Hello

I am studying genotyping by RAD-seq.

I have interests in population genetic structure within wild plant species.

So I would like to use GATK for genotyping / variant calling.

However,

I felt in a problem.

My working sentence is

"java -jar gatk-package-4.1.2.0-local.jar HaplotypeCaller -R /mnt/c/Popgen -I /mnt/c/Popgen/samtools-1.9/sample18.bam -O /mnt/c/Popgen/GATK/sample18.vcf"

and then,

I got this result.

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11:45:13.056 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/c/popgen/GATK/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

May 07, 2020 11:45:14 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

INFO: Failed to detect whether we are running on Google Compute Engine.

11:45:14.793 INFO HaplotypeCaller - ------------------------------------------------------------

11:45:14.793 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.2.0

11:45:14.794 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/

11:45:14.795 INFO HaplotypeCaller - Executing as bwook1243@bwook1243 on Linux v4.4.0-18362-Microsoft amd64

11:45:14.795 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08

11:45:14.796 INFO HaplotypeCaller - Start Date/Time: May 7, 2020 11:45:13 AM KST

11:45:14.797 INFO HaplotypeCaller - ------------------------------------------------------------

11:45:14.798 INFO HaplotypeCaller - ------------------------------------------------------------

11:45:14.799 INFO HaplotypeCaller - HTSJDK Version: 2.19.0

11:45:14.799 INFO HaplotypeCaller - Picard Version: 2.19.0

11:45:14.800 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2

11:45:14.801 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

11:45:14.801 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

11:45:14.802 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

11:45:14.804 INFO HaplotypeCaller - Deflater: IntelDeflater

11:45:14.808 INFO HaplotypeCaller - Inflater: IntelInflater

11:45:14.809 INFO HaplotypeCaller - GCS max retries/reopens: 20

11:45:14.809 INFO HaplotypeCaller - Requester pays: disabled

11:45:14.810 INFO HaplotypeCaller - Initializing engine

11:45:14.815 INFO HaplotypeCaller - Shutting down engine

[May 7, 2020 11:45:14 AM KST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.03 minutes.

Runtime.totalMemory()=288882688

java.lang.IllegalArgumentException: File is not a supported reference file type: /mnt/c/Popgen

at htsjdk.samtools.reference.ReferenceSequenceFileFactory.lambda$getFastaExtension$0(ReferenceSequenceFileFactory.java:252)

at java.util.Optional.orElseGet(Optional.java:267)

at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getFastaExtension(ReferenceSequenceFileFactory.java:252)

at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getDefaultDictionaryForReferenceSequence(ReferenceSequenceFileFactory.java:222)

at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.checkFastaPath(CachingIndexedFastaSequenceFile.java:166)

at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.(CachingIndexedFastaSequenceFile.java:129)

at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.(CachingIndexedFastaSequenceFile.java:111)

at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.(CachingIndexedFastaSequenceFile.java:96)

at org.broadinstitute.hellbender.engine.ReferenceFileSource.(ReferenceFileSource.java:35)

at org.broadinstitute.hellbender.engine.ReferenceDataSource.of(ReferenceDataSource.java:27)

at org.broadinstitute.hellbender.engine.GATKTool.initializeReference(GATKTool.java:423)

at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:693)

at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:161)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)

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:162)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)

at org.broadinstitute.hellbender.Main.main(Main.java:291)

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I think that the connection to Google compute engine is not working on my computer. Isn't it?

I prepared reference files (fasta (*.fa), *fa.fai, *.dict).

How can I solve this problem?

Please give your kind help.