[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - HaplotypeGraphBuilderPlugin Parameters configFile: db.config methods: mummer4 includeSequences: true includeVariantContexts: false haplotypeIds: null chromosomes: null taxa: null [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - first connection: dbName from config file = /datalus/weiyu/projects/phg/data/maize/maize.db host: localHost user: sqlite type: sqlite [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Database URL: jdbc:sqlite:/datalus/weiyu/projects/phg/data/maize/maize.db [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Connected to database: [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: query statement: select reference_ranges.ref_range_id, chrom, range_start, range_end, methods.name from reference_ranges INNER JOIN ref_range_ref_range_method on ref_range_ref_range_method.ref_range_id=reference_ranges.ref_range_id INNER JOIN methods on ref_range_ref_range_method.method_id = methods.method_id AND methods.method_type = 7 ORDER BY reference_ranges.ref_range_id methods size: 1 [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: number of reference ranges: 76615 [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: time: 0.392329307 secs. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: query statement: SELECT gamete_haplotypes.gamete_grp_id, genotypes.line_name FROM gamete_haplotypes INNER JOIN gametes ON gamete_haplotypes.gameteid = gametes.gameteid INNER JOIN genotypes on gametes.genoid = genotypes.genoid ORDER BY gamete_haplotypes.gamete_grp_id; [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: number of taxa lists: 3 [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: time: 0.005390985 secs. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: haplotype method: mummer4 range group method: null [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: query statement: SELECT haplotypes_id, gamete_grp_id, haplotypes.ref_range_id, asm_contig, asm_start_coordinate, asm_end_coordinate, genome_file_id, sequence, seq_hash, seq_len FROM haplotypes WHERE method_id = 4; [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - addNodes: number of nodes: 36047 [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - addNodes: number of reference ranges: 18981 [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: time: 1.139970656 secs. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.HaplotypeGraph - Created graph edges: created when requested number of nodes: 36047 number of reference ranges: 18981 [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: time: May 22, 2021 11:34:6 [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin: time: May 22, 2021 11:34:6 [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - RunHapConsensusPipelinePlugin Parameters referenceFasta: inputDir/reference/Ref.fa dbConfigFile: db.config collapseMethod: CONSENSUS collapseMethodDetails: CONSENSUS for creating Consensus minFreq: 0.5 rankingFile: rank.tsv maxClusters: 30 minSites: 30 minCoverage: 0.1 maxThreads: 1000 minTaxa: 1 mxDiv: 0.01 clusteringMode: upgma_assembly kmerSize: 7 distanceCalculation: Euclidean Genome FASTA character conversion: ACGTNacgtn to ACGTNacgtn [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin - RunHapConsensusPipelinePlugin: checking masterVariantMap for empty [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - first connection: dbName from config file = /datalus/weiyu/projects/phg/data/maize/maize.db host: localHost user: sqlite type: sqlite [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Database URL: jdbc:sqlite:/datalus/weiyu/projects/phg/data/maize/maize.db [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Connected to database: [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin - RunHapConsensusPipelinePlugin: masterVariantMap is empty - call addGraphVariantsToVariantMap [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.VariantUtils - getAllVariantIds: size of varidSet to return: 4035072 [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin - time to create masterVariantMap in seconds: 2180.473868764 [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin - runHapConsensusPipelinePlugin: after masterVariantMap check, size of masterVariantMap: 4035072 [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin - Starting up the threadpool [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin - Thread Pool started [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin - Loading up the ranking file ... ... ... [ForkJoinPool.commonPool-worker-101] DEBUG net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils - 0 taxa used to build distance matrix [ForkJoinPool.commonPool-worker-69] DEBUG net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils - 0 taxa used to build distance matrix [ForkJoinPool.commonPool-worker-101] DEBUG net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin - Finished builder distance matrix for ref range 1 [ForkJoinPool.commonPool-worker-69] DEBUG net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin - Finished builder distance matrix for ref range 49 [ForkJoinPool.commonPool-worker-101] ERROR net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin - Error processing ReferenceRange:1:1-44288 ErrorMessage:Index 0 out of bounds for length 0 [ForkJoinPool.commonPool-worker-101] DEBUG net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin - Index 0 out of bounds for length 0 java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0 at net.maizegenetics.taxa.tree.UPGMATree.getDist(UPGMATree.java:63) at net.maizegenetics.taxa.tree.UPGMATree.findNextPair(UPGMATree.java:97) at net.maizegenetics.taxa.tree.UPGMATree.(UPGMATree.java:39) at net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin$RunMergeAndCluster.clusterAssemblies(RunHapConsensusPipelinePlugin.java:823) at net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin$RunMergeAndCluster.call(RunHapConsensusPipelinePlugin.java:480) at net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin$RunMergeAndCluster.call(RunHapConsensusPipelinePlugin.java:438) at java.base/java.util.concurrent.ForkJoinTask$AdaptedCallable.exec(ForkJoinTask.java:1448) at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290) at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020) at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) ...