FastaAlternateReferenceMaker generates same sequence for multisample vcf
REQUIRED for all errors and issues:
a) GATK version used: v4.2.5.0
b) Exact command used: I used SelectVariants to generate one vcf file per sample and then used:
FastaAlternateReferenceMaker -R genomic.fna -O sample.fasta -L chromosome -V sample.vcf
c) Entire program log:
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 user/bin/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar
FastaAlternateReferenceMaker -R genomic.fna -O sample.fasta -L chromosome -V sample.vcf
09:02:24.157 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/user/bin/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Mar 17, 2023 9:02:24 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
09:02:24.270 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------
09:02:24.271 INFO FastaAlternateReferenceMaker - The Genome Analysis Toolkit (GATK) v4.2.5.0
09:02:24.271 INFO FastaAlternateReferenceMaker - For support and documentation go to https://software.broadinstitute.org/gatk/
09:02:24.271 INFO FastaAlternateReferenceMaker - Executing as user@compute-1-1734.local on Linux v3.10.0-693.5.2.el7.x86_64 amd64
09:02:24.271 INFO FastaAlternateReferenceMaker - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12
09:02:24.271 INFO FastaAlternateReferenceMaker - Start Date/Time: March 17, 2023 9:02:24 AM CDT
09:02:24.271 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------
09:02:24.271 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------
09:02:24.271 INFO FastaAlternateReferenceMaker - HTSJDK Version: 2.24.1
09:02:24.272 INFO FastaAlternateReferenceMaker - Picard Version: 2.25.4
09:02:24.272 INFO FastaAlternateReferenceMaker - Built for Spark Version: 2.4.5
09:02:24.272 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
09:02:24.272 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
09:02:24.272 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
09:02:24.272 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
09:02:24.272 INFO FastaAlternateReferenceMaker - Deflater: IntelDeflater
09:02:24.272 INFO FastaAlternateReferenceMaker - Inflater: IntelInflater
09:02:24.272 INFO FastaAlternateReferenceMaker - GCS max retries/reopens: 20
09:02:24.272 INFO FastaAlternateReferenceMaker - Requester pays: disabled
09:02:24.272 INFO FastaAlternateReferenceMaker - Initializing engine
09:02:24.751 INFO FeatureManager - Using codec VCFCodec to read file file:///sample.vcf
09:02:24.783 INFO IntervalArgumentCollection - Processing 49793703 bp from intervals
09:02:24.786 INFO FastaAlternateReferenceMaker - Done initializing engine
09:02:24.794 INFO ProgressMeter - Starting traversal
09:02:24.794 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
09:02:34.798 INFO ProgressMeter - chromosome 0.2 32033000 192159568.1
09:02:40.564 INFO ProgressMeter - chromosome 0.3 49793703 189449726.1
09:02:40.565 INFO ProgressMeter - Traversal complete. Processed 49793703 total bases in 0.3 minutes.
09:02:41.668 INFO FastaAlternateReferenceMaker - Shutting down engine
[March 17, 2023 9:02:41 AM CDT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.29 minutes.
Runtime.totalMemory()=6493831168
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I am sorry for the trouble you are having getting your variants to merge with your reference. Based on the log file and your invocation, it would seem that the method executed successfully in spite of there being no change to the sequence in your output file. In order to further assist you, would you please attach a similar log showing how you invoked SelectVariants, and its subsequent output? Thanks.
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