Hey!

I am trying to apply filters to a certain VCF file, however, it keeps returning that the VFC file is not readable or doesn't exist. 

What do I do?

(gatk) root@07f32a086bc6:/gatk#  gatk VariantFiltration -V /Users/sanatmishra27/Downloads/ALL.chr20.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf -O output.vcf --genotype-filter-expression "GQ>10" --filter-name "my_filters"

Using GATK jar /gatk/gatk-package-4.1.7.0-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 /gatk/gatk-package-4.1.7.0-local.jar VariantFiltration -V /Users/sanatmishra27/Downloads/ALL.chr20.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf -O output.vcf --genotype-filter-expression GQ>10 --filter-name my_filters

19:21:26.605 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

May 31, 2020 7:21:28 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

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

19:21:28.228 INFO  VariantFiltration - ------------------------------------------------------------

19:21:28.236 INFO  VariantFiltration - The Genome Analysis Toolkit (GATK) v4.1.7.0

19:21:28.238 INFO  VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/

19:21:28.239 INFO  VariantFiltration - Executing as root@07f32a086bc6 on Linux v4.19.76-linuxkit amd64

19:21:28.240 INFO  VariantFiltration - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03

19:21:28.240 INFO  VariantFiltration - Start Date/Time: May 31, 2020 7:21:26 PM UTC

19:21:28.241 INFO  VariantFiltration - ------------------------------------------------------------

19:21:28.241 INFO  VariantFiltration - ------------------------------------------------------------

19:21:28.252 INFO  VariantFiltration - HTSJDK Version: 2.21.2

19:21:28.252 INFO  VariantFiltration - Picard Version: 2.21.9

19:21:28.252 INFO  VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2

19:21:28.253 INFO  VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

19:21:28.253 INFO  VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

19:21:28.253 INFO  VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

19:21:28.254 INFO  VariantFiltration - Deflater: IntelDeflater

19:21:28.255 INFO  VariantFiltration - Inflater: IntelInflater

19:21:28.255 INFO  VariantFiltration - GCS max retries/reopens: 20

19:21:28.257 INFO  VariantFiltration - Requester pays: disabled

19:21:28.258 INFO  VariantFiltration - Initializing engine

19:21:29.184 INFO  VariantFiltration - Shutting down engine

[May 31, 2020 7:21:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 0.05 minutes.

Runtime.totalMemory()=188743680

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A USER ERROR has occurred: Couldn't read file file:///Users/sanatmishra27/Downloads/ALL.chr20.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf. Error was: It doesn't exist.

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Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.