2016/11/06 14:57:44: DEBUG Enqueuing command:
#TASK tags=Sample_5
gatk -T VariantFiltration \
-R /scratch/Reference_Genomes/Public/Vertebrate_mammalian/Homo_sapiens/ENSEMBL-release-81-GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa \
-I /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_haplotype.realigned.withrg.csorted.cleaned.aligned.vcf \
–filterExpression “QD ‘<’ 2.0 || FS ‘>’ 60.0 || MQ ‘<’ 40.0 || MQRankSum ‘<’ -12.5 || ReadPosRankSum ‘<’ -8.0” \
–filterName “my_snp_filter” \
-o /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_my_snp_filter.haplotype.realigned.mdup.csorted.cleaned.aligned.vcf
2016/11/06 14:57:48: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 04 seconds
2016/11/06 14:57:44: INFO Starting Job: 20
Cmd is #TASK tags=Sample_5
gatk -T VariantFiltration \
-R /scratch/Reference_Genomes/Public/Vertebrate_mammalian/Homo_sapiens/ENSEMBL-release-81-GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa \
-I /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_haplotype.realigned.withrg.csorted.cleaned.aligned.vcf \
–filterExpression “QD ‘<’ 2.0 || FS ‘>’ 60.0 || MQ ‘<’ 40.0 || MQRankSum ‘<’ -12.5 || ReadPosRankSum ‘<’ -8.0” \
–filterName “my_snp_filter” \
-o /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_my_snp_filter.haplotype.realigned.mdup.csorted.cleaned.aligned.vcf
2016/11/06 14:57:48: ERROR ##### ERROR ——————————————————————————————
2016/11/06 14:57:48: ERROR
2016/11/06 14:57:48: ERROR /scratch/gencore/.local/easybuild/software/gencore_variant_detection/1.0/bin/gatk: line 67: FS: command not found
2016/11/06 14:57:48: ERROR /scratch/gencore/.local/easybuild/software/gencore_variant_detection/1.0/bin/gatk: line 67: MQ: command not found
2016/11/06 14:57:48: ERROR /scratch/gencore/.local/easybuild/software/gencore_variant_detection/1.0/bin/gatk: line 67: MQRankSum: command not found
2016/11/06 14:57:48: ERROR /scratch/gencore/.local/easybuild/software/gencore_variant_detection/1.0/bin/gatk: line 67: ReadPosRankSum: command not found
2016/11/06 14:57:48: INFO Finishing job 20 with ExitCode -1
2016/11/06 14:57:48: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 04 seconds
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
2016/11/06 14:05:42: ERROR INFO 14:05:41,239 ProgressMeter - CHR_HSCHR4_1_CTG4:99671200 3.1110506141E10 2.2 h 0.0 s 71.9% 3.1 h 51.5 m
2016/11/06 14:06:11: ERROR INFO 14:06:11,267 ProgressMeter - CHR_HSCHR4_1_CTG6:31008421 3.1300727898E10 2.2 h 0.0 s 72.1% 3.1 h 51.0 m
2016/11/06 14:06:41: ERROR INFO 14:06:41,281 ProgressMeter - CHR_HSCHR4_1_CTG6:151460398 3.1300727898E10 2.2 h 0.0 s 72.4% 3.1 h 50.5 m
2016/11/06 14:07:11: ERROR INFO 14:07:11,331 ProgressMeter - CHR_HSCHR4_1_CTG8_1:74628994 3.1490952736E10 2.2 h 0.0 s 72.7% 3.1 h 50.0 m
2016/11/06 14:07:41: ERROR INFO 14:07:41,349 ProgressMeter - CHR_HSCHR4_1_CTG8_1:189079133 3.1490952736E10 2.2 h 0.0 s 72.9% 3.1 h 49.6 m
2016/11/06 14:08:11: ERROR INFO 14:08:11,389 ProgressMeter - CHR_HSCHR4_1_CTG9:112898500 3.1681171574E10 2.2 h 0.0 s 73.2% 3.1 h 49.1 m
2016/11/06 14:08:41: ERROR INFO 14:08:41,419 ProgressMeter - CHR_HSCHR4_2_CTG12:38600385 3.1871268506E10 2.2 h 0.0 s 73.5% 3.1 h 48.6 m
2016/11/06 14:09:11: ERROR INFO 14:09:11,470 ProgressMeter - CHR_HSCHR4_2_CTG12:161458505 3.1871268506E10 2.3 h 0.0 s 73.8% 3.1 h 48.1 m
2016/11/06 14:09:41: ERROR INFO 14:09:41,487 ProgressMeter - CHR_HSCHR4_3_CTG12:88677945 3.2061475303E10 2.3 h 0.0 s 74.0% 3.1 h 47.6 m
2016/11/06 14:10:11: ERROR INFO 14:10:11,509 ProgressMeter - CHR_HSCHR4_4_CTG12:13517005 3.2251693331E10 2.3 h 0.0 s 74.3% 3.1 h 47.1 m
2016/11/06 14:10:41: ERROR INFO 14:10:41,540 ProgressMeter - CHR_HSCHR4_4_CTG12:139614892 3.2251693331E10 2.3 h 0.0 s 74.6% 3.1 h 46.6 m
2016/11/06 14:11:11: ERROR INFO 14:11:11,619 ProgressMeter - CHR_HSCHR4_5_CTG12:66212019 3.2441914035E10 2.3 h 0.0 s 74.9% 3.1 h 46.1 m
2016/11/06 14:11:41: ERROR INFO 14:11:41,647 ProgressMeter - CHR_HSCHR4_5_CTG12:187099166 3.2441914035E10 2.3 h 0.0 s 75.1% 3.1 h 45.6 m
2016/11/06 14:12:11: ERROR INFO 14:12:11,678 ProgressMeter - CHR_HSCHR4_6_CTG12:109214362 3.2632133597E10 2.3 h 0.0 s 75.4% 3.1 h 45.1 m
2016/11/06 14:12:41: ERROR INFO 14:12:41,699 ProgressMeter - CHR_HSCHR4_7_CTG12:29967895 3.282235213E10 2.3 h 0.0 s 75.6% 3.1 h 44.6 m
2016/11/06 14:13:11: ERROR INFO 14:13:11,708 ProgressMeter - CHR_HSCHR4_7_CTG12:154794534 3.282235213E10 2.3 h 0.0 s 75.9% 3.1 h 44.1 m
2016/11/06 14:13:41: ERROR INFO 14:13:41,737 ProgressMeter - CHR_HSCHR5_1_CTG1:81383919 3.3012577271E10 2.3 h 0.0 s 76.2% 3.1 h 43.6 m
2016/11/06 14:14:11: ERROR INFO 14:14:11,758 ProgressMeter - CHR_HSCHR5_1_CTG1_1:14484708 3.3194135673E10 2.3 h 0.0 s 76.5% 3.1 h 43.1 m
2016/11/06 14:14:41: ERROR INFO 14:14:41,777 ProgressMeter - CHR_HSCHR5_1_CTG1_1:140426282 3.3194135673E10 2.3 h 0.0 s 76.8% 3.1 h 42.6 m
2016/11/06 14:15:11: ERROR INFO 14:15:11,797 ProgressMeter - CHR_HSCHR5_1_CTG5:78560351 3.3374999243E10 2.4 h 0.0 s 77.0% 3.1 h 42.1 m
2016/11/06 14:15:41: ERROR INFO 14:15:41,858 ProgressMeter - CHR_HSCHR5_2_CTG1:15644036 3.3556542979E10 2.4 h 0.0 s 77.3% 3.1 h 41.6 m
2016/11/06 14:16:11: ERROR INFO 14:16:11,879 ProgressMeter - CHR_HSCHR5_2_CTG1:135658935 3.3556542979E10 2.4 h 0.0 s 77.6% 3.1 h 41.1 m
2016/11/06 14:16:41: ERROR INFO 14:16:41,918 ProgressMeter - CHR_HSCHR5_2_CTG1_1:70734649 3.3738090118E10 2.4 h 0.0 s 77.9% 3.1 h 40.6 m
2016/11/06 14:17:11: ERROR INFO 14:17:11,948 ProgressMeter - CHR_HSCHR5_2_CTG5:9191800 3.391884368E10 2.4 h 0.0 s 78.1% 3.1 h 40.1 m
2016/11/06 14:17:41: ERROR INFO 14:17:41,980 ProgressMeter - CHR_HSCHR5_2_CTG5:133970200 3.391884368E10 2.4 h 0.0 s 78.4% 3.1 h 39.6 m
2016/11/06 14:18:12: ERROR INFO 14:18:12,018 ProgressMeter - CHR_HSCHR5_3_CTG1:69583987 3.4100385886E10 2.4 h 0.0 s 78.7% 3.1 h 39.1 m
2016/11/06 14:18:42: ERROR INFO 14:18:42,029 ProgressMeter - CHR_HSCHR5_3_CTG1_1:2883091 3.4281928381E10 2.4 h 0.0 s 78.9% 3.1 h 38.6 m
2016/11/06 14:19:12: ERROR INFO 14:19:12,077 ProgressMeter - CHR_HSCHR5_3_CTG1_1:129443915 3.4281928381E10 2.4 h 0.0 s 79.2% 3.1 h 38.0 m
2016/11/06 14:19:42: ERROR INFO 14:19:42,107 ProgressMeter - CHR_HSCHR5_3_CTG5:66546132 3.4463483246E10 2.4 h 0.0 s 79.5% 3.1 h 37.5 m
2016/11/06 14:20:12: ERROR INFO 14:20:12,149 ProgressMeter - CHR_HSCHR5_4_CTG1:494555 3.4645021815E10 2.4 h 0.0 s 79.8% 3.1 h 37.1 m
2016/11/06 14:20:42: ERROR INFO 14:20:42,188 ProgressMeter - CHR_HSCHR5_4_CTG1:125387618 3.4645021815E10 2.4 h 0.0 s 80.1% 3.1 h 36.5 m
2016/11/06 14:21:12: ERROR INFO 14:21:12,218 ProgressMeter - CHR_HSCHR5_4_CTG1_1:64984405 3.4826559249E10 2.5 h 0.0 s 80.3% 3.1 h 36.0 m
2016/11/06 14:21:42: ERROR INFO 14:21:42,248 ProgressMeter - CHR_HSCHR5_5_CTG1:5618623 3.500810553E10 2.5 h 0.0 s 80.6% 3.1 h 35.5 m
2016/11/06 14:22:12: ERROR INFO 14:22:12,288 ProgressMeter - CHR_HSCHR5_5_CTG1:125883314 3.500810553E10 2.5 h 0.0 s 80.9% 3.1 h 35.0 m
2016/11/06 13:37:09: ERROR INFO 13:37:08,537 ProgressMeter - CHR_HSCHR2_1_CTG15:10645339 2.4356718734E10 103.1 m 0.0 s 56.1% 3.1 h 80.7 m
2016/11/06 13:37:38: ERROR INFO 13:37:38,598 ProgressMeter - CHR_HSCHR2_1_CTG15:137273283 2.4356718734E10 103.6 m 0.0 s 56.4% 3.1 h 80.1 m
2016/11/06 13:38:08: ERROR INFO 13:38:08,619 ProgressMeter - CHR_HSCHR2_1_CTG5:16885271 2.4598917638E10 104.1 m 0.0 s 56.7% 3.1 h 79.6 m
2016/11/06 13:38:38: ERROR INFO 13:38:38,649 ProgressMeter - CHR_HSCHR2_1_CTG5:133524100 2.4598917638E10 104.7 m 0.0 s 57.0% 3.1 h 79.1 m
2016/11/06 13:39:09: ERROR INFO 13:39:09,138 ProgressMeter - CHR_HSCHR2_1_CTG7:235131 2.48411172E10 105.2 m 0.0 s 57.2% 3.1 h 78.7 m
2016/11/06 13:39:39: ERROR INFO 13:39:39,160 ProgressMeter - CHR_HSCHR2_1_CTG7:124321081 2.48411172E10 105.7 m 0.0 s 57.5% 3.1 h 78.1 m
2016/11/06 13:40:09: ERROR INFO 13:40:09,198 ProgressMeter - CHR_HSCHR2_1_CTG7_2:2884013 2.508331074E10 106.2 m 0.0 s 57.8% 3.1 h 77.6 m
2016/11/06 13:40:39: ERROR INFO 13:40:39,227 ProgressMeter - CHR_HSCHR2_1_CTG7_2:122588882 2.508331074E10 106.7 m 0.0 s 58.0% 3.1 h 77.1 m
2016/11/06 13:41:09: ERROR INFO 13:41:09,249 ProgressMeter - CHR_HSCHR2_1_CTG7_2:242210518 2.508331074E10 107.2 m 0.0 s 58.3% 3.1 h 76.6 m
2016/11/06 13:41:39: ERROR INFO 13:41:39,289 ProgressMeter - CHR_HSCHR2_2_CTG1:123258665 2.5325521258E10 107.7 m 0.0 s 58.6% 3.1 h 76.0 m
2016/11/06 13:42:09: ERROR INFO 13:42:09,318 ProgressMeter - CHR_HSCHR2_2_CTG15:3624117 2.5567719604E10 108.2 m 0.0 s 58.9% 3.1 h 75.5 m
2016/11/06 13:42:39: ERROR INFO 13:42:39,357 ProgressMeter - CHR_HSCHR2_2_CTG15:120591578 2.5567719604E10 108.7 m 0.0 s 59.2% 3.1 h 75.0 m
2016/11/06 13:43:09: ERROR INFO 13:43:09,408 ProgressMeter - CHR_HSCHR2_2_CTG15:237196900 2.5567719604E10 109.2 m 0.0 s 59.4% 3.1 h 74.5 m
2016/11/06 13:43:39: ERROR INFO 13:43:39,432 ProgressMeter - CHR_HSCHR2_2_CTG7:118129900 2.5809918148E10 109.7 m 0.0 s 59.7% 3.1 h 74.0 m
2016/11/06 13:44:09: ERROR INFO 13:44:09,497 ProgressMeter - CHR_HSCHR2_2_CTG7_2:70798 2.605214166E10 110.2 m 0.0 s 60.0% 3.1 h 73.5 m
2016/11/06 13:44:39: ERROR INFO 13:44:39,517 ProgressMeter - CHR_HSCHR2_2_CTG7_2:121068298 2.605214166E10 110.7 m 0.0 s 60.3% 3.1 h 72.9 m
2016/11/06 13:45:09: ERROR INFO 13:45:09,538 ProgressMeter - CHR_HSCHR2_2_CTG7_2:241309456 2.605214166E10 111.2 m 0.0 s 60.5% 3.1 h 72.4 m
2016/11/06 13:45:39: ERROR INFO 13:45:39,548 ProgressMeter - CHR_HSCHR2_3_CTG1:121684739 2.6294341269E10 111.7 m 0.0 s 60.8% 3.1 h 71.9 m
2016/11/06 13:46:09: ERROR INFO 13:46:09,578 ProgressMeter - CHR_HSCHR2_3_CTG15:1564783 2.6536536895E10 112.2 m 0.0 s 61.1% 3.1 h 71.4 m
2016/11/06 13:46:39: ERROR INFO 13:46:39,607 ProgressMeter - CHR_HSCHR2_3_CTG15:122772972 2.6536536895E10 112.7 m 0.0 s 61.4% 3.1 h 70.9 m
2016/11/06 13:47:09: ERROR INFO 13:47:09,627 ProgressMeter - CHR_HSCHR2_3_CTG15:242194292 2.6536536895E10 113.2 m 0.0 s 61.7% 3.1 h 70.3 m
2016/11/06 13:47:39: ERROR INFO 13:47:39,727 ProgressMeter - CHR_HSCHR2_3_CTG7_2:124173857 2.6778731187E10 113.7 m 0.0 s 61.9% 3.1 h 69.8 m
2016/11/06 13:48:09: ERROR INFO 13:48:09,747 ProgressMeter - CHR_HSCHR2_4_CTG1:6017192 2.7020925744E10 114.2 m 0.0 s 62.2% 3.1 h 69.3 m
2016/11/06 13:48:39: ERROR INFO 13:48:39,817 ProgressMeter - CHR_HSCHR2_4_CTG1:127262833 2.7020925744E10 114.7 m 0.0 s 62.5% 3.1 h 68.8 m
2016/11/06 13:49:10: ERROR INFO 13:49:10,038 ProgressMeter - CHR_HSCHR2_4_CTG7_2:245437 2.726311682E10 115.2 m 0.0 s 62.8% 3.1 h 68.3 m
2016/11/06 13:49:40: ERROR INFO 13:49:40,058 ProgressMeter - CHR_HSCHR2_4_CTG7_2:126447247 2.726311682E10 115.7 m 0.0 s 63.1% 3.1 h 67.7 m
2016/11/06 13:50:10: ERROR INFO 13:50:10,088 ProgressMeter - CHR_HSCHR2_5_CTG7_2:7890134 2.7505313409E10 116.2 m 0.0 s 63.4% 3.1 h 67.2 m
2016/11/06 13:50:40: ERROR INFO 13:50:40,099 ProgressMeter - CHR_HSCHR2_5_CTG7_2:126824532 2.7505313409E10 116.7 m 0.0 s 63.6% 3.1 h 66.7 m
2016/11/06 13:51:10: ERROR INFO 13:51:10,159 ProgressMeter - CHR_HSCHR2_5_CTG7_2:242199685 2.7505313409E10 117.2 m 0.0 s 63.9% 3.1 h 66.2 m
2016/11/06 13:51:40: ERROR INFO 13:51:40,197 ProgressMeter - CHR_HSCHR3_1_CTG1:116633737 2.7747513094E10 117.7 m 0.0 s 64.2% 3.1 h 65.7 m
2016/11/06 13:52:10: ERROR INFO 13:52:10,227 ProgressMeter - CHR_HSCHR3_1_CTG2_1:36598039 2.7945810574E10 118.2 m 0.0 s 64.4% 3.1 h 65.2 m
2016/11/06 13:52:40: ERROR INFO 13:52:40,243 ProgressMeter - CHR_HSCHR3_1_CTG2_1:157633643 2.7945810574E10 118.7 m 0.0 s 64.7% 3.1 h 64.7 m
2016/11/06 13:53:10: ERROR INFO 13:53:10,268 ProgressMeter - CHR_HSCHR3_1_CTG3:71190100 2.8144116671E10 119.2 m 0.0 s 65.0% 3.1 h 64.2 m
2016/11/06 13:53:40: ERROR INFO 13:53:40,279 ProgressMeter - CHR_HSCHR3_1_CTG3:193482079 2.8144116671E10 119.7 m 0.0 s 65.3% 3.1 h 63.7 m
2016/11/06 13:09:07: ERROR INFO 13:09:06,788 ProgressMeter - CHR_HSCHR19KIR_ABC08_AB_HAP_C_P_CTG3_1:53571518 1.7521499218E10 75.1 m 0.0 s 40.5% 3.1 h 110.5 m
2016/11/06 13:09:36: ERROR INFO 13:09:36,809 ProgressMeter - CHR_HSCHR19KIR_FH05_B_HAP_CTG3_1:2575358 1.7697351657E10 75.6 m 0.0 s 40.8% 3.1 h 109.9 m
2016/11/06 13:10:06: ERROR INFO 13:10:06,837 ProgressMeter - CHR_HSCHR19KIR_FH06_BA1_HAP_CTG3_1:8960389 1.781465826E10 76.1 m 0.0 s 41.0% 3.1 h 109.3 m
2016/11/06 13:10:36: ERROR INFO 13:10:36,859 ProgressMeter - CHR_HSCHR19KIR_FH08_BAX_HAP_CTG3_1:13375309 1.7931879912E10 76.6 m 0.0 s 41.3% 3.1 h 108.8 m
2016/11/06 13:11:06: ERROR INFO 13:11:06,898 ProgressMeter - CHR_HSCHR19KIR_FH13_BA2_HAP_CTG3_1:16688068 1.8049144346E10 77.1 m 0.0 s 41.6% 3.1 h 108.3 m
2016/11/06 13:11:36: ERROR INFO 13:11:36,928 ProgressMeter - CHR_HSCHR19KIR_FH15_B_HAP_CTG3_1:22430670 1.8166424149E10 77.6 m 0.0 s 41.9% 3.1 h 107.7 m
2016/11/06 13:12:06: ERROR INFO 13:12:06,938 ProgressMeter - CHR_HSCHR19KIR_G085_BA1_HAP_CTG3_1:22015600 1.8283731034E10 78.1 m 0.0 s 42.2% 3.1 h 107.2 m
2016/11/06 13:12:36: ERROR INFO 13:12:36,957 ProgressMeter - CHR_HSCHR19KIR_G248_BA2_HAP_CTG3_1:25331796 1.8400952486E10 78.6 m 0.0 s 42.4% 3.1 h 106.7 m
2016/11/06 13:13:07: ERROR INFO 13:13:07,002 ProgressMeter - CHR_HSCHR19KIR_GRC212_BA1_HAP_CTG3_1:31356588 1.8518258165E10 79.1 m 0.0 s 42.7% 3.1 h 106.1 m
2016/11/06 13:13:37: ERROR INFO 13:13:37,028 ProgressMeter - CHR_HSCHR19KIR_LUCE_BDEL_HAP_CTG3_1:39705565 1.8635478394E10 79.6 m 0.0 s 43.0% 3.1 h 105.5 m
2016/11/06 13:14:07: ERROR INFO 13:14:07,057 ProgressMeter - CHR_HSCHR19KIR_RSH_A_HAP_CTG3_1:43169101 1.8752741242E10 80.1 m 0.0 s 43.3% 3.1 h 105.0 m
2016/11/06 13:14:37: ERROR INFO 13:14:37,097 ProgressMeter - CHR_HSCHR19KIR_T7526_A_HAP_CTG3_1:45360599 1.8870021095E10 80.6 m 0.0 s 43.6% 3.1 h 104.5 m
2016/11/06 13:15:07: ERROR INFO 13:15:07,109 ProgressMeter - CHR_HSCHR19LRC_COX1_CTG3_1:51114401 1.8987269902E10 81.1 m 0.0 s 43.8% 3.1 h 103.9 m
2016/11/06 13:15:40: ERROR INFO 13:15:37,149 ProgressMeter - CHR_HSCHR19LRC_LRC_I_CTG3_1:58599096 1.9104105E10 81.6 m 0.0 s 44.1% 3.1 h 103.3 m
2016/11/06 13:16:07: ERROR INFO 13:16:07,218 ProgressMeter - CHR_HSCHR19LRC_LRC_T_CTG3_1:1615203 1.9280004328E10 82.1 m 0.0 s 44.4% 3.1 h 102.8 m
2016/11/06 13:16:37: ERROR INFO 13:16:37,238 ProgressMeter - CHR_HSCHR19LRC_PGF1_CTG3_1:58546031 1.9338565942E10 82.6 m 0.0 s 44.7% 3.1 h 102.3 m
2016/11/06 13:17:07: ERROR INFO 13:17:07,247 ProgressMeter - CHR_HSCHR19_1_CTG3_1:5750811 1.9514091415E10 83.1 m 0.0 s 44.9% 3.1 h 101.8 m
2016/11/06 13:17:37: ERROR INFO 13:17:37,288 ProgressMeter - CHR_HSCHR19_2_CTG3_1:11164563 1.9631343299E10 83.6 m 0.0 s 45.2% 3.1 h 101.2 m
2016/11/06 13:18:07: ERROR INFO 13:18:07,309 ProgressMeter - CHR_HSCHR19_3_CTG3_1:13758420 1.9748587723E10 84.1 m 0.0 s 45.5% 3.1 h 100.7 m
2016/11/06 13:18:37: ERROR INFO 13:18:37,368 ProgressMeter - CHR_HSCHR19_4_CTG3_1:16982052 1.9865833484E10 84.6 m 0.0 s 45.8% 3.1 h 100.2 m
2016/11/06 13:19:07: ERROR INFO 13:19:07,377 ProgressMeter - CHR_HSCHR1_1_CTG11:23712700 1.998307831E10 85.1 m 0.0 s 46.1% 3.1 h 99.6 m
2016/11/06 13:19:37: ERROR INFO 13:19:37,399 ProgressMeter - CHR_HSCHR1_1_CTG11:146391327 1.998307831E10 85.6 m 0.0 s 46.4% 3.1 h 99.1 m
2016/11/06 13:20:07: ERROR INFO 13:20:07,439 ProgressMeter - CHR_HSCHR1_1_CTG3:15710462 2.0232039849E10 86.1 m 0.0 s 46.6% 3.1 h 98.6 m
2016/11/06 13:20:37: ERROR INFO 13:20:37,478 ProgressMeter - CHR_HSCHR1_1_CTG3:143986125 2.0232039849E10 86.6 m 0.0 s 46.9% 3.1 h 98.0 m
2016/11/06 13:21:07: ERROR INFO 13:21:07,518 ProgressMeter - CHR_HSCHR1_1_CTG31:18148728 2.0481008255E10 87.1 m 0.0 s 47.2% 3.1 h 97.4 m
2016/11/06 13:21:37: ERROR INFO 13:21:37,558 ProgressMeter - CHR_HSCHR1_1_CTG31:135366809 2.0481008255E10 87.6 m 0.0 s 47.5% 3.1 h 96.9 m
2016/11/06 13:22:07: ERROR INFO 13:22:07,598 ProgressMeter - CHR_HSCHR1_1_CTG31:248973653 2.0481008255E10 88.1 m 0.0 s 47.7% 3.1 h 96.5 m
2016/11/06 13:22:37: ERROR INFO 13:22:37,657 ProgressMeter - CHR_HSCHR1_1_CTG32_1:126900801 2.0729981908E10 88.6 m 0.0 s 48.0% 3.1 h 95.9 m
2016/11/06 13:23:07: ERROR INFO 13:23:07,677 ProgressMeter - CHR_HSCHR1_2_CTG3:2760100 2.0978942051E10 89.1 m 0.0 s 48.3% 3.1 h 95.4 m
2016/11/06 13:23:37: ERROR INFO 13:23:37,697 ProgressMeter - CHR_HSCHR1_2_CTG3:119399510 2.0978942051E10 89.6 m 0.0 s 48.6% 3.1 h 94.9 m
2016/11/06 13:24:07: ERROR INFO 13:24:07,758 ProgressMeter - CHR_HSCHR1_2_CTG3:236923600 2.0978942051E10 90.1 m 0.0 s 48.9% 3.1 h 94.4 m
2016/11/06 13:24:37: ERROR INFO 13:24:37,788 ProgressMeter - CHR_HSCHR1_2_CTG31:108804003 2.1227917053E10 90.6 m 0.0 s 49.1% 3.1 h 93.8 m
2016/11/06 13:25:07: ERROR INFO 13:25:07,838 ProgressMeter - CHR_HSCHR1_2_CTG31:236269698 2.1227917053E10 91.1 m 0.0 s 49.4% 3.1 h 93.3 m
2016/11/06 13:25:37: ERROR INFO 13:25:37,867 ProgressMeter - CHR_HSCHR1_2_CTG32_1:105861700 2.1476888879E10 91.6 m 0.0 s 49.7% 3.1 h 92.7 m
2016/11/06 12:40:34: ERROR INFO 12:40:33,988 ProgressMeter - CHR_HSCHR11_3_CTG1:82953793 1.0526129539E10 46.6 m 0.0 s 24.4% 3.2 h 2.4 h
2016/11/06 12:41:04: ERROR INFO 12:41:04,018 ProgressMeter - CHR_HSCHR12_1_CTG1:66827500 1.0661221719E10 47.1 m 0.0 s 24.7% 3.2 h 2.4 h
2016/11/06 12:41:34: ERROR INFO 12:41:34,059 ProgressMeter - CHR_HSCHR12_1_CTG2:57598192 1.0794501043E10 47.6 m 0.0 s 25.0% 3.2 h 2.4 h
2016/11/06 12:42:04: ERROR INFO 12:42:04,188 ProgressMeter - CHR_HSCHR12_1_CTG2_1:46085208 1.0927782411E10 48.1 m 0.0 s 25.3% 3.2 h 2.4 h
2016/11/06 12:42:34: ERROR INFO 12:42:34,228 ProgressMeter - CHR_HSCHR12_2_CTG2:32691958 1.1061066879E10 48.6 m 0.0 s 25.5% 3.2 h 2.4 h
2016/11/06 12:43:04: ERROR INFO 12:43:04,239 ProgressMeter - CHR_HSCHR12_2_CTG2_1:24823615 1.1194374136E10 49.1 m 0.0 s 25.8% 3.2 h 2.3 h
2016/11/06 12:43:34: ERROR INFO 12:43:34,293 ProgressMeter - CHR_HSCHR12_3_CTG2:13791700 1.1327656494E10 49.6 m 0.0 s 26.1% 3.2 h 2.3 h
2016/11/06 12:44:04: ERROR INFO 12:44:04,339 ProgressMeter - CHR_HSCHR12_3_CTG2:133271566 1.1327656494E10 50.1 m 0.0 s 26.4% 3.2 h 2.3 h
2016/11/06 12:44:34: ERROR INFO 12:44:34,388 ProgressMeter - CHR_HSCHR12_3_CTG2_1:125264615 1.146092806E10 50.6 m 0.0 s 26.7% 3.2 h 2.3 h
2016/11/06 12:45:04: ERROR INFO 12:45:04,397 ProgressMeter - CHR_HSCHR12_4_CTG2:114652426 1.1594209546E10 51.1 m 0.0 s 27.0% 3.2 h 2.3 h
2016/11/06 12:45:34: ERROR INFO 12:45:34,422 ProgressMeter - CHR_HSCHR12_4_CTG2_1:101962997 1.1727487128E10 51.6 m 0.0 s 27.2% 3.2 h 2.3 h
2016/11/06 12:46:04: ERROR INFO 12:46:04,458 ProgressMeter - CHR_HSCHR12_5_CTG2:89757053 1.1860768479E10 52.1 m 0.0 s 27.5% 3.2 h 2.3 h
2016/11/06 12:46:34: ERROR INFO 12:46:34,498 ProgressMeter - CHR_HSCHR12_5_CTG2_1:79945687 1.1994043716E10 52.6 m 0.0 s 27.8% 3.2 h 2.3 h
2016/11/06 12:47:04: ERROR INFO 12:47:04,529 ProgressMeter - CHR_HSCHR12_6_CTG2_1:65788900 1.2127323194E10 53.1 m 0.0 s 28.1% 3.2 h 2.3 h
2016/11/06 12:47:34: ERROR INFO 12:47:34,558 ProgressMeter - CHR_HSCHR12_7_CTG2_1:53324425 1.2260598555E10 53.6 m 0.0 s 28.4% 3.1 h 2.3 h
2016/11/06 12:48:04: ERROR INFO 12:48:04,579 ProgressMeter - CHR_HSCHR13_1_CTG1:45091044 1.2393888033E10 54.1 m 0.0 s 28.6% 3.1 h 2.2 h
2016/11/06 12:48:34: ERROR INFO 12:48:34,599 ProgressMeter - CHR_HSCHR13_1_CTG2:52430200 1.2508236205E10 54.6 m 0.0 s 28.9% 3.1 h 2.2 h
2016/11/06 12:49:04: ERROR INFO 12:49:04,627 ProgressMeter - CHR_HSCHR13_1_CTG3:59287602 1.262260452E10 55.1 m 0.0 s 29.2% 3.1 h 2.2 h
2016/11/06 12:49:34: ERROR INFO 12:49:34,629 ProgressMeter - CHR_HSCHR13_1_CTG4:63743874 1.2736974746E10 55.6 m 0.0 s 29.5% 3.1 h 2.2 h
2016/11/06 12:50:04: ERROR INFO 12:50:04,672 ProgressMeter - CHR_HSCHR13_1_CTG5:71820400 1.2851343078E10 56.1 m 0.0 s 29.8% 3.1 h 2.2 h
2016/11/06 12:50:34: ERROR INFO 12:50:34,707 ProgressMeter - CHR_HSCHR13_1_CTG6:78863629 1.2965708428E10 56.6 m 0.0 s 30.0% 3.1 h 2.2 h
2016/11/06 12:51:04: ERROR INFO 12:51:04,747 ProgressMeter - CHR_HSCHR14_1_CTG1:85543300 1.3080075597E10 57.1 m 0.0 s 30.3% 3.1 h 2.2 h
2016/11/06 12:51:34: ERROR INFO 12:51:34,788 ProgressMeter - CHR_HSCHR14_2_CTG1:100012999 1.3187122974E10 57.6 m 0.0 s 30.6% 3.1 h 2.2 h
2016/11/06 12:52:04: ERROR INFO 12:52:04,799 ProgressMeter - CHR_HSCHR14_7_CTG1:9923094 1.340124173E10 58.1 m 0.0 s 30.9% 3.1 h 2.2 h
2016/11/06 12:52:34: ERROR INFO 12:52:34,829 ProgressMeter - CHR_HSCHR15_1_CTG1:26070592 1.3508287458E10 58.6 m 0.0 s 31.2% 3.1 h 2.2 h
2016/11/06 12:53:04: ERROR INFO 12:53:04,878 ProgressMeter - CHR_HSCHR15_1_CTG3:41503276 1.3610285733E10 59.1 m 0.0 s 31.4% 3.1 h 2.1 h
2016/11/06 12:53:34: ERROR INFO 12:53:34,889 ProgressMeter - CHR_HSCHR15_1_CTG8:62448376 1.371228039E10 59.6 m 0.0 s 31.7% 3.1 h 2.1 h
2016/11/06 12:54:04: ERROR INFO 12:54:04,907 ProgressMeter - CHR_HSCHR15_2_CTG3:84784419 1.3814283199E10 60.1 m 0.0 s 32.0% 3.1 h 2.1 h
2016/11/06 12:54:35: ERROR INFO 12:54:35,491 ProgressMeter - CHR_HSCHR15_3_CTG3:42400 1.4018282491E10 60.6 m 0.0 s 32.3% 3.1 h 2.1 h
2016/11/06 12:55:05: ERROR INFO 12:55:05,538 ProgressMeter - CHR_HSCHR15_3_CTG8:22287700 1.4120276254E10 61.1 m 0.0 s 32.6% 3.1 h 2.1 h
2016/11/06 12:55:35: ERROR INFO 12:55:35,579 ProgressMeter - CHR_HSCHR15_4_CTG8:43536295 1.422227597E10 61.6 m 0.0 s 32.8% 3.1 h 2.1 h
2016/11/06 12:56:05: ERROR INFO 12:56:05,627 ProgressMeter - CHR_HSCHR15_5_CTG8:64069544 1.4324347357E10 62.1 m 0.0 s 33.1% 3.1 h 2.1 h
2016/11/06 12:56:35: ERROR INFO 12:56:35,859 ProgressMeter - CHR_HSCHR15_6_CTG8:86755069 1.4426417635E10 62.6 m 0.0 s 33.4% 3.1 h 2.1 h
2016/11/06 12:57:05: ERROR INFO 12:57:05,899 ProgressMeter - CHR_HSCHR16_1_CTG3_1:19163912 1.4618366013E10 63.1 m 0.0 s 33.7% 3.1 h 2.1 h
2016/11/06 12:11:32: ERROR INFO 12:11:31,658 ProgressMeter - CHR_HG151_NOVEL_TEST:44517221 3.590596221E9 17.5 m 0.0 s 8.4% 3.5 h 3.2 h
2016/11/06 12:12:01: ERROR INFO 12:12:01,688 ProgressMeter - CHR_HG1651_PATCH:25248427 3.725693917E9 18.0 m 0.0 s 8.6% 3.5 h 3.2 h
2016/11/06 12:12:31: ERROR INFO 12:12:31,707 ProgressMeter - CHR_HG1651_PATCH:151787350 3.725693917E9 18.5 m 0.0 s 8.9% 3.5 h 3.2 h
2016/11/06 12:13:01: ERROR INFO 12:13:01,712 ProgressMeter - CHR_HG1832_PATCH:98589294 3.896473567E9 19.0 m 0.0 s 9.2% 3.4 h 3.1 h
2016/11/06 12:13:31: ERROR INFO 12:13:31,748 ProgressMeter - CHR_HG1832_PATCH:218668384 3.896473567E9 19.5 m 0.0 s 9.5% 3.4 h 3.1 h
2016/11/06 12:14:01: ERROR INFO 12:14:01,777 ProgressMeter - CHR_HG2022_PATCH:26473411 4.204066229E9 20.0 m 0.0 s 9.7% 3.4 h 3.1 h
2016/11/06 12:14:31: ERROR INFO 12:14:31,807 ProgressMeter - CHR_HG2022_PATCH:153011320 4.204066229E9 20.5 m 0.0 s 10.0% 3.4 h 3.1 h
2016/11/06 12:15:01: ERROR INFO 12:15:01,829 ProgressMeter - CHR_HG2030_PATCH:75864130 4.40236217E9 21.0 m 0.0 s 10.3% 3.4 h 3.0 h
2016/11/06 12:15:31: ERROR INFO 12:15:31,859 ProgressMeter - CHR_HG2058_PATCH:55889267 4.540757035E9 21.5 m 0.0 s 10.6% 3.4 h 3.0 h
2016/11/06 12:16:01: ERROR INFO 12:16:01,898 ProgressMeter - CHR_HG2058_PATCH:174826000 4.540757035E9 22.0 m 0.0 s 10.9% 3.4 h 3.0 h
2016/11/06 12:16:31: ERROR INFO 12:16:31,947 ProgressMeter - CHR_HG2062_PATCH:46959746 4.789713457E9 22.5 m 0.0 s 11.1% 3.4 h 3.0 h
2016/11/06 12:17:01: ERROR INFO 12:17:01,977 ProgressMeter - CHR_HG2066_PATCH:111263797 4.846975629E9 23.0 m 0.0 s 11.4% 3.4 h 3.0 h
2016/11/06 12:17:31: ERROR INFO 12:17:31,998 ProgressMeter - CHR_HG2095_PATCH:34177900 5.045271184E9 23.5 m 0.0 s 11.7% 3.4 h 3.0 h
2016/11/06 12:18:02: ERROR INFO 12:18:02,045 ProgressMeter - CHR_HG2095_PATCH:153855100 5.045271184E9 24.0 m 0.0 s 12.0% 3.3 h 2.9 h
2016/11/06 12:18:32: ERROR INFO 12:18:32,089 ProgressMeter - CHR_HG2104_PATCH:21730129 5.294230315E9 24.5 m 0.0 s 12.2% 3.3 h 2.9 h
2016/11/06 12:19:02: ERROR INFO 12:19:02,137 ProgressMeter - CHR_HG2104_PATCH:149136400 5.294230315E9 25.0 m 0.0 s 12.5% 3.3 h 2.9 h
2016/11/06 12:19:32: ERROR INFO 12:19:32,150 ProgressMeter - CHR_HG2128_PATCH:21807286 5.543188574E9 25.5 m 0.0 s 12.8% 3.3 h 2.9 h
2016/11/06 12:20:02: ERROR INFO 12:20:02,188 ProgressMeter - CHR_HG2128_PATCH:144773873 5.543188574E9 26.0 m 0.0 s 13.1% 3.3 h 2.9 h
2016/11/06 12:20:32: ERROR INFO 12:20:32,209 ProgressMeter - CHR_HG2191_PATCH:94685424 5.714000258E9 26.5 m 0.0 s 13.4% 3.3 h 2.9 h
2016/11/06 12:21:02: ERROR INFO 12:21:02,248 ProgressMeter - CHR_HG2216_PATCH:85580464 5.847799737E9 27.0 m 0.0 s 13.7% 3.3 h 2.8 h
2016/11/06 12:21:32: ERROR INFO 12:21:32,289 ProgressMeter - CHR_HG2217_PATCH:92188423 5.962176165E9 27.5 m 0.0 s 13.9% 3.3 h 2.8 h
2016/11/06 12:22:02: ERROR INFO 12:22:02,351 ProgressMeter - CHR_HG2232_PATCH:77461794 6.097262786E9 28.0 m 0.0 s 14.2% 3.3 h 2.8 h
2016/11/06 12:22:32: ERROR INFO 12:22:32,378 ProgressMeter - CHR_HG2232_PATCH:204171001 6.097262786E9 28.5 m 0.0 s 14.5% 3.3 h 2.8 h
2016/11/06 12:23:02: ERROR INFO 12:23:02,418 ProgressMeter - CHR_HG2233_PATCH:80529215 6.339456315E9 29.0 m 0.0 s 14.8% 3.3 h 2.8 h
2016/11/06 12:23:32: ERROR INFO 12:23:32,439 ProgressMeter - CHR_HG2233_PATCH:200036500 6.339456315E9 29.5 m 0.0 s 15.1% 3.3 h 2.8 h
2016/11/06 12:24:02: ERROR INFO 12:24:02,468 ProgressMeter - CHR_HG2235_PATCH:75788500 6.58164985E9 30.0 m 0.0 s 15.3% 3.3 h 2.8 h
2016/11/06 12:24:32: ERROR INFO 12:24:32,894 ProgressMeter - CHR_HG2237_PATCH:221331 6.779945505E9 30.6 m 0.0 s 15.6% 3.3 h 2.8 h
2016/11/06 12:25:02: ERROR INFO 12:25:02,928 ProgressMeter - CHR_HG2237_PATCH:122562593 6.779945505E9 31.1 m 0.0 s 15.9% 3.3 h 2.7 h
2016/11/06 12:25:32: ERROR INFO 12:25:32,939 ProgressMeter - CHR_HG2239_PATCH:42279919 6.978235834E9 31.6 m 0.0 s 16.2% 3.3 h 2.7 h
2016/11/06 12:26:02: ERROR INFO 12:26:02,959 ProgressMeter - CHR_HG2241_PATCH:5953232 7.137581153E9 32.1 m 0.0 s 16.4% 3.2 h 2.7 h
2016/11/06 12:26:32: ERROR INFO 12:26:32,979 ProgressMeter - CHR_HG2241_PATCH:130671345 7.137581153E9 32.6 m 0.0 s 16.7% 3.2 h 2.7 h
2016/11/06 12:27:03: ERROR INFO 12:27:03,007 ProgressMeter - CHR_HG2242_HG2243_PATCH:117109698 7.271373875E9 33.1 m 0.0 s 17.0% 3.2 h 2.7 h
2016/11/06 12:27:33: ERROR INFO 12:27:33,067 ProgressMeter - CHR_HG2244_HG2245_PATCH:104613489 7.405171172E9 33.6 m 0.0 s 17.3% 3.2 h 2.7 h
2016/11/06 12:28:03: ERROR INFO 12:28:03,078 ProgressMeter - CHR_HG2247_PATCH:93625352 7.538968597E9 34.1 m 0.0 s 17.6% 3.2 h 2.7 h
2016/11/06 12:10:13: DEBUG Enqueuing command:
#TASK tags=Sample_5
mkdir -p /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/freebayes && \
vcffilter -f “QUAL > 1 & QUAL / AO > 10 & SAF > 0 & SAR > 0 & RPR > 1 & RPL > 1” \
/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/freebayes/Sample_5_freebayes_raw.vcf > /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/freebayes/Sample_5_filtered.freebayes.vcf
2016/11/06 12:10:14: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 01 seconds