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Hi, I tried to run Funcotator on my VCF file, for this I have downloaded the datasources v1.7 provided, but now I ran into an error for the gencode hg19 file which I don't know how to fix, because the error is not clear to me, is the gencode file provided incorrect and should I replace it by another file or is there another problem? I hope somebody can help. I have provided the errormessage below with in bold the lines which I think are the most important. 

Thanks in advance for looking into it, If there are any questions about the error please let me know.

a) I am using GATK version 4.1.7.0)
b) The specific command(s) I used is gatk funcotator \
--variant $inputfile\
--reference $refhg19 \
--ref-version hg19 \
--data-sources-path $dbPATH \
--output $output \
--output-file-format VCF
c) Please post error log here

11:39:11.273 INFO Funcotator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01
11:39:11.273 INFO Funcotator - Start Date/Time: August 7, 2020 11:39:10 AM CEST
11:39:11.273 INFO Funcotator - ------------------------------------------------------------
11:39:11.273 INFO Funcotator - ------------------------------------------------------------
11:39:11.274 INFO Funcotator - HTSJDK Version: 2.21.2
11:39:11.274 INFO Funcotator - Picard Version: 2.21.9
11:39:11.274 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:39:11.274 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:39:11.274 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:39:11.274 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:39:11.274 INFO Funcotator - Deflater: IntelDeflater
11:39:11.274 INFO Funcotator - Inflater: IntelInflater
11:39:11.274 INFO Funcotator - GCS max retries/reopens: 20
11:39:11.274 INFO Funcotator - Requester pays: disabled
11:39:11.274 INFO Funcotator - Initializing engine

...

resolved all datasource files

ENCODE GTF Header line 1 has a version number that is above maximum tested version (v 28)
(given: 34): ##description: evidence-based annotation of the human genome (GRCh38), version 34 (Ensembl 100), mapped to GRCh37
with gencode-backmap Continuing, but errors may occur.
11:39:15.609 WARN GencodeGtfCodec - GENCODE GTF Header line 1 has a version number that is above maximum tested version (v 28)
(given: 34): ##description: evidence-based annotation of the human genome (GRCh38), version 34 (Ensembl 100), mapped to GRCh37
with gencode-backmap Continuing, but errors may occur.
11:39:15.610 INFO FeatureManager - Using codec GencodeGtfCodec to read file file:///
db/funcotator_dataSources.v1.7.20200521s/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf
11:39:15.631 WARN GencodeGtfCodec - GENCODE GTF Header line 1 has a version number that is above maximum tested version (v 28)
(given: 34): ##description: evidence-based annotation of the human genome (GRCh38), version 34 (Ensembl 100), mapped to GRCh37
with gencode-backmap Continuing, but errors may occur.

11:39:22.190 INFO Funcotator - Initializing Funcotator Engine...
11:39:22.220 INFO Funcotator - Creating a VCF file for output: file:funcotated.vcf
11:39:22.292 INFO ProgressMeter - Starting traversal
11:39:22.293 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
11:39:22.356 INFO VcfFuncotationFactory - ClinVar_VCF 20180401 cache hits/total: 0/0
11:39:22.364 INFO VcfFuncotationFactory - dbSNP 9606_b151 cache hits/total: 0/0
11:39:22.395 INFO Funcotator - Shutting down engine
[August 7, 2020 11:39:22 AM CEST] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.19 minutes.
Runtime.totalMemory()=3196059648

htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line: LineIteratorImpl(SynchronousLineReader), for input so
urce: file:///MY/FILE/PATH/funcotator_dataSources.v1.7.20200521s/gencode/hg19/gencode.v34lift37
.annotation.REORDERED.gtf
at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.java:510)
at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.<init>(TribbleIndexedFeatureReader.java:426)
at htsjdk.tribble.TribbleIndexedFeatureReader.query(TribbleIndexedFeatureReader.java:297)
at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:567)
at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:536)
at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:353)
at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:173)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.queryFeaturesFromFeatureContext(DataSour
ceFuncotationFactory.java:304)

at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.getFeaturesFromFeatureContext(D[22/9009]
FuncotationFactory.java:219)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotation
Factory.java:197)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotation
Factory.java:172)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.lambda$createFuncotationMapForVariant$0(FuncotatorEn
gine.java:147)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java
:157)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:903)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:857)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)

at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)
Caused by: java.lang.NumberFormatException: For input string: "chr1:-:586071-586358"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Long.parseLong(Long.java:589)
at java.lang.Long.valueOf(Long.java:803)
at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.<init>(GencodeGtfFeature.java:224)
at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature.<init>(GencodeGtfExonFeature.java:19)
at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature.create(GencodeGtfExonFeature.java:23)
at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature$FeatureType$4.create(GencodeGtfFeature.java:777)
at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.create(GencodeGtfFeature.java:320)
at org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec.decode(AbstractGtfCodec.java:138)
at org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec.decode(AbstractGtfCodec.java:23)
at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.java:486)