[Funcotator] java.lang.IllegalArgumentException: Unexpected value: lncRNA
Can you please provide
a) GATK version used; "broadinstitute/gatk:latest" (gatk 4.1.8.1)
Hello
I'm running funcotator on germline samples but keeps throwing this error `
java.lang.IllegalArgumentException: Unexpected value: lncRNA
`
b) Exact GATK commands used
`
# Run Funcotator: gatk --java-options "-Xmx2048m" Funcotator \ --data-sources-path $DATA_SOURCES_FOLDER \ --ref-version hg38 \ --output-file-format MAF \ -R /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta \ -V /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/a34c5bca-bf0b-4e65-98d5-700df12a8d64/JointGenotyping/2f79a259-d134-4dd5-88eb-a4c44a6be42b/call-FinalGatherVcf/Germline_108.vcf.gz \ -O XXXX_108_Germline.maf \ -L /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/Exome-Agilent_V6_UTR.bedTo.list.interval_list \ --annotation-default normal_barcode:Unknown \ --annotation-default tumor_barcode:Unknown \ --annotation-default Center:"CUIMC" \ --annotation-default source:"CUIMC" \
`
funcotator data_sources_tar_gz gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200521g.tar.gz
c) The entire error log if applicable below
`
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.b2726ba4 17:55:22.132 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so 17:55:24.377 INFO Funcotator - ------------------------------------------------------------ 17:55:24.378 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.1.8.1 17:55:24.381 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/ 17:55:24.383 INFO Funcotator - Executing as root@171ac3a4f27a on Linux v4.19.112+ amd64 17:55:24.384 INFO Funcotator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08 17:55:24.385 INFO Funcotator - Start Date/Time: July 30, 2020 5:55:21 PM GMT 17:55:24.392 INFO Funcotator - ------------------------------------------------------------ 17:55:24.393 INFO Funcotator - ------------------------------------------------------------ 17:55:24.396 INFO Funcotator - HTSJDK Version: 2.23.0 17:55:24.396 INFO Funcotator - Picard Version: 2.22.8 17:55:24.396 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 17:55:24.397 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 17:55:24.399 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 17:55:24.400 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 17:55:24.400 INFO Funcotator - Deflater: IntelDeflater 17:55:24.400 INFO Funcotator - Inflater: IntelInflater 17:55:24.400 INFO Funcotator - GCS max retries/reopens: 20 17:55:24.407 INFO Funcotator - Requester pays: disabled 17:55:24.408 INFO Funcotator - Initializing engine 17:55:25.936 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/a34c5bca-bf0b-4e65-98d5-700df12a8d64/JointGenotyping/2f79a259-d134-4dd5-88eb-a4c44a6be42b/call-FinalGatherVcf/Germline_108.vcf.gz 17:55:26.596 INFO FeatureManager - Using codec IntervalListCodec to read file file:///cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/Exome-Agilent_V6_UTR.bedTo.list.interval_list 17:55:30.307 INFO IntervalArgumentCollection - Processing 90499549 bp from intervals 17:55:30.483 INFO Funcotator - Done initializing engine 17:55:30.484 INFO Funcotator - Validating Sequence Dictionaries... 17:55:30.558 INFO Funcotator - Processing user transcripts/defaults/overrides... 17:55:30.563 INFO Funcotator - Initializing data sources... 17:55:30.566 INFO DataSourceUtils - Initializing data sources from directory: /cromwell_root/datasources_dir 17:55:30.570 INFO DataSourceUtils - Data sources version: 1.7.2020521g 17:55:30.571 INFO DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.7.20200521g.tar.gz 17:55:30.571 INFO DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200521.tar.gz 17:55:30.585 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf -> file:///cromwell_root/datasources_dir/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf 17:55:33.211 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/gencode.v34.annotation.REORDERED.gtf -> file:///cromwell_root/datasources_dir/gencode/hg38/gencode.v34.annotation.REORDERED.gtf 17:55:33.212 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/gencode.v34.pc_transcripts.fa -> file:///cromwell_root/datasources_dir/gencode/hg38/gencode.v34.pc_transcripts.fa 17:55:33.327 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/clinvar_20180429_hg38.vcf -> file:///cromwell_root/datasources_dir/clinvar/hg38/clinvar_20180429_hg38.vcf 17:55:33.329 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/acmg59_test_cleaned.txt -> file:///cromwell_root/datasources_dir/acmg_rec/hg38/acmg59_test_cleaned.txt 17:55:33.330 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/acmg_lof.tsv -> file:///cromwell_root/datasources_dir/acmg_lof/hg38/acmg_lof.tsv 17:55:33.331 INFO Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)... 17:55:33.332 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf -> file:///cromwell_root/datasources_dir/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf 17:55:33.332 INFO DataSourceUtils - Setting lookahead cache for data source: LMMKnown : 100000 17:55:33.336 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/datasources_dir/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf 17:55:33.357 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf -> file:///cromwell_root/datasources_dir/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf 17:55:33.377 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/datasources_dir/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf 17:55:33.396 INFO DataSourceUtils - Setting lookahead cache for data source: gnomAD_exome : 100000 17:55:35.811 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 17:55:40.121 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 17:55:40.507 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/gencode.v34.annotation.REORDERED.gtf -> file:///cromwell_root/datasources_dir/gencode/hg38/gencode.v34.annotation.REORDERED.gtf 17:55:40.508 INFO DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000 17:55:40.535 WARN GencodeGtfCodec - GENCODE GTF Header line 1 has a version number that is above maximum tested version (v 28) (given: 34): ##description: evidence-based annotation of the human genome (GRCh38), version 34 (Ensembl 100) Continuing, but errors may occur. 17:55:40.536 WARN GencodeGtfCodec - GENCODE GTF Header line 1 has a version number that is above maximum tested version (v 28) (given: 34): ##description: evidence-based annotation of the human genome (GRCh38), version 34 (Ensembl 100) Continuing, but errors may occur. 17:55:40.537 INFO FeatureManager - Using codec GencodeGtfCodec to read file file:///cromwell_root/datasources_dir/gencode/hg38/gencode.v34.annotation.REORDERED.gtf 17:55:40.589 WARN GencodeGtfCodec - GENCODE GTF Header line 1 has a version number that is above maximum tested version (v 28) (given: 34): ##description: evidence-based annotation of the human genome (GRCh38), version 34 (Ensembl 100) Continuing, but errors may occur. 17:55:40.740 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/gencode.v34.pc_transcripts.fa -> file:///cromwell_root/datasources_dir/gencode/hg38/gencode.v34.pc_transcripts.fa 17:55:48.604 INFO DataSourceUtils - Setting lookahead cache for data source: gnomAD_genome : 100000 17:55:50.080 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 17:55:54.384 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 17:55:54.818 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/clinvar_20180429_hg38.vcf -> file:///cromwell_root/datasources_dir/clinvar/hg38/clinvar_20180429_hg38.vcf 17:55:54.818 INFO DataSourceUtils - Setting lookahead cache for data source: ClinVar_VCF : 100000 17:55:54.823 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/datasources_dir/clinvar/hg38/clinvar_20180429_hg38.vcf 17:55:54.910 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/clinvar_20180429_hg38.vcf -> file:///cromwell_root/datasources_dir/clinvar/hg38/clinvar_20180429_hg38.vcf 17:55:54.975 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/datasources_dir/clinvar/hg38/clinvar_20180429_hg38.vcf 17:55:55.038 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/acmg59_test_cleaned.txt -> file:///cromwell_root/datasources_dir/acmg_rec/hg38/acmg59_test_cleaned.txt 17:55:55.051 INFO DataSourceUtils - Resolved data source file path: file:///cromwell_root/acmg_lof.tsv -> file:///cromwell_root/datasources_dir/acmg_lof/hg38/acmg_lof.tsv 17:55:55.052 INFO Funcotator - Initializing Funcotator Engine... 17:55:55.094 INFO Funcotator - Creating a MAF file for output: file:/cromwell_root/BRCA_CUIMC108_Germline.maf 17:55:55.173 WARN MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count). Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header 17:55:55.189 INFO ProgressMeter - Starting traversal 17:55:55.190 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 17:55:55.310 INFO VcfFuncotationFactory - ClinVar_VCF 20180429_hg38 cache hits/total: 0/0 17:55:55.311 INFO VcfFuncotationFactory - LMMKnown 20180618 cache hits/total: 0/0 17:55:55.311 INFO VcfFuncotationFactory - gnomAD_exome 2.1 cache hits/total: 0/0 17:55:55.311 INFO VcfFuncotationFactory - gnomAD_genome 2.1 cache hits/total: 0/0 17:55:55.393 INFO Funcotator - Shutting down engine [July 30, 2020 5:55:55 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.56 minutes. Runtime.totalMemory()=920244224 java.lang.IllegalArgumentException: Unexpected value: lncRNA at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature$GeneTranscriptType.getEnum(GencodeGtfFeature.java:1052) at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.<init>(GencodeGtfFeature.java:158) at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfGeneFeature.<init>(GencodeGtfGeneFeature.java:19) at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfGeneFeature.create(GencodeGtfGeneFeature.java:23) at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature$FeatureType$1.create(GencodeGtfFeature.java:753) at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.create(GencodeGtfFeature.java:320) at org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec.decode(AbstractGtfCodec.java:138) at org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec.decode(AbstractGtfCodec.java:23) at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.java:501) at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.next(TribbleIndexedFeatureReader.java:457) at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.next(TribbleIndexedFeatureReader.java:420) at org.broadinstitute.hellbender.engine.FeatureCache.fill(FeatureCache.java:142) at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:568) at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:536) at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:352) at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:173) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.queryFeaturesFromFeatureContext(DataSourceFuncotationFactory.java:314) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.getFeaturesFromFeatureContext(DataSourceFuncotationFactory.java:229) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:207) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:182) at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.lambda$createFuncotationMapForVariant$0(FuncotatorEngine.java:147) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472) at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566) at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:157) at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:904) at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:858) at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104) at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.Iterator.forEachRemaining(Iterator.java:116) at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472) at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150) at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485) at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140) 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) Using GATK jar /root/gatk.jar defined in environment variable GATK_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 -Xmx2048m -jar /root/gatk.jar Funcotator --data-sources-path /cromwell_root/datasources_dir --ref-version hg38 --output-file-format MAF -R /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta -V /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/a34c5bca-bf0b-4e65-98d5-700df12a8d64/JointGenotyping/2f79a259-d134-4dd5-88eb-a4c44a6be42b/call-FinalGatherVcf/Germline_108.vcf.gz -O BRCA_CUIMC108_Germline.maf -L /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/Exome-Agilent_V6_UTR.bedTo.list.interval_list --annotation-default normal_barcode:Unknown --annotation-default tumor_barcode:Unknown --annotation-default Center:CUIMC --annotation-default source:CUIMC
`
Thanks for your help
Sam
-
Hi sahuno,
Thanks for writing in. Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace?
- Add GROUP_FireCloud-Support@firecloud.org to the User email field and press enter on your keyboard.
- Click Save.
Let us know the workspace name, as well as the relevant submission and workflow IDs. We’ll be happy to take a closer look as soon as we can.
Thanks,
Samantha
-
I've added ` GROUP_FireCloud-Support@firecloud.org ` to the current workspace and sent submission details to email.
could you please confirm you have it?
Kind regards
SA
-
Hi sahuno,
Confirming I received your email, thank you for sending that information over. I will take a look and get back to you.
Best,
Samantha
-
Hi sahuno,
It looks like the issue may have been that the GATK docker you were using was a different version than the workflow you were running (4.1.8.1 vs 4.1.7.0). I've noticed that you recently ran the workflow again with GATK 4.1.7.0 and the submission was successful. It looks like you've solved the issue on your own, but if you need any further assistance, please let me know.
Best,
Samantha
-
I appreciate your time looking at the workflow and logs. You are right about conflicts in gatk docker versions in workflow and as attribute I specified.
but i I don't think alignment of gatk docker version to `4.1.7.0` was the only issue for the error;
java.lang.IllegalArgumentException: Unexpected value: lncRNA
You could see that when i used gatk docker `4.1.7.0` with latest functotator datasource it failed (Submission ID- 226cc74b-46aa-4ccf-bca3-d1ac61fe8877)
Rather downgrading the Funcotator datasource used in the workflow from funcotator_dataSources.v1.7.20200521s.tar.gz to funcotator_dataSources.v1.6.20190124s.tar.gz helped.
Submission ID - 50fbf53a-baa1-49b7-8e34-d7f90b2d5532or maybe I'm not doing something right again?
Kind regards
Sam -
Hi sahuno,
It looks like what you are experiencing is a known issue with funcotator_dataSources.v1.7.20200521s - see the following thread for more info: https://github.com/broadinstitute/gatk/issues/6708.
You should continue to use funcotator_dataSources.v1.6.20190124 until GATK version 4.1.9.0 is released.
Please let me know if you have any other questions or issues.
Best,
Samantha
-
Samantha (she/her) Great! thanks for pointing this out!
Sam
-
Hi sahuno,
Happy to help! If you need any further assistance, please let us know.
Best,
Samantha
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