221 - INFO - Processed 98600000 reads so far
2011-05-19 23:54:45,812 - INFO - Processed 98700000 reads so far
2011-05-19 23:54:54,700 - INFO - Processed 98800000 reads so far
2011-05-19 23:55:05,010 - INFO - Processed 98900000 reads so far
2011-05-19 23:55:14,477 - INFO - Processed 99000000 reads so far
2011-05-19 23:55:23,910 - INFO - Processed 99100000 reads so far
2011-05-19 23:55:55,671 - INFO - Processed 99200000 reads so far
2011-05-19 23:56:05,738 - INFO - Processed 99300000 reads so far
2011-05-19 23:56:14,478 - INFO - Processed 99400000 reads so far
2011-05-19 23:56:24,351 - INFO - Processed 99500000 reads so far
2011-05-19 23:56:34,703 - INFO - Processed 99600000 reads so far
2011-05-19 23:56:36,372 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:82990017-103010017
2011-05-19 23:56:45,244 - INFO - Processed 99700000 reads so far
2011-05-19 23:56:56,595 - INFO - Processed 99800000 reads so far
2011-05-19 23:57:08,989 - INFO - Processed 99900000 reads so far
2011-05-19 23:57:19,923 - INFO - Processed 100000000 reads so far
2011-05-19 23:57:33,490 - INFO - Processed 100100000 reads so far
2011-05-19 23:57:41,932 - INFO - Processed 100200000 reads so far
2011-05-19 23:57:51,615 - INFO - Processed 100300000 reads so far
2011-05-19 23:58:02,810 - INFO - Processed 100400000 reads so far
2011-05-19 23:58:15,248 - INFO - Processed 100500000 reads so far
2011-05-19 23:58:26,773 - INFO - Processed 100600000 reads so far
2011-05-19 23:58:38,070 - INFO - Processed 100700000 reads so far
2011-05-19 23:58:39,293 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:102990021-123010021
2011-05-19 23:58:48,878 - INFO - Processed 100800000 reads so far
2011-05-19 23:58:59,181 - INFO - Processed 100900000 reads so far
2011-05-19 23:59:09,085 - INFO - Processed 101000000 reads so far
2011-05-19 23:59:19,083 - INFO - Processed 101100000 reads so far
2011-05-19 23:59:28,295 - INFO - Processed 101200000 reads so far
2011-05-19 23:59:41,501 - INFO - Processed 101300000 reads so far
2011-05-19 23:59:53,552 - INFO - Processed 101400000 reads so far
2011-05-20 00:00:05,505 - INFO - Processed 101500000 reads so far
2011-05-20 00:00:16,854 - INFO - Processed 101600000 reads so far
2011-05-20 00:00:30,303 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:122990035-143010035
2011-05-20 00:00:31,335 - INFO - Processed 101700000 reads so far
2011-05-20 00:00:42,657 - INFO - Processed 101800000 reads so far
2011-05-20 00:00:53,969 - INFO - Processed 101900000 reads so far
2011-05-20 00:01:04,653 - INFO - Processed 102000000 reads so far
2011-05-20 00:01:15,756 - INFO - Processed 102100000 reads so far
2011-05-20 00:01:28,770 - INFO - Processed 102200000 reads so far
2011-05-20 00:01:41,795 - INFO - Processed 102300000 reads so far
2011-05-20 00:01:52,047 - INFO - Processed 102400000 reads so far
2011-05-20 00:02:03,585 - INFO - Processed 102500000 reads so far
2011-05-20 00:02:14,724 - INFO - Processed 102600000 reads so far
2011-05-20 00:02:26,555 - INFO - Processed 102700000 reads so far
2011-05-20 00:02:30,137 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:142990073-163010073
2011-05-20 00:02:37,526 - INFO - Processed 102800000 reads so far
2011-05-20 00:02:47,839 - INFO - Processed 102900000 reads so far
2011-05-20 00:02:58,219 - INFO - Processed 103000000 reads so far
2011-05-20 00:03:09,231 - INFO - Processed 103100000 reads so far
2011-05-20 00:03:20,703 - INFO - Processed 103200000 reads so far
2011-05-20 00:03:32,981 - INFO - Processed 103300000 reads so far
2011-05-20 00:04:12,863 - INFO - Processed 103400000 reads so far
2011-05-20 00:04:27,680 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4_random:0-20010195
2011-05-20 00:04:28,071 - INFO - Processed 103500000 reads so far
2011-05-20 00:04:28,546 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:2990037-23010037
2011-05-20 00:04:40,822 - INFO - Processed 103600000 reads so far
2011-05-20 00:04:52,062 - INFO - Processed 103700000 reads so far
2011-05-20 00:05:04,645 - INFO - Processed 103800000 reads so far
2011-05-20 00:05:16,887 - INFO - Processed 103900000 reads so far
2011-05-20 00:05:30,541 - INFO - Processed 104000000 reads so far
2011-05-20 00:05:42,383 - INFO - Processed 104100000 reads so far
2011-05-20 00:05:53,552 - INFO - Processed 104200000 reads so far
2011-05-20 00:06:09,711 - INFO - Processed 104300000 reads so far
2011-05-20 00:06:20,499 - INFO - Processed 104400000 reads so far
2011-05-20 00:06:32,408 - INFO - Processed 104500000 reads so far
2011-05-20 00:06:43,088 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:22990514-43010514
2011-05-20 00:06:44,728 - INFO - Processed 104600000 reads so far
2011-05-20 00:06:58,715 - INFO - Processed 104700000 reads so far
2011-05-20 00:07:09,367 - INFO - Processed 104800000 reads so far
2011-05-20 00:07:22,590 - INFO - Processed 104900000 reads so far
2011-05-20 00:07:31,769 - INFO - Processed 105000000 reads so far
2011-05-20 00:07:42,197 - INFO - Processed 105100000 reads so far
2011-05-20 00:07:54,999 - INFO - Processed 105200000 reads so far
2011-05-20 00:08:06,872 - INFO - Processed 105300000 reads so far
2011-05-20 00:08:18,455 - INFO - Processed 105400000 reads so far
2011-05-20 00:08:28,831 - INFO - Processed 105500000 reads so far
2011-05-20 00:08:39,778 - INFO - Processed 105600000 reads so far
2011-05-20 00:08:44,377 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:42990546-63010546
2011-05-20 00:08:49,874 - INFO - Processed 105700000 reads so far
2011-05-20 00:09:03,650 - INFO - Processed 105800000 reads so far
2011-05-20 00:09:13,180 - INFO - Processed 105900000 reads so far
2011-05-20 00:09:23,611 - INFO - Processed 106000000 reads so far
2011-05-20 00:09:32,879 - INFO - Processed 106100000 reads so far
2011-05-20 00:09:44,021 - INFO - Processed 106200000 reads so far
2011-05-20 00:09:55,061 - INFO - Processed 106300000 reads so far
2011-05-20 00:10:06,666 - INFO - Processed 106400000 reads so far
2011-05-20 00:10:26,424 - INFO - Processed 106500000 reads so far
2011-05-20 00:10:46,556 - INFO - Processed 106600000 reads so far
2011-05-20 00:11:03,172 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:62990551-83010551
2011-05-20 00:11:04,147 - INFO - Processed 106700000 reads so far
2011-05-20 00:11:17,656 - INFO - Processed 106800000 reads so far
2011-05-20 00:11:27,047 - INFO - Processed 106900000 reads so far
2011-05-20 00:11:35,621 - INFO - Processed 107000000 reads so far
2011-05-20 00:11:45,079 - INFO - Processed 107100000 reads so far
2011-05-20 00:11:53,814 - INFO - Processed 107200000 reads so far
2011-05-20 00:12:20,430 - INFO - Processed 107300000 reads so far
2011-05-20 00:12:33,581 - INFO - Processed 107400000 reads so far
2011-05-20 00:12:58,925 - INFO - Processed 107500000 reads so far
2011-05-20 00:13:10,813 - INFO - Processed 107600000 reads so far
2011-05-20 00:13:22,082 - INFO - Processed 107700000 reads so far
2011-05-20 00:13:27,891 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:82990581-103010581
2011-05-20 00:13:36,596 - INFO - Processed 107800000 reads so far
2011-05-20 00:13:47,767 - INFO - Processed 107900000 reads so far
2011-05-20 00:13:58,453 - INFO - Processed 108000000 reads so far
2011-05-20 00:14:07,815 - INFO - Processed 108100000 reads so far
2011-05-20 00:14:19,539 - INFO - Processed 108200000 reads so far
2011-05-20 00:14:31,269 - INFO - Processed 108300000 reads so far
2011-05-20 00:14:40,428 - INFO - Processed 108400000 reads so far
2011-05-20 00:14:49,924 - INFO - Processed 108500000 reads so far
2011-05-20 00:15:13,802 - INFO - Processed 108600000 reads so far
2011-05-20 00:15:22,518 - INFO - Processed 108700000 reads so far
2011-05-20 00:15:29,554 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:102990589-123010589
2011-05-20 00:15:33,050 - INFO - Processed 108800000 reads so far
2011-05-20 00:15:42,941 - INFO - Processed 108900000 reads so far
2011-05-20 00:15:54,633 - INFO - Processed 109000000 reads so far
2011-05-20 00:16:06,726 - INFO - Processed 109100000 reads so far
2011-05-20 00:16:17,480 - INFO - Processed 109200000 reads so far
2011-05-20 00:16:30,001 - INFO - Processed 109300000 reads so far
2011-05-20 00:16:43,089 - INFO - Processed 109400000 reads so far
2011-05-20 00:16:53,363 - INFO - Processed 109500000 reads so far
2011-05-20 00:17:03,557 - INFO - Processed 109600000 reads so far
2011-05-20 00:17:13,914 - INFO - Processed 109700000 reads so far
2011-05-20 00:17:23,399 - INFO - Processed 109800000 reads so far
2011-05-20 00:17:27,458 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:122990596-143010596
2011-05-20 00:17:34,023 - INFO - Processed 109900000 reads so far
2011-05-20 00:17:43,020 - INFO - Processed 110000000 reads so far
2011-05-20 00:17:51,989 - INFO - Processed 110100000 reads so far
2011-05-20 00:18:02,120 - INFO - Processed 110200000 reads so far
2011-05-20 00:18:14,970 - INFO - Processed 110300000 reads so far
2011-05-20 00:18:24,241 - INFO - Processed 110400000 reads so far
2011-05-20 00:18:34,541 - INFO - Processed 110500000 reads so far
2011-05-20 00:18:44,462 - INFO - Processed 110600000 reads so far
2011-05-20 00:18:55,803 - INFO - Processed 110700000 reads so far
2011-05-20 00:19:10,596 - INFO - Processed 110800000 reads so far
2011-05-20 00:19:23,647 - INFO - Processed 110900000 reads so far
2011-05-20 00:19:26,326 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:142990614-163010614
2011-05-20 00:19:34,579 - INFO - Processed 111000000 reads so far
2011-05-20 00:19:45,859 - INFO - Processed 111100000 reads so far
2011-05-20 00:19:54,647 - INFO - Processed 111200000 reads so far
2011-05-20 00:20:05,277 - INFO - Processed 111300000 reads so far
2011-05-20 00:20:15,287 - INFO - Processed 111400000 reads so far
2011-05-20 00:20:19,730 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5_random:0-20010018
2011-05-20 00:20:20,410 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:2989988-23009988
2011-05-20 00:20:26,425 - INFO - Processed 111500000 reads so far
2011-05-20 00:20:37,365 - INFO - Processed 111600000 reads so far
2011-05-20 00:20:49,477 - INFO - Processed 111700000 reads so far
2011-05-20 00:21:02,119 - INFO - Processed 111800000 reads so far
2011-05-20 00:21:13,362 - INFO - Processed 111900000 reads so far
2011-05-20 00:21:24,551 - INFO - Processed 112000000 reads so far
2011-05-20 00:21:35,517 - INFO - Processed 112100000 reads so far
2011-05-20 00:21:46,078 - INFO - Processed 112200000 reads so far
2011-05-20 00:21:57,958 - INFO - Processed 112300000 reads so far
2011-05-20 00:22:08,628 - INFO - Processed 112400000 reads so far
2011-05-20 00:22:22,428 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:22990001-43010001
2011-05-20 00:22:23,006 - INFO - Processed 112500000 reads so far
2011-05-20 00:22:34,868 - INFO - Processed 112600000 reads so far
2011-05-20 00:22:46,284 - INFO - Processed 112700000 reads so far
2011-05-20 00:22:59,752 - INFO - Processed 112800000 reads so far
2011-05-20 00:23:12,787 - INFO - Processed 112900000 reads so far
2011-05-20 00:23:28,956 - INFO - Processed 113000000 reads so far
2011-05-20 00:23:41,837 - INFO - Processed 113100000 reads so far
2011-05-20 00:23:52,968 - INFO - Processed 113200000 reads so far
2011-05-20 00:24:04,642 - INFO - Processed 113300000 reads so far
2011-05-20 00:24:15,813 - INFO - Processed 113400000 reads so far
2011-05-20 00:24:27,101 - INFO - Processed 113500000 reads so far
2011-05-20 00:24:38,324 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:42990026-63010026
2011-05-20 00:24:40,170 - INFO - Processed 113600000 reads so far
2011-05-20 00:24:51,982 - INFO - Processed 113700000 reads so far
2011-05-20 00:25:02,641 - INFO - Processed 113800000 reads so far
2011-05-20 00:25:13,295 - INFO - Processed 113900000 reads so far
2011-05-20 00:25:24,441 - INFO - Processed 114000000 reads so far
2011-05-20 00:25:35,506 - INFO - Processed 114100000 reads so far
2011-05-20 00:25:48,150 - INFO - Processed 114200000 reads so far
2011-05-20 00:26:00,437 - INFO - Processed 114300000 reads so far
2011-05-20 00:26:13,806 - INFO - Processed 114400000 reads so far
2011-05-20 00:26:25,953 - INFO - Processed 114500000 reads so far
2011-05-20 00:26:36,744 - INFO - Processed 114600000 reads so far
2011-05-20 00:26:43,725 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:62990035-83010035
2011-05-20 00:26:48,736 - INFO - Processed 114700000 reads so far
2011-05-20 00:27:00,439 - INFO - Processed 114800000 reads so far
2011-05-20 00:27:10,517 - INFO - Processed 114900000 reads so far
2011-05-20 00:27:21,343 - INFO - Processed 115000000 reads so far
2011-05-20 00:27:36,153 - INFO - Processed 115100000 reads so far
2011-05-20 00:27:47,769 - INFO - Processed 115200000 reads so far
2011-05-20 00:28:23,350 - INFO - Processed 115300000 reads so far
2011-05-20 00:28:34,050 - INFO - Processed 115400000 reads so far
2011-05-20 00:28:46,948 - INFO - Processed 115500000 reads so far
2011-05-20 00:28:59,075 - INFO - Processed 115600000 reads so far
2011-05-20 00:29:09,094 - INFO - Processed 115700000 reads so far
2011-05-20 00:29:09,888 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:82990038-103010038
2011-05-20 00:29:20,416 - INFO - Processed 115800000 reads so far
2011-05-20 00:29:29,476 - INFO - Processed 115900000 reads so far
2011-05-20 00:29:41,840 - INFO - Processed 116000000 reads so far
2011-05-20 00:29:52,915 - INFO - Processed 116100000 reads so far
2011-05-20 00:30:01,931 - INFO - Processed 116200000 reads so far
2011-05-20 00:30:12,553 - INFO - Processed 116300000 reads so far
2011-05-20 00:30:21,582 - INFO - Processed 116400000 reads so far
2011-05-20 00:30:30,627 - INFO - Processed 116500000 reads so far
2011-05-20 00:30:39,357 - INFO - Processed 116600000 reads so far
2011-05-20 00:30:48,125 - INFO - Processed 116700000 reads so far
2011-05-20 00:30:59,199 - INFO - Processed 116800000 reads so far
2011-05-20 00:31:00,346 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:102990106-123010106
2011-05-20 00:31:08,918 - INFO - Processed 116900000 reads so far
2011-05-20 00:31:18,615 - INFO - Processed 117000000 reads so far
2011-05-20 00:31:26,085 - INFO - Processed 117100000 reads so far
2011-05-20 00:31:35,753 - INFO - Processed 117200000 reads so far
2011-05-20 00:31:43,808 - INFO - Processed 117300000 reads so far
2011-05-20 00:31:50,770 - INFO - Processed 117400000 reads so far
2011-05-20 00:31:58,528 - INFO - Processed 117500000 reads so far
2011-05-20 00:32:05,281 - INFO - Processed 117600000 reads so far
2011-05-20 00:32:13,885 - INFO - Processed 117700000 reads so far
2011-05-20 00:32:20,938 - INFO - Processed 117800000 reads so far
2011-05-20 00:32:27,409 - INFO - Processed 117900000 reads so far
2011-05-20 00:32:35,054 - INFO - Processed 118000000 reads so far
2011-05-20 00:32:47,254 - INFO - Processed 118100000 reads so far
2011-05-20 00:32:57,724 - INFO - Processed 118200000 reads so far
2011-05-20 00:33:07,433 - INFO - Processed 118300000 reads so far
2011-05-20 00:33:15,715 - INFO - Processed 118400000 reads so far
2011-05-20 00:33:27,801 - INFO - Processed 118500000 reads so far
2011-05-20 00:33:38,820 - INFO - Processed 118600000 reads so far
2011-05-20 00:33:47,468 - INFO - Processed 118700000 reads so far
2011-05-20 00:33:59,935 - INFO - Processed 118800000 reads so far
2011-05-20 00:34:10,639 - INFO - Processed 118900000 reads so far
2011-05-20 00:34:19,152 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:122990126-143010126
2011-05-20 00:34:21,073 - INFO - Processed 119000000 reads so far
2011-05-20 00:34:33,260 - INFO - Processed 119100000 reads so far
2011-05-20 00:34:43,531 - INFO - Processed 119200000 reads so far
2011-05-20 00:34:53,786 - INFO - Processed 119300000 reads so far
2011-05-20 00:35:03,852 - INFO - Processed 119400000 reads so far
2011-05-20 00:35:12,523 - INFO - Processed 119500000 reads so far
2011-05-20 00:35:23,154 - INFO - Processed 119600000 reads so far
2011-05-20 00:35:32,095 - INFO - Processed 119700000 reads so far
2011-05-20 00:35:41,397 - INFO - Processed 119800000 reads so far
2011-05-20 00:35:51,312 - INFO - Processed 119900000 reads so far
2011-05-20 00:36:01,321 - INFO - Processed 120000000 reads so far
2011-05-20 00:36:09,914 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:142990130-163010130
2011-05-20 00:36:11,635 - INFO - Processed 120100000 reads so far
2011-05-20 00:36:21,416 - INFO - Processed 120200000 reads so far
2011-05-20 00:36:31,314 - INFO - Processed 120300000 reads so far
2011-05-20 00:36:40,835 - INFO - Processed 120400000 reads so far
2011-05-20 00:36:45,793 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:2990018-23010018
2011-05-20 00:36:52,241 - INFO - Processed 120500000 reads so far
2011-05-20 00:37:02,209 - INFO - Processed 120600000 reads so far
2011-05-20 00:37:12,413 - INFO - Processed 120700000 reads so far
2011-05-20 00:37:23,045 - INFO - Processed 120800000 reads so far
2011-05-20 00:37:34,133 - INFO - Processed 120900000 reads so far
2011-05-20 00:37:43,863 - INFO - Processed 121000000 reads so far
2011-05-20 00:37:52,519 - INFO - Processed 121100000 reads so far
2011-05-20 00:38:03,438 - INFO - Processed 121200000 reads so far
2011-05-20 00:38:12,359 - INFO - Processed 121300000 reads so far
2011-05-20 00:38:19,100 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:22990099-43010099
2011-05-20 00:38:22,494 - INFO - Processed 121400000 reads so far
2011-05-20 00:38:34,081 - INFO - Processed 121500000 reads so far
2011-05-20 00:38:44,467 - INFO - Processed 121600000 reads so far
2011-05-20 00:38:55,971 - INFO - Processed 121700000 reads so far
2011-05-20 00:39:06,379 - INFO - Processed 121800000 reads so far
2011-05-20 00:39:17,303 - INFO - Processed 121900000 reads so far
2011-05-20 00:39:26,427 - INFO - Processed 122000000 reads so far
2011-05-20 00:39:34,639 - INFO - Processed 122100000 reads so far
2011-05-20 00:39:37,965 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:46351860-66371860
2011-05-20 00:39:45,958 - INFO - Processed 122200000 reads so far
2011-05-20 00:39:59,056 - INFO - Processed 122300000 reads so far
2011-05-20 00:40:10,585 - INFO - Processed 122400000 reads so far
2011-05-20 00:40:23,406 - INFO - Processed 122500000 reads so far
2011-05-20 00:40:35,167 - INFO - Processed 122600000 reads so far
2011-05-20 00:40:46,895 - INFO - Processed 122700000 reads so far
2011-05-20 00:40:58,298 - INFO - Processed 122800000 reads so far
2011-05-20 00:41:08,560 - INFO - Processed 122900000 reads so far
2011-05-20 00:41:16,731 - INFO - Processed 123000000 reads so far
2011-05-20 00:41:24,479 - INFO - Processed 123100000 reads so far
2011-05-20 00:41:31,475 - INFO - Processed 123200000 reads so far
2011-05-20 00:41:32,379 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:66351880-86371880
2011-05-20 00:41:45,206 - INFO - Processed 123300000 reads so far
2011-05-20 00:41:56,285 - INFO - Processed 123400000 reads so far
2011-05-20 00:42:04,523 - INFO - Processed 123500000 reads so far
2011-05-20 00:42:13,011 - INFO - Processed 123600000 reads so far
2011-05-20 00:42:24,161 - INFO - Processed 123700000 reads so far
2011-05-20 00:42:32,723 - INFO - Processed 123800000 reads so far
2011-05-20 00:42:41,387 - INFO - Processed 123900000 reads so far
2011-05-20 00:42:52,101 - INFO - Processed 124000000 reads so far
2011-05-20 00:43:03,621 - INFO - Processed 124100000 reads so far
2011-05-20 00:43:11,591 - INFO - Processed 124200000 reads so far
2011-05-20 00:43:19,405 - INFO - Processed 124300000 reads so far
2011-05-20 00:43:21,719 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:86351888-106371888
2011-05-20 00:43:30,793 - INFO - Processed 124400000 reads so far
2011-05-20 00:43:42,052 - INFO - Processed 124500000 reads so far
2011-05-20 00:43:53,173 - INFO - Processed 124600000 reads so far
2011-05-20 00:44:05,594 - INFO - Processed 124700000 reads so far
2011-05-20 00:44:16,893 - INFO - Processed 124800000 reads so far
2011-05-20 00:44:29,788 - INFO - Processed 124900000 reads so far
2011-05-20 00:44:40,911 - INFO - Processed 125000000 reads so far
2011-05-20 00:44:50,596 - INFO - Processed 125100000 reads so far
2011-05-20 00:44:58,128 - INFO - Processed 125200000 reads so far
2011-05-20 00:45:11,013 - INFO - Processed 125300000 reads so far
2011-05-20 00:45:18,152 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:106351900-126371900
2011-05-20 00:45:19,408 - INFO - Processed 125400000 reads so far
2011-05-20 00:45:30,771 - INFO - Processed 125500000 reads so far
2011-05-20 00:45:42,928 - INFO - Processed 125600000 reads so far
2011-05-20 00:45:50,735 - INFO - Processed 125700000 reads so far
2011-05-20 00:46:02,245 - INFO - Processed 125800000 reads so far
2011-05-20 00:46:14,860 - INFO - Processed 125900000 reads so far
2011-05-20 00:46:22,426 - INFO - Processed 126000000 reads so far
2011-05-20 00:46:30,628 - INFO - Processed 126100000 reads so far
2011-05-20 00:46:41,611 - INFO - Processed 126200000 reads so far
2011-05-20 00:46:50,594 - INFO - Processed 126300000 reads so far
2011-05-20 00:46:59,386 - INFO - Processed 126400000 reads so far
2011-05-20 00:47:06,247 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:126351907-146371907
2011-05-20 00:47:10,694 - INFO - Processed 126500000 reads so far
2011-05-20 00:47:21,852 - INFO - Processed 126600000 reads so far
2011-05-20 00:47:33,239 - INFO - Processed 126700000 reads so far
2011-05-20 00:47:44,697 - INFO - Processed 126800000 reads so far
2011-05-20 00:47:55,858 - INFO - Processed 126900000 reads so far
2011-05-20 00:48:07,595 - INFO - Processed 127000000 reads so far
2011-05-20 00:48:18,648 - INFO - Processed 127100000 reads so far
2011-05-20 00:48:29,859 - INFO - Processed 127200000 reads so far
2011-05-20 00:48:39,409 - INFO - Processed 127300000 reads so far
2011-05-20 00:48:47,945 - INFO - Processed 127400000 reads so far
2011-05-20 00:48:55,947 - INFO - Processed 127500000 reads so far
2011-05-20 00:49:03,634 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:146351954-166371954
2011-05-20 00:49:05,815 - INFO - Processed 127600000 reads so far
2011-05-20 00:49:14,788 - INFO - Processed 127700000 reads so far
2011-05-20 00:49:28,850 - INFO - Processed 127800000 reads so far
2011-05-20 00:49:39,845 - INFO - Processed 127900000 reads so far
2011-05-20 00:49:41,007 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7_random:0-20010027
2011-05-20 00:49:42,261 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:2990020-23010020
2011-05-20 00:49:49,094 - INFO - Processed 128000000 reads so far
2011-05-20 00:49:59,894 - INFO - Processed 128100000 reads so far
2011-05-20 00:50:14,262 - INFO - Processed 128200000 reads so far
2011-05-20 00:50:23,667 - INFO - Processed 128300000 reads so far
2011-05-20 00:50:37,748 - INFO - Processed 128400000 reads so far
2011-05-20 00:50:48,705 - INFO - Processed 128500000 reads so far
2011-05-20 00:50:57,730 - INFO - Processed 128600000 reads so far
2011-05-20 00:51:06,445 - INFO - Processed 128700000 reads so far
2011-05-20 00:51:17,108 - INFO - Processed 128800000 reads so far
2011-05-20 00:51:26,377 - INFO - Processed 128900000 reads so far
2011-05-20 00:51:35,758 - INFO - Processed 129000000 reads so far
2011-05-20 00:51:40,283 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:22990055-43010055
2011-05-20 00:51:46,003 - INFO - Processed 129100000 reads so far
2011-05-20 00:51:58,210 - INFO - Processed 129200000 reads so far
2011-05-20 00:52:08,987 - INFO - Processed 129300000 reads so far
2011-05-20 00:52:21,120 - INFO - Processed 129400000 reads so far
2011-05-20 00:52:31,629 - INFO - Processed 129500000 reads so far
2011-05-20 00:52:44,545 - INFO - Processed 129600000 reads so far
2011-05-20 00:52:55,023 - INFO - Processed 129700000 reads so far
2011-05-20 00:53:04,727 - INFO - Processed 129800000 reads so far
2011-05-20 00:53:13,842 - INFO - Processed 129900000 reads so far
2011-05-20 00:53:25,233 - INFO - Processed 130000000 reads so far
2011-05-20 00:53:34,251 - INFO - Processed 130100000 reads so far
2011-05-20 00:53:34,713 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:42990071-63010071
2011-05-20 00:53:45,654 - INFO - Processed 130200000 reads so far
2011-05-20 00:53:54,433 - INFO - Processed 130300000 reads so far
2011-05-20 00:54:04,633 - INFO - Processed 130400000 reads so far
2011-05-20 00:54:16,312 - INFO - Processed 130500000 reads so far
2011-05-20 00:54:25,636 - INFO - Processed 130600000 reads so far
2011-05-20 00:54:33,903 - INFO - Processed 130700000 reads so far
2011-05-20 00:54:44,358 - INFO - Processed 130800000 reads so far
2011-05-20 00:54:55,136 - INFO - Processed 130900000 reads so far
2011-05-20 00:55:03,579 - INFO - Processed 131000000 reads so far
2011-05-20 00:55:08,255 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:62990082-83010082
2011-05-20 00:55:12,602 - INFO - Processed 131100000 reads so far
2011-05-20 00:55:25,411 - INFO - Processed 131200000 reads so far
2011-05-20 00:55:34,752 - INFO - Processed 131300000 reads so far
2011-05-20 00:55:46,356 - INFO - Processed 131400000 reads so far
2011-05-20 00:55:56,666 - INFO - Processed 131500000 reads so far
2011-05-20 00:56:06,108 - INFO - Processed 131600000 reads so far
2011-05-20 00:56:20,247 - INFO - Processed 131700000 reads so far
2011-05-20 00:56:32,484 - INFO - Processed 131800000 reads so far
2011-05-20 00:56:43,871 - INFO - Processed 131900000 reads so far
2011-05-20 00:56:55,658 - INFO - Processed 132000000 reads so far
2011-05-20 00:57:06,160 - INFO - Processed 132100000 reads so far
2011-05-20 00:57:09,256 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:82990102-103010102
2011-05-20 00:57:16,469 - INFO - Processed 132200000 reads so far
2011-05-20 00:57:26,461 - INFO - Processed 132300000 reads so far
2011-05-20 00:57:36,544 - INFO - Processed 132400000 reads so far
2011-05-20 00:57:47,528 - INFO - Processed 132500000 reads so far
2011-05-20 00:57:58,308 - INFO - Processed 132600000 reads so far
2011-05-20 00:58:09,756 - INFO - Processed 132700000 reads so far
2011-05-20 00:58:19,685 - INFO - Processed 132800000 reads so far
2011-05-20 00:58:30,217 - INFO - Processed 132900000 reads so far
2011-05-20 00:58:41,281 - INFO - Processed 133000000 reads so far
2011-05-20 00:58:50,680 - INFO - Processed 133100000 reads so far
2011-05-20 00:59:00,026 - INFO - Processed 133200000 reads so far
2011-05-20 00:59:00,676 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:102990122-123010122
2011-05-20 00:59:15,130 - INFO - Processed 133300000 reads so far
2011-05-20 00:59:25,239 - INFO - Processed 133400000 reads so far
2011-05-20 00:59:33,592 - INFO - Processed 133500000 reads so far
2011-05-20 00:59:46,759 - INFO - Processed 133600000 reads so far
2011-05-20 00:59:58,512 - INFO - Processed 133700000 reads so far
2011-05-20 01:00:09,688 - INFO - Processed 133800000 reads so far
2011-05-20 01:00:21,015 - INFO - Processed 133900000 reads so far
2011-05-20 01:00:31,526 - INFO - Processed 134000000 reads so far
2011-05-20 01:00:46,132 - INFO - Processed 134100000 reads so far
2011-05-20 01:00:56,147 - INFO - Processed 134200000 reads so far
2011-05-20 01:01:03,201 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:122990139-143010139
2011-05-20 01:01:04,562 - INFO - Processed 134300000 reads so far
2011-05-20 01:01:14,453 - INFO - Processed 134400000 reads so far
2011-05-20 01:01:28,464 - INFO - Processed 134500000 reads so far
2011-05-20 01:01:39,692 - INFO - Processed 134600000 reads so far
2011-05-20 01:01:50,213 - INFO - Processed 134700000 reads so far
2011-05-20 01:01:56,213 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8_random:0-20010026
2011-05-20 01:01:59,741 - INFO - Processed 134800000 reads so far
2011-05-20 01:02:06,522 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:2989968-23009968
2011-05-20 01:02:10,648 - INFO - Processed 134900000 reads so far
2011-05-20 01:02:19,111 - INFO - Processed 135000000 reads so far
2011-05-20 01:02:27,277 - INFO - Processed 135100000 reads so far
2011-05-20 01:02:35,464 - INFO - Processed 135200000 reads so far
2011-05-20 01:02:49,289 - INFO - Processed 135300000 reads so far
2011-05-20 01:02:55,496 - INFO - Processed 135400000 reads so far
2011-05-20 01:03:01,974 - INFO - Processed 135500000 reads so far
2011-05-20 01:03:10,728 - INFO - Processed 135600000 reads so far
2011-05-20 01:03:19,750 - INFO - Processed 135700000 reads so far
2011-05-20 01:03:26,767 - INFO - Processed 135800000 reads so far
2011-05-20 01:03:34,368 - INFO - Processed 135900000 reads so far
2011-05-20 01:03:42,612 - INFO - Processed 136000000 reads so far
2011-05-20 01:03:51,351 - INFO - Processed 136100000 reads so far
2011-05-20 01:04:00,263 - INFO - Processed 136200000 reads so far
2011-05-20 01:04:07,590 - INFO - Processed 136300000 reads so far
2011-05-20 01:04:14,110 - INFO - Processed 136400000 reads so far
2011-05-20 01:04:21,091 - INFO - Processed 136500000 reads so far
2011-05-20 01:04:29,586 - INFO - Processed 136600000 reads so far
2011-05-20 01:04:37,849 - INFO - Processed 136700000 reads so far
2011-05-20 01:04:48,278 - INFO - Processed 136800000 reads so far
2011-05-20 01:04:56,822 - INFO - Processed 136900000 reads so far
2011-05-20 01:05:06,712 - INFO - Processed 137000000 reads so far
2011-05-20 01:05:16,098 - INFO - Processed 137100000 reads so far
2011-05-20 01:05:26,345 - INFO - Processed 137200000 reads so far
2011-05-20 01:05:35,260 - INFO - Processed 137300000 reads so far
2011-05-20 01:05:44,275 - INFO - Processed 137400000 reads so far
2011-05-20 01:05:50,853 - INFO - Processed 137500000 reads so far
2011-05-20 01:05:58,856 - INFO - Processed 137600000 reads so far
2011-05-20 01:06:05,620 - INFO - Processed 137700000 reads so far
2011-05-20 01:06:13,340 - INFO - Processed 137800000 reads so far
2011-05-20 01:06:21,869 - INFO - Processed 137900000 reads so far
2011-05-20 01:06:28,258 - INFO - Processed 138000000 reads so far
2011-05-20 01:06:38,186 - INFO - Processed 138100000 reads so far
2011-05-20 01:06:47,273 - INFO - Processed 138200000 reads so far
2011-05-20 01:06:57,842 - INFO - Processed 138300000 reads so far
2011-05-20 01:07:06,910 - INFO - Processed 138400000 reads so far
2011-05-20 01:07:17,047 - INFO - Processed 138500000 reads so far
2011-05-20 01:07:24,310 - INFO - Processed 138600000 reads so far
2011-05-20 01:07:31,139 - INFO - Processed 138700000 reads so far
2011-05-20 01:07:38,723 - INFO - Processed 138800000 reads so far
2011-05-20 01:07:47,156 - INFO - Processed 138900000 reads so far
2011-05-20 01:07:52,642 - INFO - Processed 139000000 reads so far
2011-05-20 01:08:00,118 - INFO - Processed 139100000 reads so far
2011-05-20 01:08:06,696 - INFO - Processed 139200000 reads so far
2011-05-20 01:08:13,002 - INFO - Processed 139300000 reads so far
2011-05-20 01:08:19,731 - INFO - Processed 139400000 reads so far
2011-05-20 01:08:27,521 - INFO - Processed 139500000 reads so far
2011-05-20 01:08:36,061 - INFO - Processed 139600000 reads so far
2011-05-20 01:08:45,392 - INFO - Processed 139700000 reads so far
2011-05-20 01:08:52,068 - INFO - Processed 139800000 reads so far
2011-05-20 01:09:02,307 - INFO - Processed 139900000 reads so far
2011-05-20 01:09:11,256 - INFO - Processed 140000000 reads so far
2011-05-20 01:09:19,220 - INFO - Processed 140100000 reads so far
2011-05-20 01:09:26,561 - INFO - Processed 140200000 reads so far
2011-05-20 01:09:37,150 - INFO - Processed 140300000 reads so far
2011-05-20 01:09:45,380 - INFO - Processed 140400000 reads so far
2011-05-20 01:10:15,037 - INFO - Processed 140500000 reads so far
2011-05-20 01:10:38,127 - INFO - Processed 140600000 reads so far
2011-05-20 01:11:25,912 - INFO - Processed 140700000 reads so far
2011-05-20 01:11:56,194 - INFO - Processed 140800000 reads so far
2011-05-20 01:12:49,269 - INFO - Processed 140900000 reads so far
2011-05-20 01:13:12,723 - INFO - Processed 141000000 reads so far
2011-05-20 01:13:24,465 - INFO - Processed 141100000 reads so far
2011-05-20 01:13:32,922 - INFO - Processed 141200000 reads so far
2011-05-20 01:13:45,531 - INFO - Processed 141300000 reads so far
2011-05-20 01:13:57,315 - INFO - Processed 141400000 reads so far
2011-05-20 01:14:06,748 - INFO - Processed 141500000 reads so far
2011-05-20 01:14:17,252 - INFO - Processed 141600000 reads so far
2011-05-20 01:14:28,607 - INFO - Processed 141700000 reads so far
2011-05-20 01:14:38,249 - INFO - Processed 141800000 reads so far
2011-05-20 01:14:48,402 - INFO - Processed 141900000 reads so far
2011-05-20 01:14:57,366 - INFO - Processed 142000000 reads so far
2011-05-20 01:15:05,699 - INFO - Processed 142100000 reads so far
2011-05-20 01:15:15,221 - INFO - Processed 142200000 reads so far
2011-05-20 01:15:25,484 - INFO - Processed 142300000 reads so far
2011-05-20 01:15:36,380 - INFO - Processed 142400000 reads so far
2011-05-20 01:15:46,218 - INFO - Processed 142500000 reads so far
2011-05-20 01:15:57,459 - INFO - Processed 142600000 reads so far
2011-05-20 01:16:06,727 - INFO - Processed 142700000 reads so far
2011-05-20 01:16:15,945 - INFO - Processed 142800000 reads so far
2011-05-20 01:16:26,398 - INFO - Processed 142900000 reads so far
2011-05-20 01:16:38,723 - INFO - Processed 143000000 reads so far
2011-05-20 01:16:41,626 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:22989977-43009977
2011-05-20 01:16:50,133 - INFO - Processed 143100000 reads so far
2011-05-20 01:16:58,755 - INFO - Processed 143200000 reads so far
2011-05-20 01:17:07,241 - INFO - Processed 143300000 reads so far
2011-05-20 01:17:18,659 - INFO - Processed 143400000 reads so far
2011-05-20 01:17:29,321 - INFO - Processed 143500000 reads so far
2011-05-20 01:17:43,300 - INFO - Processed 143600000 reads so far
2011-05-20 01:17:52,490 - INFO - Processed 143700000 reads so far
2011-05-20 01:18:03,808 - INFO - Processed 143800000 reads so far
2011-05-20 01:18:13,369 - INFO - Processed 143900000 reads so far
2011-05-20 01:18:23,615 - INFO - Processed 144000000 reads so far
2011-05-20 01:18:34,172 - INFO - Processed 144100000 reads so far
2011-05-20 01:18:43,657 - INFO - Processed 144200000 reads so far
2011-05-20 01:18:53,826 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:42989990-63009990
2011-05-20 01:18:55,143 - INFO - Processed 144300000 reads so far
2011-05-20 01:19:06,713 - INFO - Processed 144400000 reads so far
2011-05-20 01:19:16,516 - INFO - Processed 144500000 reads so far
2011-05-20 01:19:29,021 - INFO - Processed 144600000 reads so far
2011-05-20 01:19:37,816 - INFO - Processed 144700000 reads so far
2011-05-20 01:19:49,055 - INFO - Processed 144800000 reads so far
2011-05-20 01:20:05,724 - INFO - Processed 144900000 reads so far
2011-05-20 01:20:16,169 - INFO - Processed 145000000 reads so far
2011-05-20 01:20:27,074 - INFO - Processed 145100000 reads so far
2011-05-20 01:20:36,533 - INFO - Processed 145200000 reads so far
2011-05-20 01:20:44,934 - INFO - Processed 145300000 reads so far
2011-05-20 01:20:52,115 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:62990011-83010011
2011-05-20 01:20:54,222 - INFO - Processed 145400000 reads so far
2011-05-20 01:21:01,746 - INFO - Processed 145500000 reads so far
2011-05-20 01:21:11,495 - INFO - Processed 145600000 reads so far
2011-05-20 01:21:20,710 - INFO - Processed 145700000 reads so far
2011-05-20 01:21:32,857 - INFO - Processed 145800000 reads so far
2011-05-20 01:21:42,176 - INFO - Processed 145900000 reads so far
2011-05-20 01:21:51,744 - INFO - Processed 146000000 reads so far
2011-05-20 01:22:02,447 - INFO - Processed 146100000 reads so far
2011-05-20 01:22:12,830 - INFO - Processed 146200000 reads so far
2011-05-20 01:22:23,128 - INFO - Processed 146300000 reads so far
2011-05-20 01:22:33,543 - INFO - Processed 146400000 reads so far
2011-05-20 01:22:38,763 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:82990012-103010012
2011-05-20 01:22:42,066 - INFO - Processed 146500000 reads so far
2011-05-20 01:22:51,958 - INFO - Processed 146600000 reads so far
2011-05-20 01:23:03,190 - INFO - Processed 146700000 reads so far
2011-05-20 01:23:15,348 - INFO - Processed 146800000 reads so far
2011-05-20 01:23:28,772 - INFO - Processed 146900000 reads so far
2011-05-20 01:23:39,613 - INFO - Processed 147000000 reads so far
2011-05-20 01:23:50,549 - INFO - Processed 147100000 reads so far
2011-05-20 01:24:03,675 - INFO - Processed 147200000 reads so far
2011-05-20 01:24:14,624 - INFO - Processed 147300000 reads so far
2011-05-20 01:24:26,298 - INFO - Processed 147400000 reads so far
2011-05-20 01:24:36,637 - INFO - Processed 147500000 reads so far
2011-05-20 01:24:39,306 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:102990016-123010016
2011-05-20 01:24:46,547 - INFO - Processed 147600000 reads so far
2011-05-20 01:24:54,294 - INFO - Processed 147700000 reads so far
2011-05-20 01:25:06,371 - INFO - Processed 147800000 reads so far
2011-05-20 01:25:19,358 - INFO - Processed 147900000 reads so far
2011-05-20 01:25:30,848 - INFO - Processed 148000000 reads so far
2011-05-20 01:25:42,010 - INFO - Processed 148100000 reads so far
2011-05-20 01:25:53,349 - INFO - Processed 148200000 reads so far
2011-05-20 01:26:04,711 - INFO - Processed 148300000 reads so far
2011-05-20 01:26:16,035 - INFO - Processed 148400000 reads so far
2011-05-20 01:26:27,950 - INFO - Processed 148500000 reads so far
2011-05-20 01:26:39,576 - INFO - Processed 148600000 reads so far
2011-05-20 01:26:44,405 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:122990022-143010022
2011-05-20 01:26:50,914 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9_random:0-20010008
2011-05-20 01:26:50,964 - INFO - Processed 148700000 reads so far
2011-05-20 01:26:54,614 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrM:0-20010000
2011-05-20 01:27:00,240 - INFO - Processed 148800000 reads so far
2011-05-20 01:27:00,687 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrUn_random:0-20010000
2011-05-20 01:27:11,928 - INFO - Processed 148900000 reads so far
2011-05-20 01:27:22,961 - INFO - Processed 149000000 reads so far
2011-05-20 01:27:32,756 - INFO - Processed 149100000 reads so far
2011-05-20 01:27:41,653 - INFO - Processed 149200000 reads so far
2011-05-20 01:27:46,283 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:2989998-23009998
2011-05-20 01:27:51,501 - INFO - Processed 149300000 reads so far
2011-05-20 01:28:03,023 - INFO - Processed 149400000 reads so far
2011-05-20 01:28:13,336 - INFO - Processed 149500000 reads so far
2011-05-20 01:28:25,439 - INFO - Processed 149600000 reads so far
2011-05-20 01:28:39,673 - INFO - Processed 149700000 reads so far
2011-05-20 01:28:52,117 - INFO - Processed 149800000 reads so far
2011-05-20 01:29:01,480 - INFO - Processed 149900000 reads so far
2011-05-20 01:29:11,735 - INFO - Processed 150000000 reads so far
2011-05-20 01:29:20,446 - INFO - Processed 150100000 reads so far
2011-05-20 01:29:28,800 - INFO - Processed 150200000 reads so far
2011-05-20 01:29:36,996 - INFO - Processed 150300000 reads so far
2011-05-20 01:29:47,090 - INFO - Processed 150400000 reads so far
2011-05-20 01:29:55,755 - INFO - Processed 150500000 reads so far
2011-05-20 01:30:04,491 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:22990048-43010048
2011-05-20 01:30:06,263 - INFO - Processed 150600000 reads so far
2011-05-20 01:30:17,143 - INFO - Processed 150700000 reads so far
2011-05-20 01:30:27,939 - INFO - Processed 150800000 reads so far
2011-05-20 01:30:37,139 - INFO - Processed 150900000 reads so far
2011-05-20 01:30:44,546 - INFO - Processed 151000000 reads so far
2011-05-20 01:30:54,228 - INFO - Processed 151100000 reads so far
2011-05-20 01:31:00,835 - INFO - Processed 151200000 reads so far
2011-05-20 01:31:07,968 - INFO - Processed 151300000 reads so far
2011-05-20 01:31:18,738 - INFO - Processed 151400000 reads so far
2011-05-20 01:31:37,245 - INFO - Processed 151500000 reads so far
2011-05-20 01:31:44,050 - INFO - Processed 151600000 reads so far
2011-05-20 01:31:51,085 - INFO - Processed 151700000 reads so far
2011-05-20 01:31:59,752 - INFO - Processed 151800000 reads so far
2011-05-20 01:32:05,988 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:42990056-63010056
2011-05-20 01:32:11,388 - INFO - Processed 151900000 reads so far
2011-05-20 01:32:20,075 - INFO - Processed 152000000 reads so far
2011-05-20 01:32:31,917 - INFO - Processed 152100000 reads so far
2011-05-20 01:32:45,373 - INFO - Processed 152200000 reads so far
2011-05-20 01:32:55,288 - INFO - Processed 152300000 reads so far
2011-05-20 01:33:02,847 - INFO - Processed 152400000 reads so far
2011-05-20 01:33:12,853 - INFO - Processed 152500000 reads so far
2011-05-20 01:33:22,938 - INFO - Processed 152600000 reads so far
2011-05-20 01:33:33,275 - INFO - Processed 152700000 reads so far
2011-05-20 01:33:42,029 - INFO - Processed 152800000 reads so far
2011-05-20 01:33:54,777 - INFO - Processed 152900000 reads so far
2011-05-20 01:33:57,270 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:62990108-83010108
2011-05-20 01:34:04,867 - INFO - Processed 153000000 reads so far
2011-05-20 01:34:15,074 - INFO - Processed 153100000 reads so far
2011-05-20 01:34:23,049 - INFO - Processed 153200000 reads so far
2011-05-20 01:34:34,079 - INFO - Processed 153300000 reads so far
2011-05-20 01:34:44,904 - INFO - Processed 153400000 reads so far
2011-05-20 01:34:53,499 - INFO - Processed 153500000 reads so far
2011-05-20 01:35:02,436 - INFO - Processed 153600000 reads so far
2011-05-20 01:35:11,800 - INFO - Processed 153700000 reads so far
2011-05-20 01:35:21,195 - INFO - Processed 153800000 reads so far
2011-05-20 01:35:30,076 - INFO - Processed 153900000 reads so far
2011-05-20 01:35:36,528 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:82990125-103010125
2011-05-20 01:35:39,641 - INFO - Processed 154000000 reads so far
2011-05-20 01:35:52,062 - INFO - Processed 154100000 reads so far
2011-05-20 01:36:01,848 - INFO - Processed 154200000 reads so far
2011-05-20 01:36:12,645 - INFO - Processed 154300000 reads so far
2011-05-20 01:36:23,241 - INFO - Processed 154400000 reads so far
2011-05-20 01:36:33,857 - INFO - Processed 154500000 reads so far
2011-05-20 01:36:42,499 - INFO - Processed 154600000 reads so far
2011-05-20 01:36:53,826 - INFO - Processed 154700000 reads so far
2011-05-20 01:37:02,352 - INFO - Processed 154800000 reads so far
2011-05-20 01:37:09,851 - INFO - Processed 154900000 reads so far
2011-05-20 01:37:18,904 - INFO - Processed 155000000 reads so far
2011-05-20 01:37:20,003 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:102990157-123010157
2011-05-20 01:37:28,960 - INFO - Processed 155100000 reads so far
2011-05-20 01:37:36,811 - INFO - Processed 155200000 reads so far
2011-05-20 01:37:47,654 - INFO - Processed 155300000 reads so far
2011-05-20 01:37:56,148 - INFO - Processed 155400000 reads so far
2011-05-20 01:38:04,628 - INFO - Processed 155500000 reads so far
2011-05-20 01:38:14,908 - INFO - Processed 155600000 reads so far
2011-05-20 01:38:26,016 - INFO - Processed 155700000 reads so far
2011-05-20 01:38:40,210 - INFO - Processed 155800000 reads so far
2011-05-20 01:38:49,227 - INFO - Processed 155900000 reads so far
2011-05-20 01:38:57,085 - INFO - Processed 156000000 reads so far
2011-05-20 01:38:58,040 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:122990179-143010179
2011-05-20 01:39:09,250 - INFO - Processed 156100000 reads so far
2011-05-20 01:39:19,866 - INFO - Processed 156200000 reads so far
2011-05-20 01:39:30,294 - INFO - Processed 156300000 reads so far
2011-05-20 01:39:41,976 - INFO - Processed 156400000 reads so far
2011-05-20 01:39:51,870 - INFO - Processed 156500000 reads so far
2011-05-20 01:40:02,400 - INFO - Processed 156600000 reads so far
2011-05-20 01:40:12,716 - INFO - Processed 156700000 reads so far
2011-05-20 01:40:22,096 - INFO - Processed 156800000 reads so far
2011-05-20 01:40:31,935 - INFO - Processed 156900000 reads so far
2011-05-20 01:40:39,299 - INFO - Processed 157000000 reads so far
2011-05-20 01:40:50,000 - INFO - Processed 157100000 reads so far
2011-05-20 01:40:51,904 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:142990194-163010194
2011-05-20 01:41:02,009 - INFO - Processed 157200000 reads so far
2011-05-20 01:41:13,833 - INFO - Processed 157300000 reads so far
2011-05-20 01:41:25,168 - INFO - Processed 157400000 reads so far
2011-05-20 01:41:34,760 - INFO - Processed 157500000 reads so far
2011-05-20 01:41:44,572 - INFO - Processed 157600000 reads so far
2011-05-20 01:41:55,614 - INFO - Processed 157700000 reads so far
2011-05-20 01:42:06,379 - INFO - Processed 157800000 reads so far
2011-05-20 01:42:16,148 - INFO - Processed 157900000 reads so far
2011-05-20 01:42:23,073 - INFO - Processed 158000000 reads so far
2011-05-20 01:42:30,151 - INFO - Processed 158100000 reads so far
2011-05-20 01:42:32,391 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:162990249-183010249
2011-05-20 01:42:37,215 - INFO - Processed 158200000 reads so far
2011-05-20 01:42:45,625 - INFO - Processed 158300000 reads so far
2011-05-20 01:42:51,747 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX_random:0-20010000
2011-05-20 01:42:52,397 - INFO - Processed 158400000 reads so far
2011-05-20 01:42:59,302 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY:10604-20030604
2011-05-20 01:43:00,298 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:13189-20033189
2011-05-20 01:43:01,831 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:20035292-40055292
2011-05-20 01:43:02,836 - INFO - Processed 158500000 reads so far
2011-05-20 01:43:02,948 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:40036652-60056652
2011-05-20 01:43:06,132 - INFO - Processed 158600000 reads so far
2011-05-20 01:43:08,558 - INFO - Processed 158700000 reads so far
2011-05-20 01:43:11,293 - INFO - Processed 158800000 reads so far
2011-05-20 01:43:14,677 - INFO - Processed 158900000 reads so far
2011-05-20 01:43:17,238 - INFO - Processed 159000000 reads so far
2011-05-20 01:43:20,655 - INFO - Processed 159100000 reads so far
2011-05-20 01:43:23,082 - INFO - Processed 159200000 reads so far
2011-05-20 01:43:26,548 - INFO - Processed 159300000 reads so far
2011-05-20 01:43:30,455 - INFO - Processed 159400000 reads so far
2011-05-20 01:43:35,222 - INFO - Processed 159500000 reads so far
2011-05-20 01:43:38,561 - INFO - Processed 159600000 reads so far
2011-05-20 01:43:41,190 - INFO - Processed 159700000 reads so far
2011-05-20 01:43:43,984 - INFO - Processed 159800000 reads so far
2011-05-20 01:43:47,632 - INFO - Processed 159900000 reads so far
2011-05-20 01:43:50,374 - INFO - Processed 160000000 reads so far
2011-05-20 01:43:56,189 - INFO - Processed 160100000 reads so far
2011-05-20 01:43:58,829 - INFO - Processed 160200000 reads so far
2011-05-20 01:44:03,045 - INFO - Processed 160300000 reads so far
2011-05-20 01:44:07,431 - INFO - Processed 160400000 reads so far
2011-05-20 01:44:10,805 - INFO - Processed 160500000 reads so far
2011-05-20 01:44:15,409 - INFO - Processed 160600000 reads so far
2011-05-20 01:44:18,423 - INFO - Processed 160700000 reads so far
2011-05-20 01:44:20,890 - INFO - Processed 160800000 reads so far
2011-05-20 01:44:22,163 - INFO - Finished loading data. Outputting QC metrics
2011-05-20 01:44:39,334 - INFO - Finished outputting QC metrics
2011-05-20 01:44:39,433 - INFO - Finished generating QC metrics