Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

UnifiedGenotyper progress halts

hrbigelowhrbigelow San FranciscoPosts: 6Member

Hi,

In the below log file of a UnifiedGenotyper run, the run made steady progress until about 95% completion, at which point the program keeps running for 3 hours. There has not been any new output to the log file or the vcf file.

In other runs, I've also seen Java GC errors.

Just wondering if something is wrong?

top reveals that the program is still working very hard.

18824 hbigelow 20 0 35.7g 33g 5452 R 94.4 52.9 167:27.83 java
18818 hbigelow 20 0 35.7g 33g 5452 R 93.7 52.9 167:44.83 java
18820 hbigelow 20 0 35.7g 33g 5452 R 93.7 52.9 167:28.44 java
18821 hbigelow 20 0 35.7g 33g 5452 R 93.7 52.9 167:24.83 java
18822 hbigelow 20 0 35.7g 33g 5452 R 93.7 52.9 167:25.96 java
18823 hbigelow 20 0 35.7g 33g 5452 R 93.7 52.9 167:26.57 java
18817 hbigelow 20 0 35.7g 33g 5452 R 93.4 52.9 167:26.73 java
18825 hbigelow 20 0 35.7g 33g 5452 R 93.4 52.9 167:24.03 java
18819 hbigelow 20 0 35.7g 33g 5452 R 93.1 52.9 167:27.78 java
18816 hbigelow 20 0 35.7g 33g 5452 R 92.7 52.9 167:33.16 java
18826 hbigelow 20 0 35.7g 33g 5452 S 5.6 52.9 4:34.92 java

INFO 08:23:21,511 HelpFormatter - --------------------------------------------------------------------------------
INFO 08:23:21,512 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-3-ge1dbcc8, Compiled 2012/08/22 18:12:18
INFO 08:23:21,513 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 08:23:21,513 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 08:23:21,515 HelpFormatter - Program Args: -nt 12 -nct 10 -L chr6:30000001-60000000 -rbs 100000 -T UnifiedGenotyper -rf BadCigar -R /dev/shm/CEUref.hg19.fasta -glm BOTH -D /dev/shm/dbsnp_135.hg19.reordered.vcf -metrics test.metrics.txt -stand_call_conf 30.0 -stand_emit_conf 10.0 -dcov 1000 --max_alternate_alleles 10 -A AlleleBalance -A AlleleBalanceBySample -A BaseCounts -A BaseQualityRankSumTest -A DepthOfCoverage -A DepthPerAlleleBySample -A FisherStrand -A HaplotypeScore -A HardyWeinberg -A IndelType -A LowMQ -A MappingQualityRankSumTest -A MappingQualityZero -A MappingQualityZeroBySample -A MappingQualityZeroFraction -A QualByDepth -A ReadPosRankSumTest -A RMSMappingQuality -A SampleList -o chunk41.vcf -I ./AC2181ACXX_DS-124072_GAGTGG_L006_001.markdup.fixed.left.recal.rehead.bam -I ./AC2181ACXX_DS-124113_GTCCGC_L001_001.markdup.fixed.left.recal.rehead.bam -I ./AC2181ACXX_DS-124080_ATTCCT_L008_001.markdup.fixed.left.recal.rehead.bam -I ./AD23GUACXX_DS-124122_AGTCAA_L005_001.markdup.fixed.left.recal.rehead.bam -I ./AD23GUACXX_DS-124118_GGCTAC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./AC2181ACXX_DS-124073_ACTGAT_L007_001.markdup.fixed.left.recal.rehead.bam -I ./AD23GUACXX_DS-124121_CTTGTA_L004_001.markdup.fixed.left.recal.rehead.bam -I ./BC21VPACXX_DS-124073_TAGCTT_L002_001.markdup.fixed.left.recal.rehead.bam -I ./AC1TY5ACXX_DS-124071_ATCACG_L001_001.markdup.fixed.left.recal.rehead.bam -I ./BC21V0ACXX_DS-124122_ATTCCT_L008_001.markdup.fixed.left.recal.rehead.bam -I ./BC21V0ACXX_DS-124121_ACTGAT_L007_001.markdup.fixed.left.recal.rehead.bam -I ./AD23GUACXX_DS-124111_TAGCTT_L002_001.markdup.fixed.left.recal.rehead.bam -I ./AC1TY5ACXX_DS-124089_TTAGGC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./BC21VPACXX_DS-124072_GATCAG_L001_001.markdup.fixed.left.recal.rehead.bam -I ./AC1TY5ACXX_DS-124063_ACTTGA_L008_001.markdup.fixed.left.recal.rehead.bam -I ./AC1TY5ACXX_DS-124085_CGATGT_L002_001.markdup.fixed.left.recal.rehead.bam -I ./AC21UYACXX_DS-124085_ATTCCT_L008_001.markdup.fixed.left.recal.rehead.bam -I ./AC21UYACXX_DS-124071_ACTGAT_L007_001.markdup.fixed.left.recal.rehead.bam -I ./AC21MLACXX_DS-124113_TGACCA_L004_001.markdup.fixed.left.recal.rehead.bam -I ./AC21MLACXX_DS-124116_ACAGTG_L005_001.markdup.fixed.left.recal.rehead.bam -I ./BC218BACXX_DS-124103_CAGATC_L007_001.markdup.fixed.left.recal.rehead.bam -I ./BC218BACXX_DS-124104_ACTTGA_L008_001.markdup.fixed.left.recal.rehead.bam -I ./BC218BACXX_DS-124099_ACAGTG_L005_001.markdup.fixed.left.recal.rehead.bam -I ./BC218BACXX_DS-124102_GCCAAT_L006_001.markdup.fixed.left.recal.rehead.bam -I ./AD23GUACXX_DS-124127_ATGTCA_L007_001.markdup.fixed.left.recal.rehead.bam -I ./AD23GUACXX_DS-124126_AGTTCC_L006_001.markdup.fixed.left.recal.rehead.bam -I ./AD23GUACXX_DS-124128_CCGTCC_L008_001.markdup.fixed.left.recal.rehead.bam -I ./AD24T2ACXX_DS-124093_GTCCGC_L001_001.markdup.fixed.left.recal.rehead.bam -I ./AC1TY5ACXX_DS-124096_TGACCA_L004_001.markdup.fixed.left.recal.rehead.bam -I ./AC219BACXX_DS-124099_GTGAAA_L002_001.markdup.fixed.left.recal.rehead.bam -I ./AC1TY5ACXX_DS-124100_ACAGTG_L005_001.markdup.fixed.left.recal.rehead.bam -I ./AC1TY5ACXX_DS-124113_GCCAAT_L006_001.markdup.fixed.left.recal.rehead.bam -I ./AC2181ACXX_DS-124116_GTGAAA_L002_001.markdup.fixed.left.recal.rehead.bam -I ./AC219BACXX_DS-124093_GTCCGC_L001_001.markdup.fixed.left.recal.rehead.bam -I ./AC219BACXX_DS-124102_GTGGCC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./AC1TY5ACXX_DS-124116_CAGATC_L007_001.markdup.fixed.left.recal.rehead.bam -I ./BC21VPACXX_DS-124088_AGTCAA_L005_001.markdup.fixed.left.recal.rehead.bam -I ./BC21VPACXX_DS-124080_GGCTAC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./BC21VPACXX_DS-124086_CTTGTA_L004_001.markdup.fixed.left.recal.rehead.bam -I ./BC21VPACXX_DS-124091_AGTTCC_L006_001.markdup.fixed.left.recal.rehead.bam -I ./AC21UYACXX_DS-124158_GTCCGC_L001_001.markdup.fixed.left.recal.rehead.bam -I ./AC21UYACXX_DS-124171_GTTTCG_L004_001.markdup.fixed.left.recal.rehead.bam -I ./AC21UYACXX_DS-124162_GTGGCC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./AC21UYACXX_DS-124161_GTGAAA_L002_001.markdup.fixed.left.recal.rehead.bam -I ./AD24T2ACXX_DS-124102_GTGGCC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./AD24T2ACXX_DS-124099_GTGAAA_L002_001.markdup.fixed.left.recal.rehead.bam -I ./AD24T2ACXX_DS-124103_GTTTCG_L004_001.markdup.fixed.left.recal.rehead.bam -I ./AD24T2ACXX_DS-124104_CGTACG_L005_001.markdup.fixed.left.recal.rehead.bam -I ./AC2178ACXX_DS-124127_CGATGT_L002_001.markdup.fixed.left.recal.rehead.bam -I ./AC2178ACXX_DS-124126_ATCACG_L001_001.markdup.fixed.left.recal.rehead.bam -I ./AC2178ACXX_DS-124128_TTAGGC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./BC219MACXX_DS-124177_GATCAG_L008_001.markdup.fixed.left.recal.rehead.bam -I ./AC2178ACXX_DS-124158_TGACCA_L004_001.markdup.fixed.left.recal.rehead.bam -I ./AC219BACXX_DS-124103_GTTTCG_L004_001.markdup.fixed.left.recal.rehead.bam -I ./BC21TPACXX_DS-124122_CGATGT_L002_001.markdup.fixed.left.recal.rehead.bam -I ./AC219BACXX_DS-124104_CGTACG_L005_001.markdup.fixed.left.recal.rehead.bam -I ./BC21TPACXX_DS-124121_ATCACG_L001_001.markdup.fixed.left.recal.rehead.bam -I ./AC219BACXX_DS-124110_GAGTGG_L006_001.markdup.fixed.left.recal.rehead.bam -I ./BC21VPACXX_DS-124093_ATGTCA_L007_001.markdup.fixed.left.recal.rehead.bam -I ./BC21VPACXX_DS-124099_CCGTCC_L008_001.markdup.fixed.left.recal.rehead.bam -I ./BC22FPACXX_DS-124085_AGTCAA_L005_001.markdup.fixed.left.recal.rehead.bam -I ./BC22FPACXX_DS-124071_CTTGTA_L004_001.markdup.fixed.left.recal.rehead.bam -I ./AC219BACXX_DS-124111_ACTGAT_L007_001.markdup.fixed.left.recal.rehead.bam -I ./AC21VNACXX_DS-124064_GATCAG_L001_001.markdup.fixed.left.recal.rehead.bam -I ./AC21UYACXX_DS-124177_GAGTGG_L006_001.markdup.fixed.left.recal.rehead.bam -I ./AC21UYACXX_DS-124174_CGTACG_L005_001.markdup.fixed.left.recal.rehead.bam -I ./AC21VNACXX_DS-124070_TAGCTT_L002_001.markdup.fixed.left.recal.rehead.bam -I ./AD24T2ACXX_DS-124110_GAGTGG_L006_001.markdup.fixed.left.recal.rehead.bam -I ./AD24T2ACXX_DS-124111_ACTGAT_L007_001.markdup.fixed.left.recal.rehead.bam -I ./AD24T2ACXX_DS-124118_ATTCCT_L008_001.markdup.fixed.left.recal.rehead.bam -I ./BC218BACXX_DS-124086_ATCACG_L001_001.markdup.fixed.left.recal.rehead.bam -I ./AC2178ACXX_DS-124161_ACAGTG_L005_001.markdup.fixed.left.recal.rehead.bam -I ./AC2178ACXX_DS-124162_GCCAAT_L006_001.markdup.fixed.left.recal.rehead.bam -I ./AC2178ACXX_DS-124171_CAGATC_L007_001.markdup.fixed.left.recal.rehead.bam -I ./AC21MLACXX_DS-124063_GCCAAT_L006_001.markdup.fixed.left.recal.rehead.bam -I ./AC2178ACXX_DS-124174_ACTTGA_L008_001.markdup.fixed.left.recal.rehead.bam -I ./AC219BACXX_DS-124118_ATTCCT_L008_001.markdup.fixed.left.recal.rehead.bam -I ./AC21MLACXX_DS-124064_CAGATC_L007_001.markdup.fixed.left.recal.rehead.bam -I ./AC21MLACXX_DS-124070_ACTTGA_L008_001.markdup.fixed.left.recal.rehead.bam -I ./BC22FPACXX_DS-124089_AGTTCC_L006_001.markdup.fixed.left.recal.rehead.bam -I ./BC22FPACXX_DS-124096_ATGTCA_L007_001.markdup.fixed.left.recal.rehead.bam -I ./BC22FPACXX_DS-124100_CCGTCC_L008_001.markdup.fixed.left.recal.rehead.bam -I ./BC22FPACXX_DS-124171_GATCAG_L001_001.markdup.fixed.left.recal.rehead.bam -I ./BC21TPACXX_DS-124128_ACAGTG_L005_001.markdup.fixed.left.recal.rehead.bam -I ./BC21TPACXX_DS-124127_TGACCA_L004_001.markdup.fixed.left.recal.rehead.bam -I ./BC21TPACXX_DS-124158_GCCAAT_L006_001.markdup.fixed.left.recal.rehead.bam -I ./BC21TPACXX_DS-124161_CAGATC_L007_001.markdup.fixed.left.recal.rehead.bam -I ./AC21VNACXX_DS-124072_GGCTAC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./AC21VNACXX_DS-124086_AGTTCC_L006_001.markdup.fixed.left.recal.rehead.bam -I ./AC21VNACXX_DS-124073_CTTGTA_L004_001.markdup.fixed.left.recal.rehead.bam -I ./AC21VNACXX_DS-124080_AGTCAA_L005_001.markdup.fixed.left.recal.rehead.bam -I ./BC218BACXX_DS-124088_CGATGT_L002_001.markdup.fixed.left.recal.rehead.bam -I ./BC218BACXX_DS-124091_TTAGGC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./BC218BACXX_DS-124093_TGACCA_L004_001.markdup.fixed.left.recal.rehead.bam -I ./AC21MLACXX_DS-124089_ATCACG_L001_001.markdup.fixed.left.recal.rehead.bam -I ./AC21MLACXX_DS-124096_CGATGT_L002_001.markdup.fixed.left.recal.rehead.bam -I ./AC21MLACXX_DS-124100_TTAGGC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./BC22FPACXX_DS-124174_TAGCTT_L002_001.markdup.fixed.left.recal.rehead.bam -I ./AC2181ACXX_DS-124063_GTGGCC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./BC22FPACXX_DS-124177_GGCTAC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./AC2181ACXX_DS-124064_GTTTCG_L004_001.markdup.fixed.left.recal.rehead.bam -I ./AC2181ACXX_DS-124070_CGTACG_L005_001.markdup.fixed.left.recal.rehead.bam -I ./AC21VNACXX_DS-124091_CCGTCC_L008_001.markdup.fixed.left.recal.rehead.bam -I ./AD23GUACXX_DS-124110_GATCAG_L001_001.markdup.fixed.left.recal.rehead.bam -I ./AC21VNACXX_DS-124088_ATGTCA_L007_001.markdup.fixed.left.recal.rehead.bam -I ./BC21TPACXX_DS-124162_ACTTGA_L008_001.markdup.fixed.left.recal.rehead.bam -I ./BC21V0ACXX_DS-124102_GTCCGC_L001_001.markdup.fixed.left.recal.rehead.bam -I ./BC21V0ACXX_DS-124103_GTGAAA_L002_001.markdup.fixed.left.recal.rehead.bam -I ./BC21V0ACXX_DS-124104_GTGGCC_L003_001.markdup.fixed.left.recal.rehead.bam -I ./BC21V0ACXX_DS-124110_GTTTCG_L004_001.markdup.fixed.left.recal.rehead.bam -I ./BC21V0ACXX_DS-124111_CGTACG_L005_001.markdup.fixed.left.recal.rehead.bam -I ./BC21V0ACXX_DS-124118_GAGTGG_L006_001.markdup.fixed.left.recal.rehead.bam -I ./BC21TPACXX_DS-124126_TTAGGC_L003_001.markdup.fixed.left.recal.rehead.bam
INFO 08:23:21,516 HelpFormatter - Date/Time: 2013/09/26 08:23:21
INFO 08:23:21,516 HelpFormatter - --------------------------------------------------------------------------------
INFO 08:23:21,516 HelpFormatter - --------------------------------------------------------------------------------
INFO 08:23:21,554 ArgumentTypeDescriptor - Dynamically determined type of /dev/shm/dbsnp_135.hg19.reordered.vcf to be VCF
INFO 08:23:21,567 GenomeAnalysisEngine - Strictness is SILENT
INFO 08:23:21,601 SAMDataSource - Running in asynchronous I/O mode; number of threads = 2
INFO 08:23:21,604 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 08:23:21,814 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.21 s, 50 of 113 in 0.21 s / 0.00 m (240.38 tasks/s). 63 remaining with est. completion in 0.26 s / 0.00 m
INFO 08:23:21,985 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.17 s, 100 of 113 in 0.38 s / 0.01 m (263.16 tasks/s). 13 remaining with est. completion in 0.05 s / 0.00 m
INFO 08:23:22,029 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.43
INFO 08:23:22,149 RMDTrackBuilder - Loading Tribble index from disk for file /dev/shm/dbsnp_135.hg19.reordered.vcf
INFO 08:23:22,285 MicroScheduler - Running the GATK in parallel mode with 10 concurrent threads
INFO 08:23:36,786 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 08:23:36,860 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.07 s, 50 of 113 in 0.07 s / 0.00 m (675.68 tasks/s). 63 remaining with est. completion in 0.09 s / 0.00 m
INFO 08:23:36,921 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.06 s, 100 of 113 in 0.14 s / 0.00 m (740.74 tasks/s). 13 remaining with est. completion in 0.02 s / 0.00 m
INFO 08:23:36,943 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.16
INFO 08:23:36,980 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 08:23:37,091 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.11 s, 50 of 113 in 0.11 s / 0.00 m (454.55 tasks/s). 63 remaining with est. completion in 0.14 s / 0.00 m
INFO 08:23:37,186 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.09 s, 100 of 113 in 0.21 s / 0.00 m (487.80 tasks/s). 13 remaining with est. completion in 0.03 s / 0.00 m
INFO 08:23:37,202 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.22
INFO 08:23:37,211 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 08:23:37,281 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.07 s, 50 of 113 in 0.07 s / 0.00 m (724.64 tasks/s). 63 remaining with est. completion in 0.09 s / 0.00 m
INFO 08:23:37,337 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.06 s, 100 of 113 in 0.13 s / 0.00 m (793.65 tasks/s). 13 remaining with est. completion in 0.02 s / 0.00 m
INFO 08:23:37,354 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14
INFO 08:23:37,362 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 08:23:37,418 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.06 s, 50 of 113 in 0.06 s / 0.00 m (909.09 tasks/s). 63 remaining with est. completion in 0.07 s / 0.00 m
INFO 08:23:37,468 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.05 s, 100 of 113 in 0.11 s / 0.00 m (943.40 tasks/s). 13 remaining with est. completion in 0.01 s / 0.00 m
INFO 08:23:37,484 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
INFO 08:23:37,492 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 08:23:37,552 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.06 s, 50 of 113 in 0.06 s / 0.00 m (847.46 tasks/s). 63 remaining with est. completion in 0.07 s / 0.00 m
INFO 08:23:37,605 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.05 s, 100 of 113 in 0.11 s / 0.00 m (884.96 tasks/s). 13 remaining with est. completion in 0.01 s / 0.00 m
INFO 08:23:37,629 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14
INFO 08:23:37,638 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 08:23:37,710 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.07 s, 50 of 113 in 0.07 s / 0.00 m (704.23 tasks/s). 63 remaining with est. completion in 0.09 s / 0.00 m
INFO 08:23:37,775 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.06 s, 100 of 113 in 0.14 s / 0.00 m (735.29 tasks/s). 13 remaining with est. completion in 0.02 s / 0.00 m
INFO 08:23:37,794 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.16
INFO 08:23:37,800 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 08:23:37,863 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.06 s, 50 of 113 in 0.06 s / 0.00 m (793.65 tasks/s). 63 remaining with est. completion in 0.08 s / 0.00 m
INFO 08:23:37,932 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.07 s, 100 of 113 in 0.13 s / 0.00 m (763.36 tasks/s). 13 remaining with est. completion in 0.02 s / 0.00 m
INFO 08:23:37,946 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.15
INFO 08:23:37,955 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 08:23:38,024 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.07 s, 50 of 113 in 0.07 s / 0.00 m (724.64 tasks/s). 63 remaining with est. completion in 0.09 s / 0.00 m
INFO 08:23:38,083 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.06 s, 100 of 113 in 0.13 s / 0.00 m (781.25 tasks/s). 13 remaining with est. completion in 0.02 s / 0.00 m
INFO 08:23:38,100 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.15
INFO 08:23:38,111 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 08:23:38,172 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.06 s, 50 of 113 in 0.06 s / 0.00 m (833.33 tasks/s). 63 remaining with est. completion in 0.08 s / 0.00 m
INFO 08:23:38,223 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.05 s, 100 of 113 in 0.11 s / 0.00 m (892.86 tasks/s). 13 remaining with est. completion in 0.01 s / 0.00 m
INFO 08:23:38,238 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
INFO 08:23:40,277 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
INFO 08:23:40,277 TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining
INFO 08:23:41,846 RMDTrackBuilder - Loading Tribble index from disk for file /dev/shm/dbsnp_135.hg19.reordered.vcf
INFO 08:23:41,906 RMDTrackBuilder - Loading Tribble index from disk for file /dev/shm/dbsnp_135.hg19.reordered.vcf
INFO 08:23:42,095 RMDTrackBuilder - Loading Tribble index from disk for file /dev/shm/dbsnp_135.hg19.reordered.vcf
INFO 08:23:42,756 RMDTrackBuilder - Loading Tribble index from disk for file /dev/shm/dbsnp_135.hg19.reordered.vcf
INFO 08:23:42,815 RMDTrackBuilder - Loading Tribble index from disk for file /dev/shm/dbsnp_135.hg19.reordered.vcf
INFO 08:23:42,876 RMDTrackBuilder - Loading Tribble index from disk for file /dev/shm/dbsnp_135.hg19.reordered.vcf
INFO 08:23:42,940 RMDTrackBuilder - Loading Tribble index from disk for file /dev/shm/dbsnp_135.hg19.reordered.vcf
INFO 08:23:43,003 RMDTrackBuilder - Loading Tribble index from disk for file /dev/shm/dbsnp_135.hg19.reordered.vcf
INFO 08:23:43,071 RMDTrackBuilder - Loading Tribble index from disk for file /dev/shm/dbsnp_135.hg19.reordered.vcf
INFO 08:24:26,712 TraversalEngine - chr6:30116458 2.67e+03 49.9 s 5.2 h 0.4% 3.6 h 3.6 h
INFO 08:24:57,294 TraversalEngine - chr6:30151544 4.98e+03 80.5 s 4.5 h 0.5% 4.4 h 4.4 h
INFO 08:25:27,414 TraversalEngine - chr6:30078455 7.94e+04 110.6 s 23.2 m 0.3% 11.8 h 11.7 h
INFO 08:26:01,304 TraversalEngine - chr6:30207424 1.58e+05 2.4 m 15.2 m 0.7% 5.8 h 5.8 h
INFO 08:26:31,314 TraversalEngine - chr6:30240151 2.07e+05 2.9 m 14.0 m 0.8% 6.1 h 6.0 h
INFO 08:27:01,327 TraversalEngine - chr6:30442757 2.95e+05 3.4 m 11.5 m 1.5% 3.8 h 3.8 h
INFO 08:27:31,499 TraversalEngine - chr6:30449352 3.67e+05 3.9 m 10.6 m 1.5% 4.4 h 4.3 h
INFO 08:28:02,353 TraversalEngine - chr6:30591358 4.60e+05 4.4 m 9.6 m 2.0% 3.7 h 3.7 h
INFO 08:28:33,020 TraversalEngine - chr6:30704038 5.73e+05 4.9 m 8.6 m 2.3% 3.5 h 3.4 h
INFO 08:29:03,166 TraversalEngine - chr6:30757202 7.08e+05 5.4 m 7.7 m 2.5% 3.6 h 3.5 h
INFO 08:29:33,511 TraversalEngine - chr6:30875948 8.10e+05 5.9 m 7.3 m 2.9% 3.4 h 3.3 h
INFO 08:30:04,560 TraversalEngine - chr6:30930472 8.98e+05 6.5 m 7.2 m 3.1% 3.5 h 3.4 h
INFO 08:30:34,561 TraversalEngine - chr6:31119846 1.01e+06 7.0 m 6.9 m 3.7% 3.1 h 3.0 h
INFO 08:31:04,608 TraversalEngine - chr6:31129141 1.11e+06 7.5 m 6.7 m 3.8% 3.3 h 3.2 h
INFO 08:31:35,056 TraversalEngine - chr6:31267895 1.19e+06 8.0 m 6.7 m 4.2% 3.1 h 3.0 h
INFO 08:32:06,800 TraversalEngine - chr6:31394444 1.25e+06 8.5 m 6.8 m 4.6% 3.0 h 2.9 h
INFO 08:32:37,026 TraversalEngine - chr6:31434315 1.32e+06 9.0 m 6.8 m 4.8% 3.1 h 3.0 h
INFO 08:33:07,053 TraversalEngine - chr6:31468931 1.44e+06 9.5 m 6.6 m 4.9% 3.2 h 3.1 h
INFO 08:33:37,148 TraversalEngine - chr6:31640746 1.53e+06 10.0 m 6.6 m 5.5% 3.0 h 2.9 h
INFO 08:34:07,255 TraversalEngine - chr6:31732803 1.70e+06 10.5 m 6.2 m 5.8% 3.0 h 2.9 h
INFO 08:34:37,324 TraversalEngine - chr6:31949427 1.82e+06 11.0 m 6.1 m 6.5% 2.8 h 2.6 h
INFO 08:35:07,332 TraversalEngine - chr6:32038748 1.96e+06 11.5 m 5.9 m 6.8% 2.8 h 2.6 h
INFO 08:35:38,115 TraversalEngine - chr6:32260917 2.11e+06 12.0 m 5.7 m 7.5% 2.7 h 2.5 h
INFO 08:36:08,304 TraversalEngine - chr6:32299837 2.20e+06 12.5 m 5.7 m 7.7% 2.7 h 2.5 h
INFO 08:36:38,418 TraversalEngine - chr6:32426140 2.31e+06 13.0 m 5.6 m 8.1% 2.7 h 2.5 h
INFO 08:37:08,567 TraversalEngine - chr6:32434978 2.40e+06 13.5 m 5.6 m 8.1% 2.8 h 2.6 h
INFO 08:37:38,614 TraversalEngine - chr6:32420173 2.44e+06 14.0 m 5.8 m 8.1% 2.9 h 2.7 h
INFO 08:38:08,935 TraversalEngine - chr6:32589965 2.46e+06 14.5 m 5.9 m 8.6% 2.8 h 2.6 h
INFO 08:38:39,144 TraversalEngine - chr6:32640862 2.49e+06 15.0 m 6.0 m 8.8% 2.8 h 2.6 h
INFO 08:39:10,577 TraversalEngine - chr6:32518967 2.54e+06 15.6 m 6.1 m 8.4% 3.1 h 2.8 h
INFO 08:39:41,771 TraversalEngine - chr6:32553892 2.57e+06 16.1 m 6.3 m 8.5% 3.1 h 2.9 h
INFO 08:40:12,056 TraversalEngine - chr6:32682675 2.62e+06 16.6 m 6.3 m 8.9% 3.1 h 2.8 h
INFO 08:40:42,555 TraversalEngine - chr6:32785968 2.64e+06 17.1 m 6.5 m 9.3% 3.1 h 2.8 h
INFO 08:41:20,092 TraversalEngine - chr6:32795824 2.70e+06 17.7 m 6.6 m 9.3% 3.2 h 2.9 h
INFO 08:41:50,291 TraversalEngine - chr6:32809878 2.74e+06 18.2 m 6.6 m 9.4% 3.2 h 2.9 h

(i've cut a few lines here to be able to post this message -- otherwise it is too long)

INFO 08:58:38,847 TraversalEngine - chr6:37809937 7.74e+06 35.0 m 4.5 m 26.0% 2.2 h 99.5 m
INFO 08:59:08,943 TraversalEngine - chr6:38032669 7.90e+06 35.5 m 4.5 m 26.8% 2.2 h 97.2 m
INFO 08:59:39,215 TraversalEngine - chr6:38178709 8.05e+06 36.0 m 4.5 m 27.3% 2.2 h 96.2 m
INFO 09:00:09,319 TraversalEngine - chr6:38223072 8.21e+06 36.5 m 4.5 m 27.4% 2.2 h 96.8 m
INFO 09:00:39,452 TraversalEngine - chr6:38433658 8.37e+06 37.0 m 4.4 m 28.1% 2.2 h 94.7 m
INFO 09:01:13,716 TraversalEngine - chr6:38590529 8.52e+06 37.6 m 4.4 m 28.6% 2.2 h 93.7 m
INFO 09:01:43,802 TraversalEngine - chr6:38675790 8.61e+06 38.1 m 4.4 m 28.9% 2.2 h 93.7 m
INFO 09:02:13,922 TraversalEngine - chr6:38912999 8.78e+06 38.6 m 4.4 m 29.7% 2.2 h 91.4 m
INFO 09:02:43,946 TraversalEngine - chr6:38924222 8.89e+06 39.1 m 4.4 m 29.7% 2.2 h 92.4 m
INFO 09:03:14,210 TraversalEngine - chr6:38976501 9.03e+06 39.6 m 4.4 m 29.9% 2.2 h 92.8 m
INFO 09:03:44,460 TraversalEngine - chr6:39186721 9.10e+06 40.1 m 4.4 m 30.6% 2.2 h 90.9 m
INFO 09:04:14,581 TraversalEngine - chr6:39286832 9.25e+06 40.6 m 4.4 m 31.0% 2.2 h 90.6 m
INFO 09:04:44,648 TraversalEngine - chr6:39513555 9.40e+06 41.1 m 4.4 m 31.7% 2.2 h 88.6 m
INFO 09:05:14,890 TraversalEngine - chr6:39643835 9.53e+06 41.6 m 4.4 m 32.1% 2.2 h 87.9 m
INFO 09:05:45,112 TraversalEngine - chr6:39726072 9.68e+06 42.1 m 4.4 m 32.4% 2.2 h 87.8 m
INFO 09:06:15,205 TraversalEngine - chr6:39843217 9.81e+06 42.6 m 4.3 m 32.8% 2.2 h 87.3 m
INFO 09:06:45,235 TraversalEngine - chr6:40035220 9.97e+06 43.1 m 4.3 m 33.5% 2.1 h 85.8 m
INFO 09:07:18,386 TraversalEngine - chr6:40118351 1.01e+07 43.7 m 4.3 m 33.7% 2.2 h 85.9 m
INFO 09:07:48,699 TraversalEngine - chr6:40295716 1.02e+07 44.2 m 4.3 m 34.3% 2.1 h 84.6 m
INFO 09:08:18,770 TraversalEngine - chr6:40443578 1.03e+07 44.7 m 4.3 m 34.8% 2.1 h 83.7 m
INFO 09:08:48,965 TraversalEngine - chr6:40513739 1.05e+07 45.2 m 4.3 m 35.0% 2.1 h 83.8 m
INFO 09:09:19,107 TraversalEngine - chr6:40731644 1.06e+07 45.7 m 4.3 m 35.8% 2.1 h 82.1 m
INFO 09:09:49,166 TraversalEngine - chr6:40746672 1.07e+07 46.2 m 4.3 m 35.8% 2.1 h 82.8 m
INFO 09:10:19,460 TraversalEngine - chr6:40922695 1.08e+07 46.7 m 4.3 m 36.4% 2.1 h 81.6 m
INFO 09:10:49,470 TraversalEngine - chr6:41053193 1.10e+07 47.2 m 4.3 m 36.8% 2.1 h 80.9 m
INFO 09:11:19,503 TraversalEngine - chr6:41258443 1.11e+07 47.7 m 4.3 m 37.5% 2.1 h 79.4 m
INFO 09:11:49,657 TraversalEngine - chr6:41373032 1.13e+07 48.2 m 4.3 m 37.9% 2.1 h 79.0 m
INFO 09:12:19,818 TraversalEngine - chr6:41519483 1.14e+07 48.7 m 4.3 m 38.4% 2.1 h 78.2 m
INFO 09:12:49,994 TraversalEngine - chr6:41607431 1.15e+07 49.2 m 4.3 m 38.7% 2.1 h 78.0 m
INFO 09:13:20,085 TraversalEngine - chr6:41829544 1.17e+07 49.7 m 4.3 m 39.4% 2.1 h 76.4 m
INFO 09:13:51,114 TraversalEngine - chr6:41976835 1.18e+07 50.2 m 4.2 m 39.9% 2.1 h 75.6 m
INFO 09:14:21,198 TraversalEngine - chr6:42042108 1.19e+07 50.7 m 4.3 m 40.1% 2.1 h 75.7 m
INFO 09:14:51,368 TraversalEngine - chr6:42145915 1.20e+07 51.2 m 4.3 m 40.5% 2.1 h 75.3 m
INFO 09:15:21,745 TraversalEngine - chr6:42230347 1.21e+07 51.7 m 4.3 m 40.8% 2.1 h 75.2 m
INFO 09:15:51,769 TraversalEngine - chr6:42312940 1.23e+07 52.2 m 4.3 m 41.0% 2.1 h 75.1 m
INFO 09:16:21,989 TraversalEngine - chr6:42521707 1.24e+07 52.8 m 4.3 m 41.7% 2.1 h 73.6 m
INFO 09:16:52,068 TraversalEngine - chr6:42667582 1.26e+07 53.3 m 4.2 m 42.2% 2.1 h 72.9 m
INFO 09:17:22,213 TraversalEngine - chr6:42596694 1.26e+07 53.8 m 4.3 m 42.0% 2.1 h 74.3 m
INFO 09:17:52,355 TraversalEngine - chr6:42912768 1.28e+07 54.3 m 4.2 m 43.0% 2.1 h 71.8 m
INFO 09:18:23,674 TraversalEngine - chr6:42940249 1.29e+07 54.8 m 4.2 m 43.1% 2.1 h 72.2 m
INFO 09:18:53,795 TraversalEngine - chr6:43164214 1.30e+07 55.3 m 4.2 m 43.9% 2.1 h 70.7 m
INFO 09:19:23,953 TraversalEngine - chr6:43296472 1.32e+07 55.8 m 4.2 m 44.3% 2.1 h 70.1 m
INFO 09:19:58,879 TraversalEngine - chr6:43393448 1.33e+07 56.4 m 4.2 m 44.6% 2.1 h 69.9 m
INFO 09:20:28,923 TraversalEngine - chr6:43584770 1.35e+07 56.9 m 4.2 m 45.3% 2.1 h 68.7 m
INFO 09:20:59,073 TraversalEngine - chr6:43643818 1.36e+07 57.4 m 4.2 m 45.5% 2.1 h 68.8 m
INFO 09:21:32,811 TraversalEngine - chr6:43832842 1.37e+07 57.9 m 4.2 m 46.1% 2.1 h 67.7 m
INFO 09:22:03,108 TraversalEngine - chr6:43929592 1.39e+07 58.4 m 4.2 m 46.4% 2.1 h 67.4 m
INFO 09:22:33,243 TraversalEngine - chr6:44125651 1.40e+07 58.9 m 4.2 m 47.1% 2.1 h 66.2 m
INFO 09:23:03,473 TraversalEngine - chr6:44165849 1.41e+07 59.4 m 4.2 m 47.2% 2.1 h 66.4 m
INFO 09:23:33,496 TraversalEngine - chr6:44273738 1.42e+07 59.9 m 4.2 m 47.6% 2.1 h 66.0 m
INFO 09:24:03,513 TraversalEngine - chr6:44394715 1.43e+07 60.4 m 4.2 m 48.0% 2.1 h 65.5 m
INFO 09:24:35,836 TraversalEngine - chr6:44524782 1.44e+07 61.0 m 4.2 m 48.4% 2.1 h 65.0 m
INFO 09:25:05,908 TraversalEngine - chr6:44593246 1.45e+07 61.5 m 4.2 m 48.6% 2.1 h 64.9 m
INFO 09:25:35,943 TraversalEngine - chr6:44724080 1.47e+07 62.0 m 4.2 m 49.1% 2.1 h 64.3 m
INFO 09:26:06,087 TraversalEngine - chr6:44842595 1.48e+07 62.5 m 4.2 m 49.5% 2.1 h 63.8 m
INFO 09:26:36,236 TraversalEngine - chr6:45061281 1.50e+07 63.0 m 4.2 m 50.2% 2.1 h 62.5 m
INFO 09:27:06,248 TraversalEngine - chr6:45195311 1.51e+07 63.5 m 4.2 m 50.7% 2.1 h 61.9 m
INFO 09:27:36,407 TraversalEngine - chr6:45374247 1.53e+07 64.0 m 4.2 m 51.2% 2.1 h 60.9 m
INFO 09:28:06,485 TraversalEngine - chr6:45429293 1.54e+07 64.5 m 4.2 m 51.4% 2.1 h 60.9 m
INFO 09:28:36,712 TraversalEngine - chr6:45624998 1.55e+07 65.0 m 4.2 m 52.1% 2.1 h 59.8 m
INFO 09:29:06,764 TraversalEngine - chr6:45811826 1.57e+07 65.5 m 4.2 m 52.7% 2.1 h 58.8 m
INFO 09:29:38,307 TraversalEngine - chr6:45959089 1.58e+07 66.0 m 4.2 m 53.2% 2.1 h 58.1 m
INFO 09:30:08,500 TraversalEngine - chr6:46032156 1.59e+07 66.5 m 4.2 m 53.4% 2.1 h 58.0 m
INFO 09:30:38,609 TraversalEngine - chr6:46117802 1.61e+07 67.0 m 4.2 m 53.7% 2.1 h 57.7 m
INFO 09:31:08,773 TraversalEngine - chr6:46356384 1.62e+07 67.5 m 4.2 m 54.5% 2.1 h 56.3 m
INFO 09:31:38,954 TraversalEngine - chr6:46391290 1.63e+07 68.0 m 4.2 m 54.6% 2.1 h 56.5 m
INFO 09:32:09,073 TraversalEngine - chr6:46542734 1.65e+07 68.5 m 4.2 m 55.1% 2.1 h 55.8 m
INFO 09:32:39,250 TraversalEngine - chr6:46762643 1.66e+07 69.0 m 4.2 m 55.9% 2.1 h 54.5 m
INFO 09:33:09,403 TraversalEngine - chr6:46774570 1.68e+07 69.5 m 4.1 m 55.9% 2.1 h 54.8 m
INFO 09:33:39,535 TraversalEngine - chr6:46947944 1.69e+07 70.0 m 4.1 m 56.5% 2.1 h 53.9 m
INFO 09:34:09,839 TraversalEngine - chr6:47156780 1.70e+07 70.6 m 4.1 m 57.2% 2.1 h 52.8 m
INFO 09:34:39,986 TraversalEngine - chr6:47317115 1.72e+07 71.1 m 4.1 m 57.7% 2.1 h 52.0 m
INFO 09:35:09,991 TraversalEngine - chr6:47416650 1.73e+07 71.6 m 4.1 m 58.1% 2.1 h 51.7 m
INFO 09:35:40,106 TraversalEngine - chr6:47471655 1.74e+07 72.1 m 4.1 m 58.2% 2.1 h 51.7 m
INFO 09:36:10,116 TraversalEngine - chr6:47591682 1.76e+07 72.6 m 4.1 m 58.6% 2.1 h 51.2 m
INFO 09:36:40,252 TraversalEngine - chr6:47735236 1.77e+07 73.1 m 4.1 m 59.1% 2.1 h 50.5 m
INFO 09:37:10,376 TraversalEngine - chr6:47882396 1.78e+07 73.6 m 4.1 m 59.6% 2.1 h 49.8 m
INFO 09:37:40,429 TraversalEngine - chr6:48031975 1.80e+07 74.1 m 4.1 m 60.1% 2.1 h 49.2 m
INFO 09:38:10,761 TraversalEngine - chr6:48148047 1.81e+07 74.6 m 4.1 m 60.5% 2.1 h 48.7 m
INFO 09:38:40,815 TraversalEngine - chr6:48358393 1.83e+07 75.1 m 4.1 m 61.2% 2.0 h 47.6 m
INFO 09:39:10,834 TraversalEngine - chr6:48520973 1.84e+07 75.6 m 4.1 m 61.7% 2.0 h 46.8 m
INFO 09:39:40,902 TraversalEngine - chr6:48590730 1.86e+07 76.1 m 4.1 m 62.0% 2.0 h 46.7 m
INFO 09:40:10,940 TraversalEngine - chr6:48771497 1.87e+07 76.6 m 4.1 m 62.6% 2.0 h 45.8 m
INFO 09:40:41,559 TraversalEngine - chr6:48872402 1.88e+07 77.1 m 4.1 m 62.9% 2.0 h 45.4 m
INFO 09:41:11,622 TraversalEngine - chr6:49063500 1.89e+07 77.6 m 4.1 m 63.5% 2.0 h 44.5 m
INFO 09:41:41,801 TraversalEngine - chr6:49192972 1.91e+07 78.1 m 4.1 m 64.0% 2.0 h 44.0 m
INFO 09:42:11,815 TraversalEngine - chr6:49386761 1.93e+07 78.6 m 4.1 m 64.6% 2.0 h 43.0 m
INFO 09:42:41,830 TraversalEngine - chr6:49440520 1.94e+07 79.1 m 4.1 m 64.8% 2.0 h 43.0 m
INFO 09:43:11,960 TraversalEngine - chr6:49644100 1.95e+07 79.6 m 4.1 m 65.5% 2.0 h 42.0 m
INFO 09:43:42,117 TraversalEngine - chr6:49791580 1.97e+07 80.1 m 4.1 m 66.0% 2.0 h 41.3 m
INFO 09:44:12,453 TraversalEngine - chr6:49942980 1.98e+07 80.6 m 4.1 m 66.5% 2.0 h 40.6 m
INFO 09:44:42,514 TraversalEngine - chr6:50080075 2.00e+07 81.1 m 4.1 m 66.9% 2.0 h 40.1 m
INFO 09:45:12,756 TraversalEngine - chr6:50132228 2.01e+07 81.6 m 4.1 m 67.1% 2.0 h 40.0 m
INFO 09:45:43,083 TraversalEngine - chr6:50341911 2.03e+07 82.1 m 4.0 m 67.8% 2.0 h 39.0 m
INFO 09:46:13,272 TraversalEngine - chr6:50459968 2.04e+07 82.6 m 4.0 m 68.2% 2.0 h 38.5 m
INFO 09:46:43,325 TraversalEngine - chr6:50654861 2.06e+07 83.1 m 4.0 m 68.8% 2.0 h 37.6 m
INFO 09:47:13,333 TraversalEngine - chr6:50770087 2.07e+07 83.6 m 4.0 m 69.2% 2.0 h 37.2 m
INFO 09:47:43,428 TraversalEngine - chr6:50958433 2.09e+07 84.1 m 4.0 m 69.9% 2.0 h 36.3 m
INFO 09:48:13,559 TraversalEngine - chr6:51052363 2.10e+07 84.6 m 4.0 m 70.2% 2.0 h 36.0 m
INFO 09:48:43,710 TraversalEngine - chr6:51269289 2.12e+07 85.1 m 4.0 m 70.9% 2.0 h 34.9 m
INFO 09:49:13,780 TraversalEngine - chr6:51325417 2.12e+07 85.6 m 4.0 m 71.1% 2.0 h 34.8 m
INFO 09:49:43,958 TraversalEngine - chr6:51427067 2.14e+07 86.1 m 4.0 m 71.4% 2.0 h 34.5 m
INFO 09:50:13,998 TraversalEngine - chr6:51618301 2.15e+07 86.6 m 4.0 m 72.1% 2.0 h 33.6 m
INFO 09:50:44,171 TraversalEngine - chr6:51769423 2.17e+07 87.1 m 4.0 m 72.6% 2.0 h 32.9 m
INFO 09:51:14,302 TraversalEngine - chr6:51921220 2.18e+07 87.6 m 4.0 m 73.1% 119.9 m 32.3 m
INFO 09:51:44,486 TraversalEngine - chr6:52053794 2.19e+07 88.1 m 4.0 m 73.5% 119.9 m 31.8 m
INFO 09:52:14,531 TraversalEngine - chr6:52084325 2.21e+07 88.6 m 4.0 m 73.6% 2.0 h 31.8 m
INFO 09:52:44,620 TraversalEngine - chr6:52318415 2.22e+07 89.1 m 4.0 m 74.4% 119.8 m 30.7 m
INFO 09:53:15,252 TraversalEngine - chr6:52495376 2.23e+07 89.6 m 4.0 m 75.0% 119.5 m 29.9 m
INFO 09:53:45,312 TraversalEngine - chr6:52508016 2.24e+07 90.1 m 4.0 m 75.0% 2.0 h 30.0 m
INFO 09:54:15,358 TraversalEngine - chr6:52523967 2.26e+07 90.6 m 4.0 m 75.1% 2.0 h 30.1 m
INFO 09:54:45,366 TraversalEngine - chr6:52825024 2.27e+07 91.1 m 4.0 m 76.1% 119.8 m 28.7 m
INFO 09:55:15,533 TraversalEngine - chr6:52957057 2.29e+07 91.6 m 4.0 m 76.5% 119.8 m 28.1 m
INFO 09:55:45,630 TraversalEngine - chr6:53090402 2.30e+07 92.1 m 4.0 m 77.0% 119.7 m 27.6 m
INFO 09:56:15,731 TraversalEngine - chr6:53116593 2.31e+07 92.6 m 4.0 m 77.1% 2.0 h 27.6 m
INFO 09:56:45,870 TraversalEngine - chr6:53306749 2.33e+07 93.2 m 4.0 m 77.7% 119.9 m 26.8 m
INFO 09:57:16,185 TraversalEngine - chr6:53480683 2.34e+07 93.7 m 4.0 m 78.3% 119.7 m 26.0 m
INFO 09:57:46,349 TraversalEngine - chr6:53674612 2.35e+07 94.2 m 4.0 m 78.9% 119.3 m 25.2 m
INFO 09:58:16,617 TraversalEngine - chr6:53728699 2.36e+07 94.7 m 4.0 m 79.1% 119.7 m 25.0 m
INFO 09:58:46,622 TraversalEngine - chr6:53889922 2.38e+07 95.2 m 4.0 m 79.6% 119.5 m 24.3 m
INFO 09:59:16,780 TraversalEngine - chr6:53995948 2.39e+07 95.7 m 4.0 m 80.0% 119.6 m 23.9 m
INFO 09:59:46,941 TraversalEngine - chr6:54171265 2.41e+07 96.2 m 4.0 m 80.6% 119.4 m 23.2 m
INFO 10:00:17,025 TraversalEngine - chr6:54346501 2.42e+07 96.7 m 4.0 m 81.2% 119.1 m 22.4 m
INFO 10:00:47,168 TraversalEngine - chr6:54416886 2.43e+07 97.2 m 4.0 m 81.4% 119.4 m 22.2 m
INFO 10:01:17,220 TraversalEngine - chr6:54612159 2.45e+07 97.7 m 4.0 m 82.0% 119.1 m 21.4 m
INFO 10:01:47,429 TraversalEngine - chr6:54741948 2.46e+07 98.2 m 4.0 m 82.5% 119.0 m 20.9 m
INFO 10:02:17,457 TraversalEngine - chr6:54875353 2.47e+07 98.7 m 4.0 m 82.9% 119.0 m 20.3 m
INFO 10:02:47,470 TraversalEngine - chr6:55034479 2.49e+07 99.2 m 4.0 m 83.4% 118.8 m 19.7 m
INFO 10:03:17,501 TraversalEngine - chr6:55077719 2.50e+07 99.7 m 4.0 m 83.6% 119.2 m 19.6 m
INFO 10:03:47,629 TraversalEngine - chr6:55239211 2.52e+07 100.2 m 4.0 m 84.1% 119.1 m 18.9 m
INFO 10:04:17,807 TraversalEngine - chr6:55261503 2.53e+07 100.7 m 4.0 m 84.2% 119.6 m 18.9 m
INFO 10:04:48,022 TraversalEngine - chr6:55529351 2.54e+07 101.2 m 4.0 m 85.1% 118.9 m 17.7 m
INFO 10:05:18,030 TraversalEngine - chr6:55690263 2.55e+07 101.7 m 4.0 m 85.6% 118.7 m 17.1 m
INFO 10:05:48,177 TraversalEngine - chr6:55872577 2.57e+07 102.2 m 4.0 m 86.2% 118.5 m 16.3 m
INFO 10:06:18,302 TraversalEngine - chr6:56066218 2.59e+07 102.7 m 4.0 m 86.9% 118.2 m 15.5 m
INFO 10:06:50,984 TraversalEngine - chr6:56095241 2.60e+07 103.2 m 4.0 m 87.0% 118.7 m 15.4 m
INFO 10:07:21,004 TraversalEngine - chr6:56254088 2.62e+07 103.7 m 4.0 m 87.5% 118.5 m 14.8 m
INFO 10:07:51,015 TraversalEngine - chr6:56358201 2.63e+07 104.2 m 4.0 m 87.9% 118.6 m 14.4 m
INFO 10:08:21,055 TraversalEngine - chr6:56521140 2.65e+07 104.7 m 4.0 m 88.4% 118.5 m 13.7 m
INFO 10:08:51,097 TraversalEngine - chr6:56653469 2.66e+07 105.2 m 4.0 m 88.8% 118.5 m 13.2 m
INFO 10:09:21,237 TraversalEngine - chr6:56919917 2.68e+07 105.7 m 3.9 m 89.7% 117.8 m 12.1 m
INFO 10:09:51,254 TraversalEngine - chr6:56995310 2.70e+07 106.2 m 3.9 m 90.0% 118.1 m 11.8 m
INFO 10:10:21,418 TraversalEngine - chr6:57123859 2.71e+07 106.7 m 3.9 m 90.4% 118.1 m 11.3 m
INFO 10:10:51,765 TraversalEngine - chr6:57297613 2.72e+07 107.2 m 3.9 m 91.0% 117.9 m 10.6 m
INFO 10:11:22,167 TraversalEngine - chr6:57254325 2.72e+07 107.8 m 4.0 m 90.8% 118.6 m 10.9 m
INFO 10:11:52,516 TraversalEngine - chr6:57270883 2.72e+07 108.3 m 4.0 m 90.9% 119.1 m 10.8 m
INFO 10:12:22,849 TraversalEngine - chr6:57274093 2.72e+07 108.8 m 4.0 m 90.9% 119.6 m 10.9 m
INFO 10:12:53,635 TraversalEngine - chr6:57428723 2.73e+07 109.3 m 4.0 m 91.4% 119.5 m 10.2 m
INFO 10:13:24,366 TraversalEngine - chr6:57366872 2.73e+07 109.8 m 4.0 m 91.2% 2.0 h 10.6 m
INFO 10:13:55,899 TraversalEngine - chr6:57444991 2.73e+07 110.3 m 4.0 m 91.5% 2.0 h 10.3 m
INFO 10:14:25,994 TraversalEngine - chr6:57415703 2.73e+07 110.8 m 4.1 m 91.4% 2.0 h 10.4 m
INFO 10:14:57,164 TraversalEngine - chr6:57450056 2.74e+07 111.3 m 4.1 m 91.5% 2.0 h 10.3 m
INFO 10:15:28,614 TraversalEngine - chr6:57373410 2.74e+07 111.9 m 4.1 m 91.2% 2.0 h 10.7 m
INFO 10:16:00,023 TraversalEngine - chr6:57376265 2.74e+07 112.4 m 4.1 m 91.3% 2.1 h 10.8 m
INFO 10:16:30,470 TraversalEngine - chr6:57390372 2.74e+07 112.9 m 4.1 m 91.3% 2.1 h 10.8 m
INFO 10:17:00,616 TraversalEngine - chr6:57473509 2.74e+07 113.4 m 4.1 m 91.6% 2.1 h 10.4 m
INFO 10:17:31,852 TraversalEngine - chr6:57408327 2.74e+07 113.9 m 4.2 m 91.4% 2.1 h 10.8 m
INFO 10:18:02,372 TraversalEngine - chr6:57624633 2.75e+07 114.4 m 4.2 m 92.1% 2.1 h 9.8 m
INFO 10:18:32,415 TraversalEngine - chr6:57619768 2.75e+07 114.9 m 4.2 m 92.1% 2.1 h 9.9 m
INFO 10:19:03,387 TraversalEngine - chr6:57672367 2.75e+07 115.4 m 4.2 m 92.2% 2.1 h 9.7 m
INFO 10:19:33,472 TraversalEngine - chr6:57713390 2.76e+07 115.9 m 4.2 m 92.4% 2.1 h 9.6 m
INFO 10:20:03,707 TraversalEngine - chr6:57588693 2.76e+07 116.4 m 4.2 m 92.0% 2.1 h 10.2 m
INFO 10:20:33,937 TraversalEngine - chr6:57805974 2.77e+07 117.0 m 4.2 m 92.7% 2.1 h 9.2 m
INFO 10:21:04,581 TraversalEngine - chr6:57854191 2.77e+07 117.5 m 4.2 m 92.8% 2.1 h 9.0 m
INFO 10:21:38,029 TraversalEngine - chr6:57846906 2.77e+07 118.0 m 4.3 m 92.8% 2.1 h 9.1 m
INFO 10:22:11,718 TraversalEngine - chr6:57880594 2.78e+07 118.6 m 4.3 m 92.9% 2.1 h 9.0 m
INFO 10:22:44,835 TraversalEngine - chr6:57895296 2.78e+07 119.1 m 4.3 m 93.0% 2.1 h 9.0 m
INFO 10:23:19,001 TraversalEngine - chr6:57950669 2.78e+07 119.7 m 4.3 m 93.2% 2.1 h 8.8 m
INFO 10:23:52,808 TraversalEngine - chr6:57970048 2.78e+07 2.0 h 4.3 m 93.2% 2.1 h 8.7 m
INFO 10:24:26,193 TraversalEngine - chr6:57519976 2.79e+07 2.0 h 4.3 m 91.7% 2.2 h 10.9 m
INFO 10:25:00,160 TraversalEngine - chr6:57995097 2.79e+07 2.0 h 4.4 m 93.3% 2.2 h 8.7 m
INFO 10:25:33,919 TraversalEngine - chr6:58050289 2.79e+07 2.0 h 4.4 m 93.5% 2.2 h 8.5 m
INFO 10:26:06,617 TraversalEngine - chr6:58073510 2.79e+07 2.0 h 4.4 m 93.6% 2.2 h 8.4 m
INFO 10:26:39,639 TraversalEngine - chr6:58165229 2.80e+07 2.1 h 4.4 m 93.9% 2.2 h 8.0 m
INFO 10:27:13,254 TraversalEngine - chr6:58152533 2.81e+07 2.1 h 4.4 m 93.8% 2.2 h 8.1 m
INFO 10:27:45,992 TraversalEngine - chr6:58247070 2.81e+07 2.1 h 4.4 m 94.2% 2.2 h 7.7 m
INFO 10:28:19,085 TraversalEngine - chr6:58195026 2.81e+07 2.1 h 4.4 m 94.0% 2.2 h 8.0 m
INFO 10:28:51,984 TraversalEngine - chr6:58315635 2.82e+07 2.1 h 4.4 m 94.4% 2.2 h 7.5 m
INFO 10:29:22,635 TraversalEngine - chr6:58310322 2.83e+07 2.1 h 4.4 m 94.4% 2.2 h 7.5 m
INFO 10:29:52,658 TraversalEngine - chr6:58454325 2.84e+07 2.1 h 4.5 m 94.8% 2.2 h 6.9 m
INFO 10:30:23,461 TraversalEngine - chr6:58583327 2.85e+07 2.1 h 4.5 m 95.3% 2.2 h 6.3 m
INFO 10:30:53,585 TraversalEngine - chr6:58744180 2.86e+07 2.1 h 4.5 m 95.8% 2.2 h 5.6 m
INFO 10:31:23,886 TraversalEngine - chr6:58765337 2.99e+07 2.1 h 4.3 m 95.9% 2.2 h 5.5 m
INFO 10:31:57,941 TraversalEngine - chr6:57604792 3.00e+07 2.1 h 4.3 m 92.0% 2.3 h 11.1 m
INFO 10:35:46,247 TraversalEngine - chr6:58776926 3.00e+07 2.2 h 4.4 m 95.9% 2.3 h 5.6 m
INFO 10:42:29,294 TraversalEngine - chr6:58777926 3.00e+07 2.3 h 4.6 m 95.9% 2.4 h 5.9 m
INFO 10:49:41,001 TraversalEngine - chr6:58778926 3.00e+07 2.4 h 4.9 m 95.9% 2.5 h 6.2 m
INFO 10:55:43,727 TraversalEngine - chr6:58779926 3.00e+07 2.5 h 5.1 m 95.9% 2.6 h 6.4 m

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,235Administrator, GSA Member admin

    It's strange that you're not seeing any new progress for so long, yes. The program may have got bogged down in a difficult area. But it's difficult to diagnose the issue based on this.

    I notice you're using an older version (2.1), which was one of the earlier versions with both -nt and -nct multithreading modes. You may experience fewer issues with a more recent versions; I would recommend you upgrade to 2.7.

    Geraldine Van der Auwera, PhD

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