Hello, After about 95 minutes my jobs was killed due to the error below. It seems it is referencing an unkown interval "Contig:chrUn_JTFH01001980v1_decoy start". My code is below as well as the fasta. I am wondering if perhaps the reference fasta is the issue here? I used GRCh38.d1.vd1.fa from the GDC since it matches the build of the files used. Do you think there would be major discrepancies if I used standard hg38 instead for funcotator? I have been using GRCh38.d1.vd1.fa for all upstream processes and just now coming across this error. Any suggestions on how to navigate this issue?

REQUIRED for all errors and issues:
a) GATK version used: 4.4.0
b) Exact command used:

java -jar ${GATK} Funcotator \

        --variant $sample \

        --reference GRCh38.d1.vd1.fa \

        --ref-version hg38 \

        --data-sources-path funcotator_dataSources.v1.7.20200521g \

        --output ${sample%.vcf}_germline.maf \

        --output-file-format MAF

c) Entire program log:

11:01:39.382 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/data/icelake-apps/software/openjdk-17.0.2/gatk/4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

11:01:39.416 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression11221408051366704058.so: /tmp/libgkl_compression11221408051366704058.so: failed to map segment from shared object)

11:01:39.419 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/data/icelake-apps/software/openjdk-17.0.2/gatk/4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

11:01:39.443 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13957371503608302880.so: /tmp/libgkl_compression13957371503608302880.so: failed to map segment from shared object)

11:01:39.445 INFO  Funcotator - ------------------------------------------------------------

11:01:39.447 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.4.0.0

11:01:39.447 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/

11:01:39.447 INFO  Funcotator - Executing as kmillan@cri22cn113.cri.uchicago.edu on Linux v4.18.0-240.22.1.el8_3.x86_64 amd64

11:01:39.447 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.2+8-86

11:01:39.447 INFO  Funcotator - Start Date/Time: March 18, 2024 at 11:01:39 AM CDT

11:01:39.447 INFO  Funcotator - ------------------------------------------------------------

11:01:39.448 INFO  Funcotator - ------------------------------------------------------------

11:01:39.449 INFO  Funcotator - HTSJDK Version: 3.0.5

11:01:39.449 INFO  Funcotator - Picard Version: 3.0.0

11:01:39.449 INFO  Funcotator - Built for Spark Version: 3.3.1

11:01:39.449 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2

11:01:39.450 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

11:01:39.450 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

11:01:39.450 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

11:01:39.450 INFO  Funcotator - Deflater: JdkDeflater

11:01:39.450 INFO  Funcotator - Inflater: JdkInflater

11:01:39.451 INFO  Funcotator - GCS max retries/reopens: 20

11:01:39.451 INFO  Funcotator - Requester pays: disabled

11:01:39.452 INFO  Funcotator - Initializing engine

11:01:39.753 INFO  FeatureManager - Using codec VCFCodec to read file file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/cohort_10_FINAL.MMRF_1021_2_PB_CD3pos_C1_KAS5U_L02374.vcf

11:01:39.903 INFO  Funcotator - Done initializing engine

11:01:39.903 INFO  Funcotator - Validating sequence dictionaries...

11:01:39.922 INFO  Funcotator - Processing user transcripts/defaults/overrides...

11:01:39.925 INFO  Funcotator - Initializing data sources...

11:01:39.940 INFO  DataSourceUtils - Initializing data sources from directory: /scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g

11:01:39.947 INFO  DataSourceUtils - Data sources version: 1.7.2020521g

11:01:39.947 INFO  DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.7.20200521g.tar.gz

11:01:39.947 INFO  DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200521.tar.gz

11:01:39.967 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/gencode.v34.annotation.REORDERED.gtf -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/gencode/hg38/gencode.v34.annotation.REORDERED.gtf

11:01:39.968 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/gencode.v34.pc_transcripts.fa -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/gencode/hg38/gencode.v34.pc_transcripts.fa

11:01:39.972 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/acmg_lof.tsv -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/acmg_lof/hg38/acmg_lof.tsv

11:01:39.975 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/clinvar_20180429_hg38.vcf -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/clinvar/hg38/clinvar_20180429_hg38.vcf

11:01:39.978 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/acmg59_test_cleaned.txt -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/acmg_rec/hg38/acmg59_test_cleaned.txt

11:01:39.980 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf

11:01:41.002 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...

11:01:41.003 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/gencode.v34.annotation.REORDERED.gtf -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/gencode/hg38/gencode.v34.annotation.REORDERED.gtf

11:01:41.015 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000

11:01:41.032 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/gencode/hg38/gencode.v34.annotation.REORDERED.gtf

11:01:41.095 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/gencode.v34.pc_transcripts.fa -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/gencode/hg38/gencode.v34.pc_transcripts.fa

11:01:44.326 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/acmg_lof.tsv -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/acmg_lof/hg38/acmg_lof.tsv

11:01:44.331 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/clinvar_20180429_hg38.vcf -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/clinvar/hg38/clinvar_20180429_hg38.vcf

11:01:44.331 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar_VCF : 100000

11:01:44.344 INFO  FeatureManager - Using codec VCFCodec to read file file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/clinvar/hg38/clinvar_20180429_hg38.vcf

11:01:44.404 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/clinvar_20180429_hg38.vcf -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/clinvar/hg38/clinvar_20180429_hg38.vcf

11:01:44.464 INFO  FeatureManager - Using codec VCFCodec to read file file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/clinvar/hg38/clinvar_20180429_hg38.vcf

11:01:44.580 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/acmg59_test_cleaned.txt -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/acmg_rec/hg38/acmg59_test_cleaned.txt

11:01:44.581 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf

11:01:44.581 INFO  DataSourceUtils - Setting lookahead cache for data source: LMMKnown : 100000

11:01:44.583 INFO  FeatureManager - Using codec VCFCodec to read file file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf

11:01:44.588 INFO  DataSourceUtils - Resolved data source file path: file:///ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf -> file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf

11:01:44.591 INFO  FeatureManager - Using codec VCFCodec to read file file:///scratch/kmillan/WES/ref_genome/germ_GATK/funcotator_dataSources.v1.7.20200521g/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf

11:01:44.592 INFO  DataSourceUtils - Setting lookahead cache for data source: gnomAD_exome : 100000

11:01:45.520 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:46.174 INFO  FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg38/gnomad.exomes.r2.1.sites.liftoverToHg38.INFO_ANNOTATIONS_FIXED.vcf.gz

11:01:46.279 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:46.363 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:46.677 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:47.549 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:47.582 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:47.761 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:48.705 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:49.188 INFO  FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg38/gnomad.exomes.r2.1.sites.liftoverToHg38.INFO_ANNOTATIONS_FIXED.vcf.gz

11:01:49.282 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:49.314 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:49.493 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:49.706 INFO  DataSourceUtils - Setting lookahead cache for data source: gnomAD_genome : 100000

11:01:50.544 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:51.131 INFO  FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg38/gnomad.genomes.r2.1.sites.liftoverToHg38.INFO_ANNOTATIONS_FIXED.vcf.gz

11:01:51.227 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:51.271 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:51.629 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:53.356 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:53.406 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:53.800 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:54.721 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:55.163 INFO  FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg38/gnomad.genomes.r2.1.sites.liftoverToHg38.INFO_ANNOTATIONS_FIXED.vcf.gz

11:01:55.291 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:55.377 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:55.676 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

11:01:55.830 INFO  Funcotator - Initializing Funcotator Engine...

11:01:55.839 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.

11:01:55.840 INFO  Funcotator - Creating a MAF file for output: file:/ess/scratch/scratch1/kmillan/WES/data/myeloma_files/Haplo_output/cohort_10/non_annotated/single_samples/group01

00:03:10.219 INFO  Funcotator - Shutting down engine

[March 19, 2024 at 12:03:10 AM CDT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 96.52 minutes.

Runtime.totalMemory()=2037448704

java.lang.IllegalArgumentException: Invalid interval. Contig:chrUn_JTFH01001980v1_decoy start:-1 end:18

at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:804)

at org.broadinstitute.hellbender.utils.SimpleInterval.validatePositions(SimpleInterval.java:59)

at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:35)

at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.createReferenceSnippet(FuncotatorUtils.java:1461)

at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createIgrFuncotation(GencodeFuncotationFactory.java:2481)

at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createIgrFuncotations(GencodeFuncotationFactory.java:2407)

at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createDefaultFuncotationsOnVariant(GencodeFuncotationFactory.java:499)

at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:217)

at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:182)

at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.lambda$createFuncotationMapForVariant$0(FuncotatorEngine.java:152)

at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)

at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)

at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1625)

at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)

at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)

at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921)

at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)

at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)

at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:162)

at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:924)

at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:878)

at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)

at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)

at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)

at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)

at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)

at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)

at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845)

at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)

at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)

at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)

at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)

at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)

at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596)

at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)

at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1098)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)

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)