Error in trying to use VariantRecalibrator

Hi,

I'm trying to use the VariantRecalibrator on SNP calls from ~160 yeast genomes. Because there are no resources for known SNPs, I had to create my own. As all the genomes are of yeast that derived in an evolution experiment, they have a (relatively small) common set of differences relative to the reference. As coverage varies between strains, and across the genome, not all common SNPs get called in all strains, so I generated one vcf file with SNPs that were called in 25% or more of the strains - manual examination of these suggests that they are all real (I called this truth.vcf - it has ~120 SNPs) - and one file of SNPs that were called in between 10-25% of strains (I called this train.vcf - it only has ~25 SNPs). I then try to do variant recalibration as:

gatk-4.0.11.0/gatk VariantRecalibrator -R Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fasta -V called_genotypes.vcf.gz --resource truth,known=false,training=true,truth=true,prior=15.0:truth.vcf --resource train,known=false,training=true,truth=false,prior=10.0:train.vcf -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -mode SNP -O output.recal --tranches-file output.tranches --rscript-file output.plots.R --max-gaussians=4

but got the following output:

Using GATK jar /Volumes/Promise_Pegasus/gatk-4.0.11.0/gatk-package-4.0.11.0-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 /Volumes/Promise_Pegasus/gatk-4.0.11.0/gatk-package-4.0.11.0-local.jar VariantRecalibrator -R Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fasta -V called_genotypes.vcf.gz --resource truth,known=false,training=true,truth=true,prior=15.0:truth.vcf --resource train,known=false,training=true,truth=false,prior=10.0:train.vcf -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -mode SNP -O output.recal --tranches-file output.tranches --rscript-file output.plots.R --max-gaussians=4
18:23:35.917 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Volumes/Promise_Pegasus/gatk-4.0.11.0/gatk-package-4.0.11.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib
18:23:37.594 INFO VariantRecalibrator - ------------------------------------------------------------
18:23:37.594 INFO VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.0.11.0
18:23:37.595 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:23:37.595 INFO VariantRecalibrator - Executing as [email protected] on Mac OS X v10.13.3 x86_64
18:23:37.595 INFO VariantRecalibrator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_51-b16
18:23:37.595 INFO VariantRecalibrator - Start Date/Time: January 9, 2019 6:23:35 PM PST
18:23:37.595 INFO VariantRecalibrator - ------------------------------------------------------------
18:23:37.595 INFO VariantRecalibrator - ------------------------------------------------------------
18:23:37.596 INFO VariantRecalibrator - HTSJDK Version: 2.16.1
18:23:37.596 INFO VariantRecalibrator - Picard Version: 2.18.13
18:23:37.596 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:23:37.596 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:23:37.596 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:23:37.596 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:23:37.596 INFO VariantRecalibrator - Deflater: IntelDeflater
18:23:37.596 INFO VariantRecalibrator - Inflater: IntelInflater
18:23:37.596 INFO VariantRecalibrator - GCS max retries/reopens: 20
18:23:37.596 INFO VariantRecalibrator - Requester pays: disabled
18:23:37.596 INFO VariantRecalibrator - Initializing engine
18:23:38.024 INFO FeatureManager - Using codec VCFCodec to read file file:///Volumes/Promise_Pegasus/Lucas/whole_genome_seq/Gavin_Haploid_Analysis/truth.vcf
18:23:38.040 INFO FeatureManager - Using codec VCFCodec to read file file:///Volumes/Promise_Pegasus/Lucas/whole_genome_seq/Gavin_Haploid_Analysis/train.vcf
18:23:38.047 INFO FeatureManager - Using codec VCFCodec to read file file:///Volumes/Promise_Pegasus/Lucas/whole_genome_seq/Gavin_Haploid_Analysis/called_genotypes.vcf.gz
18:23:38.082 INFO VariantRecalibrator - Done initializing engine
18:23:38.086 INFO TrainingSet - Found truth track: Known = false Training = true Truth = true Prior = Q15.0
18:23:38.086 INFO TrainingSet - Found train track: Known = false Training = true Truth = false Prior = Q10.0
18:23:38.092 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "recal". Defaulting to VCF.
18:23:38.107 INFO ProgressMeter - Starting traversal
18:23:38.108 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:23:38.347 INFO VariantRecalibrator - No variants filtered by: AllowAllVariantsVariantFilter
18:23:38.348 INFO ProgressMeter - XI:67773 0.0 1598 399500.0
18:23:38.348 INFO ProgressMeter - Traversal complete. Processed 1598 total variants in 0.0 minutes.
18:23:38.349 INFO VariantDataManager - QD: mean = 31.03 standard deviation = 2.13
18:23:38.349 INFO VariantDataManager - MQ: mean = 56.26 standard deviation = 5.91
18:23:38.349 INFO VariantDataManager - MQRankSum: mean = 0.17 standard deviation = 0.65
18:23:38.350 INFO VariantDataManager - ReadPosRankSum: mean = 0.22 standard deviation = 0.89
18:23:38.350 INFO VariantDataManager - FS: mean = 0.53 standard deviation = 3.12
18:23:38.351 INFO VariantDataManager - SOR: mean = 1.03 standard deviation = 0.77
18:23:38.351 INFO VariantDataManager - DP: mean = 3260.79 standard deviation = 10238.34
18:23:38.358 INFO VariantDataManager - Annotation order is: [DP, MQ, QD, FS, ReadPosRankSum, MQRankSum, SOR]
18:23:38.358 INFO VariantDataManager - Training with 112 variants after standard deviation thresholding.
18:23:38.358 WARN VariantDataManager - WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable.
18:23:38.361 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:23:38.394 INFO VariantRecalibratorEngine - Finished iteration 0.
18:23:38.412 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.04664
18:23:38.419 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.05034
18:23:38.421 INFO VariantRecalibratorEngine - Convergence after 11 iterations!
18:23:38.424 WARN VariantRecalibratorEngine - Model could not pre-compute denominators.
18:23:38.424 INFO VariantDataManager - Selected worst 0 scoring variants --> variants with LOD <= -5.0000.
18:23:38.427 INFO VariantRecalibrator - Shutting down engine
[January 9, 2019 6:23:38 PM PST] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1202192384
java.lang.IllegalArgumentException: No data found.
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:34)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.onTraversalSuccess(VariantRecalibrator.java:656)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:968)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)

I don't understand what the "No data found" error at the end means, but it results in me having no SNPs in the output.recal file (should that be a vcf file?) , and I get no .R file from which to generate any plots.

Answers

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