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hail-is / hail

Cloud-native genomic dataframes and batch computing
https://hail.is
MIT License
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Error summary: HailException: cannot set missing field for required type +PCStruct{info:PCStruct{ALLELEID:PInt32}} #8469

Closed bw2 closed 4 years ago

bw2 commented 4 years ago

Running this pipeline https://github.com/macarthur-lab/hail-elasticsearch-pipelines/blob/master/luigi_pipeline/seqr_loading.py#L39 on a non-Broad VCF with this header and several example variants:

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller  --genotyping-mode DISCOVERY --output /mnt/fast/3P5CH/3P5CH/PHASER_SVCALLER_CS/PHASER_SVCALLER/_SNPINDEL_PHASER/_SNPINDEL_CALLER/CALL_SNPINDELS/fork0/chnk00-u77951d7808/files/default.vcf --intervals /mnt/fast/3P5CH/3P5CH/PHASER_SVCALLER_CS/PHASER_SVCALLER/_SNPINDEL_PHASER/_SNPINDEL_CALLER/CALL_SNPINDELS/fork0/chnk00-u77951d7808/files/default.vcf.bed --input /mnt/fast/3P5CH/3P5CH/PHASER_SVCALLER_CS/PHASER_SVCALLER/_LINKED_READS_ALIGNER/MERGE_POS_BAM/fork0/join-u77951d1e3c/files/pos_sorted_bam.bam --reference /home/fgc4/10x/refdata-GRCh38-2.1.0/fasta/genome.fa  --emit-ref-confidence NONE --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.0.7.0,Date="December 21, 2018 6:32:37 PM EST">
##source=HaplotypeCaller
##source=10X/pipelines/stages/snpindels/attach_bcs_snpindels 2.2.2
##source=10X/pipelines/stages/snpindels/phase_snpindels 2.2.2
##bcftools_filterVersion=1.1-3-g9058fce+htslib-1.1-1-g03a4427
##bcftools_filterCommand=filter canonicalized.vcftmp.vcf
##bcftools_filterCommand=filter -O v --soft-filter 10X_RESCUED_MOLECULE_HIGH_DIVERSITY -e '(((RESCUED+NOT_RESCUED) > 0 & RESCUED/(RESCUED+NOT_RESCUED) > 0.1) & (MMD == -1 | MMD >= 3.0)) ' -m '+' /mnt/fast/3P5CH/3P5CH/PHASER_SVCALLER_CS/PHASER_SVCALLER/_SNPINDEL_PHASER/_SNPINDEL_CALLER/POPULATE_INFO_FIELDS/fork0/chnk00-u77951dd300/files/default.vcf.gztmp2.vcf
##bcftools_filterCommand=filter -O v --soft-filter 10X_QUAL_FILTER -e '(%QUAL <= 15 || (AF[0] > 0.5 && %QUAL < 50))' -m '+' /mnt/fast/3P5CH/3P5CH/PHASER_SVCALLER_CS/PHASER_SVCALLER/_SNPINDEL_PHASER/_SNPINDEL_CALLER/POPULATE_INFO_FIELDS/fork0/chnk00-u77951dd300/files/default.vcf.gztmp2.vcf
##bcftools_filterCommand=filter -O v --soft-filter 10X_ALLELE_FRACTION_FILTER -e '(AO[0] < 2 || AO[0]/(AO[0] + RO) < 0.15)' -m '+' /mnt/fast/3P5CH/3P5CH/PHASER_SVCALLER_CS/PHASER_SVCALLER/_SNPINDEL_PHASER/_SNPINDEL_CALLER/POPULATE_INFO_FIELDS/fork0/chnk00-u77951dd300/files/default.vcf.gztmp2.vcf
##bcftools_filterCommand=filter -O v --soft-filter 10X_RESCUED_MOLECULE_HIGH_DIVERSITY -e '(((RESCUED+NOT_RESCUED) > 0 & RESCUED/(RESCUED+NOT_RESCUED) > 0.1) & (MMD == -1 | MMD >= 3.0)) ' -m '+' /mnt/fast/3P5CH/3P5CH/PHASER_SVCALLER_CS/PHASER_SVCALLER/_SNPINDEL_PHASER/POPULATE_INFO_FIELDS/fork0/chnk00-u77951f096b/files/default.vcf.gztmp3.vcf
##bcftools_filterCommand=filter -O v --soft-filter 10X_QUAL_FILTER -e '(%QUAL <= 15 || (AF[0] > 0.5 && %QUAL < 50))' -m '+' /mnt/fast/3P5CH/3P5CH/PHASER_SVCALLER_CS/PHASER_SVCALLER/_SNPINDEL_PHASER/POPULATE_INFO_FIELDS/fork0/chnk00-u77951f096b/files/default.vcf.gztmp2.vcf
##bcftools_filterCommand=filter -O v --soft-filter 10X_ALLELE_FRACTION_FILTER -e '(AO[0] < 2 || AO[0]/(AO[0] + RO) < 0.15)' -m '+' /mnt/fast/3P5CH/3P5CH/PHASER_SVCALLER_CS/PHASER_SVCALLER/_SNPINDEL_PHASER/POPULATE_INFO_FIELDS/fork0/chnk00-u77951f096b/files/default.vcf.gztmp2.vcf
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
##INFO=<ID=VCFALLELICPRIMITIVE,Number=0,Type=Flag,Description="The allele was parsed using vcfallelicprimitives.">
##INFO=<ID=TENX,Number=0,Type=Flag,Description="called by 10X">
##INFO=<ID=POSTHPC,Number=.,Type=Integer,Description="Postvariant homopolymer count">
##INFO=<ID=POSTHPB,Number=.,Type=Character,Description="Postvariant homopolymer base">
##INFO=<ID=MUMAP_REF,Number=1,Type=Float,Description="Mean mapping score of ref allele">
##INFO=<ID=MUMAP_ALT,Number=.,Type=Float,Description="Mean mapping scores of alt alleles">
##INFO=<ID=AO,Number=.,Type=Integer,Description="Alternate allele observed count">
##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observed count">
##INFO=<ID=MMD,Number=.,Type=Float,Description="Mean molecule divergence from reference per read">
##INFO=<ID=RESCUED,Number=.,Type=Integer,Description="How many reads were rescued via cross barcode mapq correction">
##INFO=<ID=NOT_RESCUED,Number=.,Type=Integer,Description="How many reads were not rescued via cross barcode mapq correction">
##INFO=<ID=POSTDNB,Number=.,Type=String,Description="Post variant dinucleotide repeat sequence">
##INFO=<ID=POSTDNC,Number=.,Type=Integer,Description="Post variant dinucleotide repeat count">
##INFO=<ID=POSTTNB,Number=.,Type=String,Description="Post variant trinucleotide repeat sequence">
##INFO=<ID=POSTTNC,Number=.,Type=Integer,Description="Post variant trinucleotide repeat count">
##INFO=<ID=HAPLOCALLED,Number=1,Type=Integer,Description="1 for variants that were called after phasing via splitting the bam into its component haplotypes and calling variants in haploid mode">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=BX,Number=.,Type=String,Description="Barcodes and Associated Qual-Scores Supporting Alleles">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="ID of Phase Set for Variant">
##FORMAT=<ID=PQ,Number=1,Type=Integer,Description="Phred QV indicating probability at this variant is incorrectly phased">
##FORMAT=<ID=JQ,Number=1,Type=Integer,Description="Phred QV indicating probability of a phasing switch error in gap prior to this variant">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=UNSUPPORTED_GENOTYPE,Description="If genotype field contains '.' we assume that this is due to making a single sample vcf from a multiple sample vcf in which this sample does not contain the variant.">
##FILTER=<ID=10X_RESCUED_MOLECULE_HIGH_DIVERSITY,Description="Set if true: (((RESCUED+NOT_RESCUED) > 0 & RESCUED/(RESCUED+NOT_RESCUED) > 0.1) & (MMD == -1 | MMD >= 3.0))">
##FILTER=<ID=10X_QUAL_FILTER,Description="Set if true: (%QUAL <= 15 || (AF[0] > 0.5 && %QUAL < 50))">
##FILTER=<ID=10X_ALLELE_FRACTION_FILTER,Description="Set if true: (AO[0] < 2 || AO[0]/(AO[0] + RO) < 0.15)">
##FILTER=<ID=10X_PHASING_INCONSISTENT,Description="Uses haplotype information from the fragments and the alleles to filter some variants that are not consistent with phasing.">
##FILTER=<ID=10X_HOMOPOLYMER_UNPHASED_INSERTION,Description="Unphased insertions in homopolymer regions tend to be false positives">
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
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##contig=<ID=chrUn_KI270338v1,length=1428>
##contig=<ID=chrUn_KI270340v1,length=1428>
##contig=<ID=chrUn_KI270336v1,length=1026>
##contig=<ID=chrUn_KI270337v1,length=1121>
##contig=<ID=chrUn_KI270363v1,length=1803>
##contig=<ID=chrUn_KI270364v1,length=2855>
##contig=<ID=chrUn_KI270362v1,length=3530>
##contig=<ID=chrUn_KI270366v1,length=8320>
##contig=<ID=chrUn_KI270378v1,length=1048>
##contig=<ID=chrUn_KI270379v1,length=1045>
##contig=<ID=chrUn_KI270389v1,length=1298>
##contig=<ID=chrUn_KI270390v1,length=2387>
##contig=<ID=chrUn_KI270387v1,length=1537>
##contig=<ID=chrUn_KI270395v1,length=1143>
##contig=<ID=chrUn_KI270396v1,length=1880>
##contig=<ID=chrUn_KI270388v1,length=1216>
##contig=<ID=chrUn_KI270394v1,length=970>
##contig=<ID=chrUn_KI270386v1,length=1788>
##contig=<ID=chrUn_KI270391v1,length=1484>
##contig=<ID=chrUn_KI270383v1,length=1750>
##contig=<ID=chrUn_KI270393v1,length=1308>
##contig=<ID=chrUn_KI270384v1,length=1658>
##contig=<ID=chrUn_KI270392v1,length=971>
##contig=<ID=chrUn_KI270381v1,length=1930>
##contig=<ID=chrUn_KI270385v1,length=990>
##contig=<ID=chrUn_KI270382v1,length=4215>
##contig=<ID=chrUn_KI270376v1,length=1136>
##contig=<ID=chrUn_KI270374v1,length=2656>
##contig=<ID=chrUn_KI270372v1,length=1650>
##contig=<ID=chrUn_KI270373v1,length=1451>
##contig=<ID=chrUn_KI270375v1,length=2378>
##contig=<ID=chrUn_KI270371v1,length=2805>
##contig=<ID=chrUn_KI270448v1,length=7992>
##contig=<ID=chrUn_KI270521v1,length=7642>
##contig=<ID=chrUn_GL000195v1,length=182896>
##contig=<ID=chrUn_GL000219v1,length=179198>
##contig=<ID=chrUn_GL000220v1,length=161802>
##contig=<ID=chrUn_GL000224v1,length=179693>
##contig=<ID=chrUn_KI270741v1,length=157432>
##contig=<ID=chrUn_GL000226v1,length=15008>
##contig=<ID=chrUn_GL000213v1,length=164239>
##contig=<ID=chrUn_KI270743v1,length=210658>
##contig=<ID=chrUn_KI270744v1,length=168472>
##contig=<ID=chrUn_KI270745v1,length=41891>
##contig=<ID=chrUn_KI270746v1,length=66486>
##contig=<ID=chrUn_KI270747v1,length=198735>
##contig=<ID=chrUn_KI270748v1,length=93321>
##contig=<ID=chrUn_KI270749v1,length=158759>
##contig=<ID=chrUn_KI270750v1,length=148850>
##contig=<ID=chrUn_KI270751v1,length=150742>
##contig=<ID=chrUn_KI270752v1,length=27745>
##contig=<ID=chrUn_KI270753v1,length=62944>
##contig=<ID=chrUn_KI270754v1,length=40191>
##contig=<ID=chrUn_KI270755v1,length=36723>
##contig=<ID=chrUn_KI270756v1,length=79590>
##contig=<ID=chrUn_KI270757v1,length=71251>
##contig=<ID=chrUn_GL000214v1,length=137718>
##contig=<ID=chrUn_KI270742v1,length=186739>
##contig=<ID=chrUn_GL000216v2,length=176608>
##contig=<ID=chrUn_GL000218v1,length=161147>
##contig=<ID=chrEBV,length=171823>
##contig=<ID=hs38d1,length=10560522>
##bcftools_pluginVersion=1.9+htslib-1.9
##bcftools_pluginCommand=plugin fill-AN-AC; Date=Sat Dec 29 14:52:44 2018
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output 3P5CH.new.vcf --use-new-qual-calculator true --annotation-group StandardAnnotation --annotation-group StandardHCAnnotation --dbsnp /home/fgc3/dbsnp/150/GRCh38/All_20170710.vcf.gz --variant 3P5CH.new.g.vcf.gz --reference /home/fgc3/10x/refdata-GRCh38-2.1.0/fasta/genome.fa --create-output-variant-index false --verbosity ERROR  --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --disable-tool-default-annotations false --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.1.2,Date="March 22, 2018 1:12:03 AM EDT">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##VEP="v91" time="2018-03-22 04:15:25" cache="/media/SE5/.vep/homo_sapiens/91_GRCh38" db="homo_sapiens_core_91_38@ensembldb.ensembl.org" ensembl-variation=91.c78d8b4 ensembl-funcgen=91.4681d69 ensembl-io=91.923d668 ensembl=91.18ee742 1000genomes="phase3" COSMIC="82" ClinVar="201710" ESP="V2-SSA137" HGMD-PUBLIC="20172" assembly="GRCh38.p10" dbSNP="150" gencode="GENCODE 27" genebuild="2014-07" gnomAD="170228" polyphen="2.2.2" regbuild="16" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|SIFT|PolyPhen|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE">
##bcftools_mergeVersion=1.7+htslib-1.7-2
##bcftools_mergeCommand=merge -m none -Oz -o merged_phased_3P5CH.vcf.gz phased_variants.ACfix_LR.vcf.gz 3P5CH.vep.vcf.gz; Date=Sun Dec 30 00:01:56 2018
##INFO=<ID=OLD_MULTIALLELIC,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding">
##INFO=<ID=OLD_VARIANT,Number=.,Type=String,Description="Original chr:pos:ref:alt encoding">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  3P5CH-LR    3P5CH
chr1    10247   .   TAAACCCTA   T   48.52   10X_QUAL_FILTER;10X_RESCUED_MOLECULE_HIGH_DIVERSITY ExcessHet=3.0103;FS=0;MQ=53.76;QD=16.17;SOR=1.179;POSTHPC=2;POSTHPB=A;MUMAP_REF=41.2304;MUMAP_ALT=42.8452;AO=491;RO=143;MMD=3.51306;RESCUED=497;NOT_RESCUED=398;POSTDNB=AA;POSTDNC=1;POSTTNB=AAC;POSTTNC=1;HAPLOCALLED=1;DP=27;AF=0.5;MLEAC=2;MLEAF=1;AN=2;AC=1 GT:AD:DP:GQ:PL:PS:PQ:JQ:BX  0|1:0,3:3:7:85,7,0:1:25:25:CTCATTACACCGCTAG-1_45;CTGCGTTGTCGGGAAT-1_45;CAGTATGGTTTAGCAC-1_45;AGGGATGTCCCAGGTG-1_45;CGCTATCCATCACTGA-1_45;TGTGGGCTCCTCTGCA-1_45_45_45_45;ACTGGGCTCGAGCAGA-1_45;TACTCCGTCACCGCAG-1_45;AGCATTGTCTCTTTAG-1_45;TGTCGCTAGCTAAGAT-1_45;GATTCAGCATACTAGC-1_45;TCCTCAGAGCTGCATT-1_45;TGTACGAAGAATGTGT-1_45;GAAGACGGTGACAATA-1_45;GGGCATCAGTGTTTGC-1_45_45;AGTGAAACATGGTCTA-1_45;GTACTCCGTTAGACCT-1_45;CGATGATAGGATATAC-1_45;CCACATCAGAGTAATC-1_45;GACTACAAGACTAACA-1_45;ACTGTAGCATGGGCCT-1_45;GGAGCAACAAGCCAAG-1_45;CAGTGCGGTTATGGAA-1_45;GGGACCTAGAGGTAGA-1_45;GTCGAATTCGGTTCGG-1_45;TCATGTTGTAAACAGT-1_45;TTAGGACCAAGGCGTA-1_45_45;CCGTTCAAGGCTAGAC-1_45;AAGACGGGTGCATCTA-1_45;TAATCTCCACTTAAGC-1_45;ATGCGGCCATGTAGCT-1_45;TTAAGGCGTAGAGTTA-1_45;AGCTGATAGGGTTTCT-1_45_45;TAGGCCGAGAACCTGG-1_45;CCTCAGTCAGGTACGA-1_45;TTAACTCAGAGTGAGA-1_45_45;GGCAACCCAGACAGGT-1_45;CCCACATAGGCACGTA-1_45;GCTCCTATCACGACGC-1_45;TCTCGGTGTTTACTCT-1_45;CGATCAAGTCCTTCTG-1_45;CCTAGCTTCTGGAGCC-1_45;GTAGGGATCCTCGACT-1_45;GTCTCGTTCCATGCGG-1_45;CCTGGTTGTCACCGTG-1_45;TGACGGCAGGCCACTC-1_45;CTTAGGAGTTAGCTCA-1_45;TTGTTGTTCTCAGGAT-1_45;CCGTACTTCTGCCAGG-1_45_45;TGTCACCTCTCATACT-1_45;GTATTTCAGGAGCGAG-1_45;GCGCTGAAGGAATGAG-1_45;TAGGCCGTCCATGCGG-1_45;CGACGTGCAGTGACAG-1_45;TGGACGCTCTGCACTC-1_45;CACATAGCATCGTCAA-1_45;GCCTATCGTCCTCCAT-1_45;ACCGTAATCTGACGCG-1_45;TGTGGGCAGTGAGATT-1_45;CAGGCGTAGAGTTAGT-1_45;CTAAGTGTCGTCCTAC-1_45_45;AAAGCTCAGCAATCTC-1_45;AGGTCCGAGTGGCGAT-1_45;CAGTACAGTTCCAGTA-1_45;AGTACCAGTCCCACAG-1_45;TTCGACCAGACGTCTT-1_45;TACGGGCCAAGACGTG-1_45_45;AGCTGCGTCGGCGCTA-1_45;ACGGGTCGTACACAGG-1_45;TCCTCGAAGTCAACAA-1_45;ACATGGTAGTCAAGGC-1_45;TTAGTCTGTGGTTAAA-1_45_45_45;CATCGAATCCTCTAGC-1_45;GATCGATGTATAATGG-1_45;TCGCTTGTCGATGAGG-1_45;ACCGCTTTCCGCATAA-1_45;TTAACTCCAACGGAGT-1_45;CTGGTCTTCTGTCCGT-1_45;CGATAACTCCCTAACC-1_45;CGGATGCAGGAGAACA-1_45;GTGGGTCAGTCCCGAC-1_45;GCACATATCACGGTTA-1_45;CGAGCCATCTACCAGA-1_45;CCCGAAGAGTGGGTAC-1_45;AGTCCAACAGTCACTA-1_45;GGTACATCATATGAGA-1_45;GCATGCGGTGTAACGG-1_45;TGCGTGGTCCCTAATT-1_45;ACCCGTTAGCTCTGGC-1_45;GCCGTTTAGCCAGTTT-1_45;CAGAGCCAGATATGCA-1_45;TCTTAGTGTCCTTGGG-1_45;CGCACTTCATTCCGTC-1_45;CTATGAGCATTAGGTC-1_45;TAGAACCGTGCGTGCT-1_45;ATTTCCACACATGGCC-1_45;GTGGTGCAGCTATCAC-1_45;ACGGGCTCATCCACGG-1_45;AGAAATGCAGTTCCCT-1_45;AATCTTCGTAAACGCG-1_45;TTTGTCAAGGTTTCGT-1_45,TACCAAGTCTCACCTG-1_45_45;GAGCCGTAGGACATTA-1_45_45_45;TGGTCTCAGCTCTGCG-1_45;ATAGTGCCAGGTCCCA-1_45;ACCATTTGTTCTTTGT-1_45;CCTAGTCCAAAGGTTA-1_45;CGAACGCGTTCGGTGC-1_45;ACACGATGTTAACGTC-1_45;GCAATCAAGTCGTTTG-1_45;TTGATCTTCGTCCAGG-1_45;ATGCTTTTCCGGCTAG-1_45;AGGGATGTCCCAGGTG-1_45_45;TCGACTCAGGCGAAGG-1_45;ACCATCCTCTGCGGGT-1_45;ACGTCAAAGCTCCCTT-1_45;CTCTGTGCATCTGACA-1_45;TACTCCGTCACCGCAG-1_45;TCTTACACAGGGTTAG-1_45;TGGACGCGTATTACCG-1_45;TTTCCTCGTTCTGAAC-1_45;ACACCAAAGGGCAGGA-1_45_45_45_45;ATGAAAGCAGTCGCAC-1_45;GGATGGAAGGCCAGAT-1_45;TTTGTCAGTAATCCAC-1_45;AGAACAACAAAGTGGC-1_45_45;GAGTCCGTCCTAGAAC-1_45;TAAGAGATCAGAAACA-1_45;ACATGGTAGTCAAGGC-1_45;CTTACCGGTCTTCTCG-1_45;ACCATCCAGTACTGTC-1_45;ATATGGCCAACGCCGT-1_45;AGGAAGCTCTACGGGC-1_45;AAAGTAGAGTCACCGC-1_45;ACCCAAAAGCTGCCTG-1_45;TGCACCTAGTGATATG-1_45;TGCATCCCAGCTGGCT-1_45_45;CAGTATGAGTGCCATT-1_45_45;AGTTCCCGTCAAGGGT-1_45;AGGCCGTTCGCAGACC-1_45;GAGATAATCGTTATTC-1_45;CCTAACCGTGCTTCGG-1_45;TACTCATAGACACGAC-1_45_45;GTGACCGCAGACTTGT-1_45;AGCCCTTGTCAACATC-1_45;TTGGTGATCTCTGTCG-1_45;ACAGTGTTCGGTGTCG-1_45;GGATTTGAGAACTGCG-1_45;CGAGAAGGTTGTAAGA-1_45;CAACTTTAGTGCCATT-1_45;GGGACCTGTTGGAGCA-1_45;GTTACTTGTCCTAGGC-1_45;CATTATCCATACGTTG-1_45;CGGGTGTGTCCGGTGT-1_45;GGAGCAACAAGCCAAG-1_45_45;AGGCCGTCAGGGTTAG-1_45;GCTAAGTGTACCATCA-1_45_45_45;GGATGTTCATCTGACA-1_45;TCTGTCGTCGCCCTTA-1_45;GGGACCTGTCCTAACA-1_45;ACGCAGCAGATATACG-1_45;GTTGAACTCCCTAACC-1_45;TACTCCGTCTTATGCT-1_45;TAGTTGGTCCTAATGG-1_45;CCTCATGCAGTCTTCC-1_45;CATCGAATCAGAGGAC-1_45;ATGCTTTAGCGCCAAA-1_45;ATCAGCAAGTGAACAT-1_45;TATCAGGCATCACGTA-1_45_45_45;GTATTCTTCTGTTGAG-1_45;CGGAACCAGCTACAAA-1_45;TCTAGTTGTCATGCCG-1_45;GGTGGCTCATCCATCC-1_45;GTCGAATTCGGTTCGG-1_45_45;ACTGTAGTCTAAAGGA-1_45;TCTGGAATCTGTTGTT-1_45_45_45;ACGGGTCTCAGTACAC-1_45_45;GAGACCCTCTGAAGTC-1_45;AGTTCTTCATTCTTCA-1_45_45;CACACAAAGGCGTGTA-1_45;TTAGGACCAAGGCGTA-1_45;TGACTGAGTTAAACGA-1_45;CGTTGAACATTACGCA-1_45_45;GCTAAGTGTAAGAAGG-1_45_45_45;ACGTACAAGAGTACCG-1_45;GTATTTCAGGAGCGAG-1_45;GCGTGTGCACTCGGCA-1_45;AGTACCACAGAGCTCC-1_45;CCTTTCTCAATAGAGT-1_45_45;GCGTGTGTCACCACGG-1_45;CCACAAAGTGTAACAA-1_45;ACTGGATCAGAGTGTG-1_45;AGCTGATAGGGTTTCT-1_45;CGTCCTAAGCTGAACG-1_45;TGACAACCACCAGGCT-1_45;CGTTTGCTCATTTCGT-1_45;ATTGGACCAAGTAGTA-1_45;GGTATTGGTACCATCA-1_45;ACGGAGATCTAAGGAA-1_45_45;CGCAACGTCGGTTCGG-1_45_45;TCGCTTGCAGCATACT-1_45;CTCTAGCCAGGCTCTG-1_45;ACACCAATCATGCTGA-1_45;TCTTCGGCAAACGGGT-1_45_45;TGAAAGATCGAAGCTT-1_45;CGCTATCCAGTCCACG-1_45;CCATGGGCACATAAAG-1_45;TACACCCGTTAGTGAA-1_45;CGTCTCATCCTTCGTG-1_45;GTCCCATTCTCCAACC-1_45;TAAAGCCCAATGGGCA-1_45;AGTTACGCAATGGACG-1_45;CCTTCGAAGGCAACAC-1_45;CCGGTAGGTTCAAGAA-1_45;CCGGTAGTCGTTGACA-1_45;CTTGGCTTCACACGTA-1_45;CCGAGACTCTGAAAGA-1_45_45_45_45;GTCTCGTTCCATGCGG-1_45;CAACTAGCAGTCAAGG-1_45;CATTTCACACCAACAT-1_45;CGGATCGGTCGTGTAT-1_45;TGGCCAGAGATAGTCA-1_45;TGACGGCAGGCCACTC-1_45;CTTAGGAGTTAGCTCA-1_45;GCACATACACTGCGCA-1_45;AGTGAGGGTCATGTTG-1_45;AGGAGACTCTAAGCCA-1_45;AGCAAGGAGGCTATCT-1_45;AAAGCAAGTGCTTTGA-1_45;ACTTTCACAGGCGATA-1_45;GGACAGACAGCTCGAC-1_45_45;GTGACCGTCACGTATG-1_45;CGTCGTTTCGTTAGGT-1_45_45_45_45_45;GCGCTGAAGGAATGAG-1_45;CTATTTGAGCGTCGAA-1_45;CCGTTCAGTGTCCGAC-1_45;ACCAGTAGTATGAATG-1_45;ATCATGGCAAGGAGTC-1_45;TCTATTGGTAAGCGCA-1_45;TTGAGCAAGTGAGACC-1_45_45;GCTAAACGTCGCTGTG-1_45;CTAGTCCTCCTGCACT-1_45;AAGATCCTCCACTTAT-1_45_45;TATCAGGTCACCGGGT-1_45_45;TTTATGCAGCCACCAC-1_45;AGGTCCGAGTGGCGAT-1_45;TGGAGCCAGTACATGA-1_45;TCATTTGTCCAAACCA-1_45;TACTTGTGTTTAACGC-1_45;GCATGCGGTGTAACGG-1_45;AGCCTCTAGATCCCGC-1_45;CTTATACTCATCGCCT-1_45;AGGTTTGTCCGAAGGA-1_45;CTGCCTATCGTAAGTC-1_45;AGGTCATTCGTTACCC-1_45;GAGTGAGAGTAGAGTT-1_45;CCCTCCTGTTGAAGGC-1_45;TGAGACTTCCAGCGAC-1_45;TTACTCACACGGTAGA-1_45;GCACATATCGTAGGAG-1_45_45;AAACCCACATATGAGA-1_45_45;ACATGGTTCTTGCGGG-1_45;TTTACTGGTCGCTCAG-1_45;ATCCGGGTCTACTATC-1_45;GATCGGCTCAGCAGCC-1_45_45_45;TCATGAGAGTAACAGT-1_45;GAGCAGATCTCGGTTC-1_45;CGGATCGCATGACGGA-1_45_45_45;TGTACGAGTCTAGCGC-1_45;GTACGATTCCACGCAG-1_45;GAACCTAAGTGAATGT-1_45;CGGATCGTCGCTGCTT-1_45_45;TATCGCCTCAGATAAG-1_45;TATATCCTCAGGCCCA-1_45;ATACTTCCACATCTTT-1_45;CAGTGCGCATCTGCCT-1_45;ATGTAGCAGTTATGAG-1_45;AACGTCAGTGTTTCAG-1_45_45;CTGATGAGTTAGTAGA-1_45;GGTACATAGTGTACGG-1_45;AGATCTGAGGCTAGTG-1_45;ACGCAGCGTCATTAGC-1_45_45;GTCTGAAGTACAGATA-1_45;AGCAGCCCATTTGCGA-1_45;CAGCATAAGTAAGAGG-1_45_45;GAAATGACATTAGGCT-1_45;TTCGCCAAGAGTCTTC-1_45;TCTCGGTTCACCAGCG-1_45_45;CCCGAAGAGTGGGTAC-1_45;TACGAACTCGAACCAT-1_45;CAGCCGATCCATGCGG-1_45_45_45;AGTCCAACAGTCACTA-1_45;TGCTATTGTAAGAGGA-1_45;GCTAAACTCTTTCGGC-1_45;ACCCGTTGTAAGAGAG-1_45;TGAGCCGAGTGTGAAT-1_45;TGTACGACAAAGGCGT-1_45;ACGGGCTAGGAGCTAC-1_45;CAAGGCCAGCGAACTG-1_45;TGAACTGGTTATCCGA-1_45;CGCAGACAGCACGCAA-1_45;AAACCTGTCCAGGCTG-1_45;TAGTCAGCAGCTGTAT-1_45;CGGGCATTCTCCTGTG-1_45;ACGCCAGGTGTAAAGT-1_45;CAGTGCGGTTATGGAA-1_45;TGCATAGGTCAAGCGA-1_45;GGTACATGTCAAAGCG-1_45;TAAGAGAAGAGGGATA-1_45;CTACCCAAGTGGCCCT-1_45;TCTTAGTGTCCTTGGG-1_45_45_45;TCTTACATCCGCCTTA-1_45_45;TTCGCCACAGAGGCAT-1_45;CGGGCATCACCAGTTA-1_45;CAGTGTAAGGCTGTAG-1_45;TACCTTAGTTTACTTC-1_45;GCGCAACTCGTTCGGG-1_45;GTGTTAGGTGCCTGGT-1_45_45;TTACCCGCATTGCCAA-1_45;CTATGAGCATTAGGTC-1_45;TAGAACCGTGCGTGCT-1_45_45;ATTTCCACACATGGCC-1_45;ACACAACTCCCTGACT-1_45;CGTTGGGTCGGGCTCA-1_45;TCCGGTTTCTCACCTG-1_45_45;TTCCATAAGGTGCGTA-1_45;ATCACCCGTCTCGGTG-1_45;GTTTAGGCAACCCGAC-1_45;AGAAATGCAGTTCCCT-1_45;TTTGAGGGTGACCAAG-1_45;GTATTCTTCACTCTTA-1_45;GCATCTCTCCGTTCAC-1_45_45;CTTACCGGTTCTCCCA-1_45;CGATATGAGGCTCTTA-1_45;TTTGTCAAGGTTTCGT-1_45_45;ATTCATCAGAGGAATG-1_45;GTCCTGTTCACAGTAC-1_45    ./.:.:.:.:.:.:.:.:.
chr1    11863   rs187669455 C   A   93.6    PASS    BaseQRankSum=-1.645;ExcessHet=3.0103;FS=0;MQ=42.43;MQRankSum=0.674;QD=6.15;ReadPosRankSum=0.524;SOR=1.179;MUMAP_REF=6.625;MUMAP_ALT=21;AO=2;RO=2;MMD=1.96017;RESCUED=0;NOT_RESCUED=23;HAPLOCALLED=0;ClippingRankSum=0;DB;CSQ=A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene||||||||||rs187669455|147|1||HGNC|HGNC:37102|||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript||||||||||rs187669455|6|1||HGNC|HGNC:37102|||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene||||||||||rs187669455|2541|-1||HGNC|HGNC:38034|||||||||||||||||||||||||||;DP=13;AF=0.5;MLEAC=1;MLEAF=0.5;AN=4;AC=2  GT:AD:DP:GQ:PL:BX:PS:PQ:JQ  0/1:2,3:5:59:59,0,63:CTTGGAACACAGTGTT-1_70_65,GAAGTCTCATCCCATC-1_45;AACGTCAGTGTTTCAG-1_74:1:19:255  0/1:2,4:6:60:101,0,60:.:.:.:.
chr1    12198   rs62635282  G   C   69.6    .   BaseQRankSum=0;ClippingRankSum=0;DB;ExcessHet=3.0103;FS=4.771;MQ=42;MQRankSum=-0.967;QD=23.2;ReadPosRankSum=0.967;SOR=2.225;CSQ=C|non_coding_transcript_exon_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|2/6||||68|||||||1||HGNC|HGNC:37102|||||||||||||||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|1/3||||330|||||||1||HGNC|HGNC:37102|||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||2206|-1||HGNC|HGNC:38034|||||||||||||||||||||||||||;DP=3;AF=0.5;MLEAC=1;MLEAF=0.5;AN=2;AC=1    GT:AD:DP:GQ:PL  ./.:.:.:.:. 0/1:1,2:3:37:77,0,37

Getting this error message:

INFO: [pid 11941] Worker Worker(salt=943636132, workers=1, host=seqr-loading-cluster-m, username=root, pid=11941) running   SeqrVCFToMTTask(source_paths=gs://seqr-bw/merged_phased_3P5CH.split.vcf.gz, dest_path=gs://seqr-bw/merged_phased_3P5CH.mt, genome_version=38, vep_runner=VEP, reference_ht_path=gs://seqr-reference-data/GRCh38/all_reference_data/combined_reference_data_grch38.ht, clinvar_ht_path=gs://seqr-reference-data/GRCh38/clinvar/clinvar.GRCh38.2020-03-29.ht, hgmd_ht_path=None, sample_type=WGS, validate=False, dataset_type=VARIANTS, remap_path=, subset_path=, vep_config_json_path=)
Initializing Spark and Hail with default parameters...
Running on Apache Spark version 2.4.5
SparkUI available at http://seqr-loading-cluster-m.c.seqr-project.internal:4040
Welcome to
     __  __     <>__
    / /_/ /__  __/ /
   / __  / _ `/ / /
  /_/ /_/\_,_/_/_/   version 0.2.34-914bd8a10ca2
LOGGING: writing to /tmp/c7e0443c47b54e91b295e2bff7b554b9/hail-20200405-1408-0.2.34-914bd8a10ca2.log
{'_Task__hash': -3818947167740532127,
 'clinvar_ht_path': 'gs://seqr-reference-data/GRCh38/clinvar/clinvar.GRCh38.2020-03-29.ht',
 'dataset_type': 'VARIANTS',
 'decrease_running_resources': <bound method TaskStatusReporter.decrease_running_resources of <luigi.worker.TaskStatusReporter object at 0x7f0583f0f588>>,
 'dest_path': 'gs://seqr-bw/merged_phased_3P5CH.mt',
 'genome_version': '38',
 'hgmd_ht_path': None,
 'param_kwargs': {'clinvar_ht_path': 'gs://seqr-reference-data/GRCh38/clinvar/clinvar.GRCh38.2020-03-29.ht',
                  'dataset_type': 'VARIANTS',
                  'dest_path': 'gs://seqr-bw/merged_phased_3P5CH.mt',
                  'genome_version': '38',
                  'hgmd_ht_path': None,
                  'reference_ht_path': 'gs://seqr-reference-data/GRCh38/all_reference_data/combined_reference_data_grch38.ht',
                  'remap_path': None,
                  'sample_type': 'WGS',
                  'source_paths': 'gs://seqr-bw/merged_phased_3P5CH.split.vcf.gz',
                  'subset_path': None,
                  'validate': False,
                  'vep_config_json_path': None,
                  'vep_runner': 'VEP'},
 'reference_ht_path': 'gs://seqr-reference-data/GRCh38/all_reference_data/combined_reference_data_grch38.ht',
 'remap_path': None,
 'sample_type': 'WGS',
 'scheduler_messages': None,
 'set_progress_percentage': <bound method TaskStatusReporter.update_progress_percentage of <luigi.worker.TaskStatusReporter object at 0x7f0583f0f588>>,
 'set_status_message': <bound method TaskStatusReporter.update_status_message of <luigi.worker.TaskStatusReporter object at 0x7f0583f0f588>>,
 'set_tracking_url': <bound method TaskStatusReporter.update_tracking_url of <luigi.worker.TaskStatusReporter object at 0x7f0583f0f588>>,
 'source_paths': ['gs://seqr-bw/merged_phased_3P5CH.split.vcf.gz'],
 'subset_path': None,
 'task_id': 'SeqrVCFToMTTask_gs___seqr_refere_VARIANTS_gs___seqr_bw_mer_b185718e87',
 'validate': False,
 'vep_config_json_path': None,
 'vep_runner': 'VEP'}
[Stage 1:======================================================>(492 + 8) / 500]2020-04-05 14:09:30 Hail: INFO: Coerced almost-sorted dataset
[Stage 2:====================================================> (485 + 15) / 500]2020-04-05 14:09:34 Hail: INFO: Coerced almost-sorted dataset
[Stage 3:==================================================>   (467 + 33) / 500]MT using schema class <class 'lib.model.seqr_mt_schema.SeqrVariantsAndGenotypesSchema'> already has vep annotation.
MT using schema class <class 'lib.model.seqr_mt_schema.SeqrVariantsAndGenotypesSchema'> already has filters annotation.
MT using schema class <class 'lib.model.seqr_mt_schema.SeqrVariantsAndGenotypesSchema'> already has rsid annotation.
MT using schema class <class 'lib.model.seqr_mt_schema.SeqrVariantsAndGenotypesSchema'> already has vep annotation.
----------------------------------------
Global fields:
    'gencodeVersion': str
    'sourceFilePath': str
    'genomeVersion': str
    'sampleType': str
    'hail_version': str
----------------------------------------
Column fields:
    's': str
----------------------------------------
Row fields:
    'locus': locus<GRCh38>
    'alleles': array<str>
    'aIndex': int32
    'AC': int32
    'AF': float64
    'alt': str
    'AN': int32
    'cadd': struct {
        PHRED: float32
    }
    'clinvar': struct {
        allele_id: int32,
        clinical_significance: str,
        gold_stars: int32
    }
    'codingGeneIds': set<str>
    'contig': str
    'dbnsfp': struct {
        SIFT_pred: str,
        Polyphen2_HVAR_pred: str,
        MutationTaster_pred: str,
        FATHMM_pred: str,
        MetaSVM_pred: str,
        REVEL_score: str,
        GERP_RS: str,
        phastCons100way_vertebrate: str
    }
    'docId': str
    'domains': set<str>
    'eigen': struct {
        Eigen_phred: float64
    }
    'end': int32
    'exac': struct {
        AF_POPMAX: float64,
        AF: float64,
        AC_Adj: int32,
        AC_Het: int32,
        AC_Hom: int32,
        AC_Hemi: int32,
        AN_Adj: int32
    }
    'filters': set<str>
    'g1k': struct {
        AC: int32,
        AF: float64,
        AN: int32,
        POPMAX_AF: float64
    }
    'geneIds': set<str>
    'geno2mp': struct {
        HPO_Count: int32
    }
    'genotypes': array<struct {
        num_alt: int32,
        gq: int32,
        ab: float64,
        dp: float64,
        sample_id: str
    }>
    'gnomad_exome_coverage': float64
    'gnomad_exomes': struct {
        AF: float64,
        AN: int32,
        AC: int32,
        FAF_AF: float64,
        AF_POPMAX_OR_GLOBAL: float64,
        Hom: int32,
        Hemi: int32
    }
    'gnomad_genome_coverage': float64
    'gnomad_genomes': struct {
        AF: float64,
        AN: int32,
        AC: int32,
        FAF_AF: float64,
        AF_POPMAX_OR_GLOBAL: float64,
        Hom: int32,
        Hemi: int32
    }
    'mainTranscript': struct {
        biotype: str,
        canonical: int32,
        category: str,
        cdna_start: int32,
        cdna_end: int32,
        codons: str,
        gene_id: str,
        gene_symbol: str,
        hgvs: str,
        hgvsc: str,
        major_consequence: str,
        major_consequence_rank: int32,
        transcript_id: str,
        amino_acids: str,
        domains: str,
        hgvsp: str,
        lof: str,
        lof_flags: str,
        lof_filter: str,
        lof_info: str,
        polyphen_prediction: str,
        protein_id: str,
        sift_prediction: str
    }
    'mpc': struct {
        MPC: str
    }
    'originalAltAlleles': array<str>
    'pos': int32
    'primate_ai': struct {
        score: float64
    }
    'ref': str
    'rsid': str
    'samples_ab': struct {
        0_to_5: set<str>,
        5_to_10: set<str>,
        10_to_15: set<str>,
        15_to_20: set<str>,
        20_to_25: set<str>,
        25_to_30: set<str>,
        30_to_35: set<str>,
        35_to_40: set<str>,
        40_to_45: set<str>
    }
    'samples_gq': struct {
        0_to_5: set<str>,
        5_to_10: set<str>,
        10_to_15: set<str>,
        15_to_20: set<str>,
        20_to_25: set<str>,
        25_to_30: set<str>,
        30_to_35: set<str>,
        35_to_40: set<str>,
        40_to_45: set<str>,
        45_to_50: set<str>,
        50_to_55: set<str>,
        55_to_60: set<str>,
        60_to_65: set<str>,
        65_to_70: set<str>,
        70_to_75: set<str>,
        75_to_80: set<str>,
        80_to_85: set<str>,
        85_to_90: set<str>,
        90_to_95: set<str>
    }
    'samples_no_call': set<str>
    'samples_num_alt': struct {
        1: set<str>,
        2: set<str>
    }
    'sortedTranscriptConsequences': array<struct {
        biotype: str,
        canonical: int32,
        cdna_start: int32,
        cdna_end: int32,
        codons: str,
        gene_id: str,
        gene_symbol: str,
        hgvsc: str,
        hgvsp: str,
        transcript_id: str,
        amino_acids: str,
        lof: str,
        lof_filter: str,
        lof_flags: str,
        lof_info: str,
        polyphen_prediction: str,
        protein_id: str,
        protein_start: int32,
        sift_prediction: str,
        consequence_terms: array<str>,
        domains: array<str>,
        major_consequence: str,
        category: str,
        hgvs: str,
        major_consequence_rank: int32,
        transcript_rank: int32
    }>
    'splice_ai': struct {
        delta_score: float64
    }
    'start': int32
    'topmed': struct {
        AC: int32,
        AF: float64,
        AN: int32,
        Hom: int32,
        Het: int32
    }
    'transcriptConsequenceTerms': set<str>
    'transcriptIds': set<str>
    'variantId': str
    'vep': struct {
        assembly_name: str,
        allele_string: str,
        ancestral: str,
        colocated_variants: array<struct {
            aa_allele: str,
            aa_maf: float64,
            afr_allele: str,
            afr_maf: float64,
            allele_string: str,
            amr_allele: str,
            amr_maf: float64,
            clin_sig: array<str>,
            end: int32,
            eas_allele: str,
            eas_maf: float64,
            ea_allele: str,
            ea_maf: float64,
            eur_allele: str,
            eur_maf: float64,
            exac_adj_allele: str,
            exac_adj_maf: float64,
            exac_allele: str,
            exac_afr_allele: str,
            exac_afr_maf: float64,
            exac_amr_allele: str,
            exac_amr_maf: float64,
            exac_eas_allele: str,
            exac_eas_maf: float64,
            exac_fin_allele: str,
            exac_fin_maf: float64,
            exac_maf: float64,
            exac_nfe_allele: str,
            exac_nfe_maf: float64,
            exac_oth_allele: str,
            exac_oth_maf: float64,
            exac_sas_allele: str,
            exac_sas_maf: float64,
            id: str,
            minor_allele: str,
            minor_allele_freq: float64,
            phenotype_or_disease: int32,
            pubmed: array<int32>,
            sas_allele: str,
            sas_maf: float64,
            somatic: int32,
            start: int32,
            strand: int32
        }>,
        context: str,
        end: int32,
        id: str,
        input: str,
        intergenic_consequences: array<struct {
            allele_num: int32,
            consequence_terms: array<str>,
            impact: str,
            minimised: int32,
            variant_allele: str
        }>,
        most_severe_consequence: str,
        motif_feature_consequences: array<struct {
            allele_num: int32,
            consequence_terms: array<str>,
            high_inf_pos: str,
            impact: str,
            minimised: int32,
            motif_feature_id: str,
            motif_name: str,
            motif_pos: int32,
            motif_score_change: float64,
            strand: int32,
            variant_allele: str
        }>,
        regulatory_feature_consequences: array<struct {
            allele_num: int32,
            biotype: str,
            consequence_terms: array<str>,
            impact: str,
            minimised: int32,
            regulatory_feature_id: str,
            variant_allele: str
        }>,
        seq_region_name: str,
        start: int32,
        strand: int32,
        transcript_consequences: array<struct {
            allele_num: int32,
            amino_acids: str,
            appris: str,
            biotype: str,
            canonical: int32,
            ccds: str,
            cdna_start: int32,
            cdna_end: int32,
            cds_end: int32,
            cds_start: int32,
            codons: str,
            consequence_terms: array<str>,
            distance: int32,
            domains: array<struct {
                db: str,
                name: str
            }>,
            exon: str,
            gene_id: str,
            gene_pheno: int32,
            gene_symbol: str,
            gene_symbol_source: str,
            hgnc_id: str,
            hgvsc: str,
            hgvsp: str,
            hgvs_offset: int32,
            impact: str,
            intron: str,
            lof: str,
            lof_flags: str,
            lof_filter: str,
            lof_info: str,
            minimised: int32,
            polyphen_prediction: str,
            polyphen_score: float64,
            protein_end: int32,
            protein_start: int32,
            protein_id: str,
            sift_prediction: str,
            sift_score: float64,
            strand: int32,
            swissprot: str,
            transcript_id: str,
            trembl: str,
            tsl: int32,
            uniparc: str,
            variant_allele: str
        }>,
        variant_class: str
    }
    'xpos': int64
    'xstart': int64
    'xstop': int64
----------------------------------------
Entry fields:
    'AD': array<int32>
    'DP': int32
    'GQ': int32
    'GT': call
    'PL': array<int32>
    'BX': array<str>
    'PS': int32
    'PQ': int32
    'JQ': int32
    'MIN_DP': int32
    'PGT': call
    'PID': str
    'RGQ': int32
    'SB': array<int32>
----------------------------------------
Column key: ['s']
Row key: ['locus', 'alleles']
----------------------------------------
[Stage 4:===================================================>  (480 + 20) / 500]2020-04-05 14:09:48 Hail: INFO: Coerced almost-sorted dataset
[Stage 5:======================================================>(498 + 2) / 500]2020-04-05 14:09:50 Hail: INFO: Coerced almost-sorted dataset
[Stage 7:>                                                      (0 + 108) / 500]ERROR: [pid 11941] Worker Worker(salt=943636132, workers=1, host=seqr-loading-cluster-m, username=root, pid=11941) failed    SeqrVCFToMTTask(source_paths=gs://seqr-bw/merged_phased_3P5CH.split.vcf.gz, dest_path=gs://seqr-bw/merged_phased_3P5CH.mt, genome_version=38, vep_runner=VEP, reference_ht_path=gs://seqr-reference-data/GRCh38/all_reference_data/combined_reference_data_grch38.ht, clinvar_ht_path=gs://seqr-reference-data/GRCh38/clinvar/clinvar.GRCh38.2020-03-29.ht, hgmd_ht_path=None, sample_type=WGS, validate=False, dataset_type=VARIANTS, remap_path=, subset_path=, vep_config_json_path=)
Traceback (most recent call last):
  File "/opt/conda/default/lib/python3.6/site-packages/luigi/worker.py", line 199, in run
    new_deps = self._run_get_new_deps()
  File "/opt/conda/default/lib/python3.6/site-packages/luigi/worker.py", line 141, in _run_get_new_deps
    task_gen = self.task.run()
  File "/tmp/c7e0443c47b54e91b295e2bff7b554b9/seqr_loading.py", line 54, in run
    self.read_vcf_write_mt()
  File "/tmp/c7e0443c47b54e91b295e2bff7b554b9/seqr_loading.py", line 84, in read_vcf_write_mt
    mt.write(self.output().path, stage_locally=True, overwrite=True)
  File "<decorator-gen-1092>", line 2, in write
  File "/opt/conda/default/lib/python3.6/site-packages/hail/typecheck/check.py", line 585, in wrapper
    return __original_func(*args_, **kwargs_)
  File "/opt/conda/default/lib/python3.6/site-packages/hail/matrixtable.py", line 2529, in write
    Env.backend().execute(MatrixWrite(self._mir, writer))
  File "/opt/conda/default/lib/python3.6/site-packages/hail/backend/backend.py", line 109, in execute
    result = json.loads(Env.hc()._jhc.backend().executeJSON(self._to_java_ir(ir)))
  File "/usr/lib/spark/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py", line 1257, in __call__
    answer, self.gateway_client, self.target_id, self.name)
  File "/opt/conda/default/lib/python3.6/site-packages/hail/utils/java.py", line 225, in deco
    'Error summary: %s' % (deepest, full, hail.__version__, deepest)) from None
hail.utils.java.FatalError: HailException: cannot set missing field for required type +PCStruct{info:PCStruct{ALLELEID:PInt32}}

Java stack trace:
java.lang.RuntimeException: error while applying lowering 'InterpretNonCompilable'
    at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:26)
    at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:18)
    at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
    at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
    at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:18)
    at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:27)
    at is.hail.backend.Backend.is$hail$backend$Backend$$_execute(Backend.scala:90)
    at is.hail.backend.Backend$$anonfun$execute$1.apply(Backend.scala:78)
    at is.hail.backend.Backend$$anonfun$execute$1.apply(Backend.scala:77)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:10)
    at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:9)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.annotations.Region$.scoped(Region.scala:18)
    at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:9)
    at is.hail.backend.Backend.execute(Backend.scala:77)
    at is.hail.backend.Backend.executeJSON(Backend.scala:96)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
    at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
    at py4j.Gateway.invoke(Gateway.java:282)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:238)
    at java.lang.Thread.run(Thread.java:748)

org.apache.spark.SparkException: Job aborted due to stage failure: Task 40 in stage 7.0 failed 20 times, most recent failure: Lost task 40.19 in stage 7.0 (TID 3171, seqr-loading-cluster-sw-z91p.c.seqr-project.internal, executor 14): is.hail.utils.HailException: cannot set missing field for required type +PCStruct{info:PCStruct{ALLELEID:PInt32}}
    at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:9)
    at is.hail.utils.package$.fatal(package.scala:74)
    at is.hail.annotations.RegionValueBuilder.setMissing(RegionValueBuilder.scala:210)
    at is.hail.rvd.RVD$$anonfun$24$$anonfun$apply$17.apply(RVD.scala:974)
    at is.hail.rvd.RVD$$anonfun$24$$anonfun$apply$17.apply(RVD.scala:967)
    at is.hail.utils.FlipbookIterator$$anon$5.<init>(FlipbookIterator.scala:176)
    at is.hail.utils.FlipbookIterator.map(FlipbookIterator.scala:174)
    at is.hail.utils.FlipbookIterator.map(FlipbookIterator.scala:145)
    at is.hail.rvd.RVD$$anonfun$24.apply(RVD.scala:967)
    at is.hail.rvd.RVD$$anonfun$24.apply(RVD.scala:963)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:147)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anonfun$3.apply(RichContextRDDRegionValue.scala:176)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anonfun$3.apply(RichContextRDDRegionValue.scala:176)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anonfun$3.apply(RichContextRDDRegionValue.scala:176)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anonfun$3.apply(RichContextRDDRegionValue.scala:176)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$class.foreach(Iterator.scala:891)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3$$anonfun$apply$4.apply(RichContextRDDRegionValue.scala:106)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3$$anonfun$apply$4.apply(RichContextRDDRegionValue.scala:102)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3.apply(RichContextRDDRegionValue.scala:102)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3.apply(RichContextRDDRegionValue.scala:101)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2.apply(RichContextRDDRegionValue.scala:101)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2.apply(RichContextRDDRegionValue.scala:99)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.io.fs.HadoopFS.writeFile(HadoopFS.scala:406)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1.apply(RichContextRDDRegionValue.scala:99)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1.apply(RichContextRDDRegionValue.scala:97)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:97)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:95)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.io.fs.HadoopFS.writeFile(HadoopFS.scala:406)
    at is.hail.io.RichContextRDDRegionValue$.writeSplitRegion(RichContextRDDRegionValue.scala:95)
    at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:922)
    at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:920)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$run$1$$anonfun$apply$5.apply(ContextRDD.scala:162)
    at is.hail.sparkextras.ContextRDD$$anonfun$run$1$$anonfun$apply$5.apply(ContextRDD.scala:162)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$class.foreach(Iterator.scala:891)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
    at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
    at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1334)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1334)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1334)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$15.apply(RDD.scala:990)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$15.apply(RDD.scala:990)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
    at org.apache.spark.scheduler.Task.run(Task.scala:123)
    at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

Driver stacktrace:
    at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1892)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1880)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1879)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1879)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927)
    at scala.Option.foreach(Option.scala:257)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:927)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2113)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2062)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2051)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
    at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:738)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2126)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:990)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
    at org.apache.spark.rdd.RDD.withScope(RDD.scala:385)
    at org.apache.spark.rdd.RDD.collect(RDD.scala:989)
    at is.hail.sparkextras.ContextRDD.collect(ContextRDD.scala:166)
    at is.hail.rvd.RVD.writeRowsSplit(RVD.scala:936)
    at is.hail.expr.ir.MatrixValue.write(MatrixValue.scala:214)
    at is.hail.expr.ir.MatrixNativeWriter.apply(MatrixWriter.scala:39)
    at is.hail.expr.ir.WrappedMatrixWriter.apply(MatrixWriter.scala:24)
    at is.hail.expr.ir.Interpret$.run(Interpret.scala:586)
    at is.hail.expr.ir.Interpret$.alreadyLowered(Interpret.scala:54)
    at is.hail.expr.ir.InterpretNonCompilable$.interpretAndCoerce$1(InterpretNonCompilable.scala:16)
    at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:53)
    at is.hail.expr.ir.InterpretNonCompilable$.apply(InterpretNonCompilable.scala:58)
    at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.transform(LoweringPass.scala:50)
    at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
    at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
    at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
    at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:15)
    at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:13)
    at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
    at is.hail.expr.ir.lowering.LoweringPass$class.apply(LoweringPass.scala:13)
    at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.apply(LoweringPass.scala:45)
    at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:20)
    at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:18)
    at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
    at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
    at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:18)
    at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:27)
    at is.hail.backend.Backend.is$hail$backend$Backend$$_execute(Backend.scala:90)
    at is.hail.backend.Backend$$anonfun$execute$1.apply(Backend.scala:78)
    at is.hail.backend.Backend$$anonfun$execute$1.apply(Backend.scala:77)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:10)
    at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:9)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.annotations.Region$.scoped(Region.scala:18)
    at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:9)
    at is.hail.backend.Backend.execute(Backend.scala:77)
    at is.hail.backend.Backend.executeJSON(Backend.scala:96)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
    at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
    at py4j.Gateway.invoke(Gateway.java:282)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:238)
    at java.lang.Thread.run(Thread.java:748)

is.hail.utils.HailException: cannot set missing field for required type +PCStruct{info:PCStruct{ALLELEID:PInt32}}
    at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:9)
    at is.hail.utils.package$.fatal(package.scala:74)
    at is.hail.annotations.RegionValueBuilder.setMissing(RegionValueBuilder.scala:210)
    at is.hail.rvd.RVD$$anonfun$24$$anonfun$apply$17.apply(RVD.scala:974)
    at is.hail.rvd.RVD$$anonfun$24$$anonfun$apply$17.apply(RVD.scala:967)
    at is.hail.utils.FlipbookIterator$$anon$5.<init>(FlipbookIterator.scala:176)
    at is.hail.utils.FlipbookIterator.map(FlipbookIterator.scala:174)
    at is.hail.utils.FlipbookIterator.map(FlipbookIterator.scala:145)
    at is.hail.rvd.RVD$$anonfun$24.apply(RVD.scala:967)
    at is.hail.rvd.RVD$$anonfun$24.apply(RVD.scala:963)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:147)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anonfun$3.apply(RichContextRDDRegionValue.scala:176)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anonfun$3.apply(RichContextRDDRegionValue.scala:176)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anonfun$3.apply(RichContextRDDRegionValue.scala:176)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anonfun$3.apply(RichContextRDDRegionValue.scala:176)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:185)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
    at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
    at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
    at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
    at is.hail.utils.FlipbookIterator$$anon$9.<init>(FlipbookIterator.scala:344)
    at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
    at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:53)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:149)
    at is.hail.rvd.KeyedRVD$$anonfun$orderedLeftJoinDistinct$1.apply(KeyedRVD.scala:146)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$19.apply(ContextRDD.scala:280)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13$$anonfun$apply$14.apply(ContextRDD.scala:223)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$class.foreach(Iterator.scala:891)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3$$anonfun$apply$4.apply(RichContextRDDRegionValue.scala:106)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3$$anonfun$apply$4.apply(RichContextRDDRegionValue.scala:102)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3.apply(RichContextRDDRegionValue.scala:102)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3.apply(RichContextRDDRegionValue.scala:101)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2.apply(RichContextRDDRegionValue.scala:101)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2.apply(RichContextRDDRegionValue.scala:99)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.io.fs.HadoopFS.writeFile(HadoopFS.scala:406)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1.apply(RichContextRDDRegionValue.scala:99)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1.apply(RichContextRDDRegionValue.scala:97)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:97)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:95)
    at is.hail.utils.package$.using(package.scala:602)
    at is.hail.io.fs.HadoopFS.writeFile(HadoopFS.scala:406)
    at is.hail.io.RichContextRDDRegionValue$.writeSplitRegion(RichContextRDDRegionValue.scala:95)
    at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:922)
    at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:920)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$13.apply(ContextRDD.scala:223)
    at is.hail.sparkextras.ContextRDD$$anonfun$run$1$$anonfun$apply$5.apply(ContextRDD.scala:162)
    at is.hail.sparkextras.ContextRDD$$anonfun$run$1$$anonfun$apply$5.apply(ContextRDD.scala:162)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at scala.collection.Iterator$class.foreach(Iterator.scala:891)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
    at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
    at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1334)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1334)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1334)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$15.apply(RDD.scala:990)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$15.apply(RDD.scala:990)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
    at org.apache.spark.scheduler.Task.run(Task.scala:123)
    at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

Hail version: 0.2.34-914bd8a10ca2
Error summary: HailException: cannot set missing field for required type +PCStruct{info:PCStruct{ALLELEID:PInt32}}
bw2 commented 4 years ago

Another thing I just realized is the genotype format varies across rows in the VCF: GT:AD:DP:GQ:PL GT:AD:DP:GQ:PL:BX:PS:PQ:JQ GT:AD:DP:GQ:PL:PS:PQ:JQ:BX GT:AD:DP:GQ:PL:BX:PS

tpoterba commented 4 years ago

Another thing I just realized is the genotype format varies across rows in the VCF

This is perfectly well-supported. I'm pretty sure the bug is with annotate(x = ht[...]), and is fixed by #8443

tpoterba commented 4 years ago

0.2.35 is a bit of a dud release

tpoterba commented 4 years ago

fixed.