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Variant Discovery in High-Throughput Sequencing Data

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Can't open VCF File

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Sanat Mishra

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

***********************************************************************

 

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.

 

***********************************************************************

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

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2 comments

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  • Avatar
    Bhanu Gandham

    Are you able to view the file? Looks like the tool is not able to find this file. Can you try opening it and ensure that the file path you provided is accurate.

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  • Avatar
    Sanat Mishra

    I ran this outside Docker and it worked. I think there was some problem with reading files when inside the container.

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