Can't open VCF File
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.
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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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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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