Hi, this is Jun

While making a new fasta file which will be used for "SNPEFF" as a database in the future, 

I have faced some error on "FastaAlternateReferenceMaker"

a) GATK version used:

gatk-4.1.8.1

b) Exact command used: 

/mnt/d/gatk-4.1.8.1/gatk FastaAlternateReferenceMaker

-R Homo_sapiens.GRCh37.75.fasta

-O Venter.fasta

-V Venter.sorted.vcf

c) Entire error log:
Using GATK jar /mnt/d/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /mnt/d/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar FastaAlternateReferenceMaker -R Homo_sapiens.GRCh37.75.fasta -O Venter.fasta -V Venter.sorted.vcf
14:56:59.881 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/d/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Sep 03, 2020 2:57:00 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
14:57:00.501 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------
14:57:00.501 INFO FastaAlternateReferenceMaker - The Genome Analysis Toolkit (GATK) v4.1.8.1
14:57:00.501 INFO FastaAlternateReferenceMaker - For support and documentation go to https://software.broadinstitute.org/gatk/
14:57:00.501 INFO FastaAlternateReferenceMaker - Executing as omg@DESKTOP-NS83LDC on Linux v4.19.104-microsoft-standard amd64
14:57:00.501 INFO FastaAlternateReferenceMaker - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~20.04-b01
14:57:00.502 INFO FastaAlternateReferenceMaker - Start Date/Time: September 3, 2020 2:56:59 PM KST
14:57:00.502 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------
14:57:00.502 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------
14:57:00.503 INFO FastaAlternateReferenceMaker - HTSJDK Version: 2.23.0
14:57:00.503 INFO FastaAlternateReferenceMaker - Picard Version: 2.22.8
14:57:00.503 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:57:00.503 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:57:00.503 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:57:00.503 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:57:00.504 INFO FastaAlternateReferenceMaker - Deflater: IntelDeflater
14:57:00.504 INFO FastaAlternateReferenceMaker - Inflater: IntelInflater
14:57:00.504 INFO FastaAlternateReferenceMaker - GCS max retries/reopens: 20
14:57:00.504 INFO FastaAlternateReferenceMaker - Requester pays: disabled
14:57:00.504 INFO FastaAlternateReferenceMaker - Initializing engine
14:57:00.954 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/d/Homo/dna/Venter.sorted.vcf
14:57:00.989 INFO FastaAlternateReferenceMaker - Shutting down engine
[September 3, 2020 2:57:00 PM KST] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=355467264
org.broadinstitute.hellbender.exceptions.GATKException: Error initializing feature reader for path Venter.sorted.vcf
at org.broadinstitute.hellbender.engine.FeatureDataSource.getTribbleFeatureReader(FeatureDataSource.java:383)
at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(FeatureDataSource.java:335)
at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:282)
at org.broadinstitute.hellbender.engine.FeatureManager.addToFeatureSources(FeatureManager.java:246)
at org.broadinstitute.hellbender.engine.FeatureManager.initializeFeatureSources(FeatureManager.java:209)
at org.broadinstitute.hellbender.engine.FeatureManager.<init>(FeatureManager.java:156)
at org.broadinstitute.hellbender.engine.GATKTool.initializeFeatures(GATKTool.java:488)
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:709)
at org.broadinstitute.hellbender.engine.ReferenceWalker.onStartup(ReferenceWalker.java:36)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Invalid count number, with fixed count the number should be 1 or higher: key=INFO name=TSA type=String desc=Type of sequence alteration. Child of term sequence_alteration as defined by the sequence ontology project. lineType=INFO count=0, for input source: Venter.sorted.vcf
at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:263)
at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:102)
at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:127)
at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:121)
at org.broadinstitute.hellbender.engine.FeatureDataSource.getTribbleFeatureReader(FeatureDataSource.java:380)
... 14 more
Caused by: java.lang.IllegalArgumentException: Invalid count number, with fixed count the number should be 1 or higher: key=INFO name=TSA type=String desc=Type of sequence alteration. Child of term sequence_alteration as defined by the sequence ontology project. lineType=INFO count=0
at htsjdk.variant.vcf.VCFCompoundHeaderLine.validate(VCFCompoundHeaderLine.java:261)
at htsjdk.variant.vcf.VCFCompoundHeaderLine.<init>(VCFCompoundHeaderLine.java:256)
at htsjdk.variant.vcf.VCFInfoHeaderLine.<init>(VCFInfoHeaderLine.java:56)
at htsjdk.variant.vcf.AbstractVCFCodec.parseHeaderFromLines(AbstractVCFCodec.java:192)
at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:111)
at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:79)
at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:37)
at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:261)
... 18 more

All of fasta data were obtained in "ensembl.org". 

Please let me know the problems. Thank you.

P.S.: I am worrying that I run gatk program on windows wsl2 ubuntu, not Linux system.

Does it make other problems?