2016/11/06 14:34:18: ERROR INFO 14:34:13,585 ProgressMeter - CHR_HSCHR6_MHC_QBL_CTG1:26571650 3.7944387208E10 2.7 h 0.0 s 87.4% 3.1 h 23.0 m
2016/11/06 14:34:43: ERROR INFO 14:34:43,829 ProgressMeter - CHR_HSCHR6_MHC_QBL_CTG1:155500900 3.7944387208E10 2.7 h 0.0 s 87.7% 3.1 h 22.5 m
2016/11/06 14:35:13: ERROR INFO 14:35:13,878 ProgressMeter - CHR_HSCHR6_MHC_SSTO_CTG1:105809766 3.8115122009E10 2.7 h 0.0 s 88.0% 3.1 h 22.0 m
2016/11/06 14:35:43: ERROR INFO 14:35:43,899 ProgressMeter - CHR_HSCHR7_1_CTG1:53328035 3.8286068145E10 2.7 h 0.0 s 88.3% 3.1 h 21.5 m
2016/11/06 14:36:13: ERROR INFO 14:36:13,929 ProgressMeter - CHR_HSCHR7_1_CTG4_4:9121769 3.8445417423E10 2.7 h 0.0 s 88.5% 3.1 h 21.0 m
2016/11/06 14:36:43: ERROR INFO 14:36:43,965 ProgressMeter - CHR_HSCHR7_1_CTG4_4:134577700 3.8445417423E10 2.7 h 0.0 s 88.8% 3.1 h 20.4 m
2016/11/06 14:37:14: ERROR INFO 14:37:13,988 ProgressMeter - CHR_HSCHR7_1_CTG6:94616591 3.8604766027E10 2.7 h 0.0 s 89.1% 3.1 h 19.9 m
2016/11/06 14:37:44: ERROR INFO 14:37:44,057 ProgressMeter - CHR_HSCHR7_1_CTG7:52850200 3.8764118008E10 2.7 h 0.0 s 89.4% 3.1 h 19.4 m
2016/11/06 14:38:14: ERROR INFO 14:38:14,107 ProgressMeter - CHR_HSCHR7_2_CTG1:10860320 3.8923464289E10 2.7 h 0.0 s 89.7% 3.1 h 19.0 m
2016/11/06 14:38:44: ERROR INFO 14:38:44,129 ProgressMeter - CHR_HSCHR7_2_CTG1:139671726 3.8923464289E10 2.7 h 0.0 s 90.0% 3.1 h 18.4 m
2016/11/06 14:39:14: ERROR INFO 14:39:14,149 ProgressMeter - CHR_HSCHR7_2_CTG4_4:97278066 3.9082812583E10 2.8 h 0.0 s 90.2% 3.1 h 17.9 m
2016/11/06 14:39:44: ERROR INFO 14:39:44,211 ProgressMeter - CHR_HSCHR7_2_CTG6:52800173 3.9242146372E10 2.8 h 0.0 s 90.5% 3.1 h 17.4 m
2016/11/06 14:40:14: ERROR INFO 14:40:14,238 ProgressMeter - CHR_HSCHR7_2_CTG7:9651137 3.9401553532E10 2.8 h 0.0 s 90.8% 3.1 h 16.9 m
2016/11/06 14:40:44: ERROR INFO 14:40:44,277 ProgressMeter - CHR_HSCHR7_2_CTG7:135598357 3.9401553532E10 2.8 h 0.0 s 91.0% 3.1 h 16.4 m
2016/11/06 14:41:14: ERROR INFO 14:41:14,308 ProgressMeter - CHR_HSCHR7_3_CTG6:98513392 3.9560902884E10 2.8 h 0.0 s 91.3% 3.1 h 15.9 m
2016/11/06 14:41:44: ERROR INFO 14:41:44,359 ProgressMeter - CHR_HSCHR8_1_CTG1:56979410 3.9720247325E10 2.8 h 0.0 s 91.6% 3.1 h 15.4 m
2016/11/06 14:42:14: ERROR INFO 14:42:14,408 ProgressMeter - CHR_HSCHR8_1_CTG6:25479174 3.9865372277E10 2.8 h 0.0 s 91.9% 3.1 h 14.9 m
2016/11/06 14:42:44: ERROR INFO 14:42:44,562 ProgressMeter - CHR_HSCHR8_1_CTG7:352454 4.0010522677E10 2.8 h 0.0 s 92.1% 3.1 h 14.4 m
2016/11/06 14:43:14: ERROR INFO 14:43:14,568 ProgressMeter - CHR_HSCHR8_1_CTG7:122806204 4.0010522677E10 2.8 h 0.0 s 92.4% 3.1 h 13.9 m
2016/11/06 14:43:44: ERROR INFO 14:43:44,589 ProgressMeter - CHR_HSCHR8_2_CTG1:97217658 4.015566471E10 2.8 h 0.0 s 92.7% 3.1 h 13.4 m
2016/11/06 14:44:14: ERROR INFO 14:44:14,599 ProgressMeter - CHR_HSCHR8_2_CTG7:69830513 4.0300806277E10 2.8 h 0.0 s 93.0% 3.1 h 12.9 m
2016/11/06 14:44:44: ERROR INFO 14:44:44,619 ProgressMeter - CHR_HSCHR8_3_CTG1:46308023 4.0445948145E10 2.8 h 0.0 s 93.2% 3.1 h 12.4 m
2016/11/06 14:45:14: ERROR INFO 14:45:14,639 ProgressMeter - CHR_HSCHR8_3_CTG7:21205716 4.0591078757E10 2.9 h 0.0 s 93.5% 3.1 h 11.9 m
2016/11/06 14:45:44: ERROR INFO 14:45:44,687 ProgressMeter - CHR_HSCHR8_3_CTG7:143366096 4.0591078757E10 2.9 h 0.0 s 93.8% 3.1 h 11.4 m
2016/11/06 14:46:14: ERROR INFO 14:46:14,709 ProgressMeter - CHR_HSCHR8_4_CTG1:121848734 4.07362044E10 2.9 h 0.0 s 94.1% 3.1 h 10.8 m
2016/11/06 14:46:44: ERROR INFO 14:46:44,747 ProgressMeter - CHR_HSCHR8_4_CTG7:99038866 4.088134541E10 2.9 h 0.0 s 94.4% 3.1 h 10.3 m
2016/11/06 14:47:14: ERROR INFO 14:47:14,784 ProgressMeter - CHR_HSCHR8_5_CTG1:74269584 4.1026489343E10 2.9 h 0.0 s 94.6% 3.1 h 9.8 m
2016/11/06 14:47:44: ERROR INFO 14:47:44,812 ProgressMeter - CHR_HSCHR8_5_CTG7:48308096 4.1171626962E10 2.9 h 0.0 s 94.9% 3.1 h 9.3 m
2016/11/06 14:48:14: ERROR INFO 14:48:14,849 ProgressMeter - CHR_HSCHR8_6_CTG1:24715647 4.13167715E10 2.9 h 0.0 s 95.2% 3.1 h 8.8 m
2016/11/06 14:48:44: ERROR INFO 14:48:44,887 ProgressMeter - CHR_HSCHR8_6_CTG1:145136257 4.13167715E10 2.9 h 0.0 s 95.5% 3.1 h 8.3 m
2016/11/06 14:49:14: ERROR INFO 14:49:14,909 ProgressMeter - CHR_HSCHR8_6_CTG7:118159407 4.1461907757E10 2.9 h 0.0 s 95.7% 3.1 h 7.8 m
2016/11/06 14:49:44: ERROR INFO 14:49:44,978 ProgressMeter - CHR_HSCHR8_7_CTG1:87814300 4.1607049594E10 2.9 h 0.0 s 96.0% 3.1 h 7.3 m
2016/11/06 14:50:15: ERROR INFO 14:50:15,018 ProgressMeter - CHR_HSCHR8_8_CTG1:61954994 4.1752187792E10 2.9 h 0.0 s 96.3% 3.1 h 6.8 m
2016/11/06 14:50:45: ERROR INFO 14:50:45,047 ProgressMeter - CHR_HSCHR8_9_CTG1:36127845 4.1897311118E10 2.9 h 0.0 s 96.6% 3.1 h 6.3 m
2016/11/06 14:51:15: ERROR INFO 14:51:15,069 ProgressMeter - CHR_HSCHR9_1_CTG1:6200792 4.2042294707E10 3.0 h 0.0 s 96.8% 3.1 h 5.8 m
2016/11/06 14:51:45: ERROR INFO 14:51:45,098 ProgressMeter - CHR_HSCHR9_1_CTG1:134850186 4.2042294707E10 3.0 h 0.0 s 97.1% 3.1 h 5.3 m
2016/11/06 14:52:15: ERROR INFO 14:52:15,119 ProgressMeter - CHR_HSCHR9_1_CTG2:118854069 4.2180704236E10 3.0 h 0.0 s 97.4% 3.1 h 4.8 m
2016/11/06 14:52:45: ERROR INFO 14:52:45,178 ProgressMeter - CHR_HSCHR9_1_CTG3:101096048 4.2319107149E10 3.0 h 0.0 s 97.7% 3.0 h 4.2 m
2016/11/06 14:53:15: ERROR INFO 14:53:15,207 ProgressMeter - CHR_HSCHR9_1_CTG4:82745252 4.2457507946E10 3.0 h 0.0 s 98.0% 3.0 h 3.7 m
2016/11/06 14:53:45: ERROR INFO 14:53:45,218 ProgressMeter - CHR_HSCHR9_1_CTG5:64685396 4.2595913761E10 3.0 h 0.0 s 98.2% 3.0 h 3.2 m
2016/11/06 14:54:15: ERROR INFO 14:54:15,247 ProgressMeter - CHR_HSCHRX_1_CTG3:47215300 4.2734318066E10 3.0 h 0.0 s 98.5% 3.0 h 2.7 m
2016/11/06 14:54:45: ERROR INFO 14:54:45,294 ProgressMeter - CHR_HSCHRX_2_CTG12:10769765 4.2890361651E10 3.0 h 0.0 s 98.8% 3.0 h 2.2 m
2016/11/06 14:55:15: ERROR INFO 14:55:15,328 ProgressMeter - CHR_HSCHRX_2_CTG12:130819625 4.2890361651E10 3.0 h 0.0 s 99.1% 3.0 h 102.0 s
2016/11/06 14:55:45: ERROR INFO 14:55:45,337 ProgressMeter - CHR_HSCHRX_2_CTG3:92382709 4.3046414823E10 3.0 h 0.0 s 99.3% 3.0 h 72.0 s
2016/11/06 14:56:15: ERROR INFO 14:56:15,380 ProgressMeter - X:52887509 4.3202471267E10 3.0 h 0.0 s 99.6% 3.0 h 43.0 s
2016/11/06 14:56:45: ERROR INFO 14:56:45,418 ProgressMeter - Y:14660419 4.3358512162E10 3.0 h 0.0 s 99.9% 3.0 h 13.0 s
2016/11/06 14:56:59: ERROR INFO 14:56:59,498 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.032789194
INFO 14:56:59,499 PairHMM - Total compute time in PairHMM computeLikelihoods() : 16.995468206
INFO 14:56:59,499 HaplotypeCaller - Ran local assembly on 2006 active regions
2016/11/06 14:56:59: ERROR INFO 14:56:59,822 ProgressMeter - done 4.3427203894E10 3.1 h 0.0 s 100.0% 3.1 h 0.0 s
INFO 14:56:59,823 ProgressMeter - Total runtime 10980.18 secs, 183.00 min, 3.05 hours
INFO 14:56:59,823 MicroScheduler - 29451 reads were filtered out during the traversal out of approximately 239438 total reads (12.30%)
INFO 14:56:59,823 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 14:56:59,823 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 14:56:59,824 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 14:56:59,824 MicroScheduler - -> 29451 reads (12.30% of total) failing HCMappingQualityFilter
INFO 14:56:59,824 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 14:56:59,824 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 14:56:59,824 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
INFO 14:56:59,824 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
2016/11/06 14:57:31: INFO Finishing job 19 with ExitCode -1
2016/11/06 14:57:31: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 183 minutes, 37 seconds