Bug report for RegenotypeVariants

Just want to report a bug in RegenotypeVariants. Adding the "AF" field in the header solved the problem, even though I don't use this field.

Stack trace:

~$ java -Xmx30g -jar $prog/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar \

--num_threads $cpu \
-R $genome \
-V $snp/snp_filtered_sorted_chr_NoLD1.vcf.gz \
-T RegenotypeVariants \
-o $snp/snp_filtered_sorted_chr_NoLD1_regenotyped.vcf

INFO 10:42:20,806 HelpFormatter - ---------------------------------------------------------------------------------
INFO 10:42:20,808 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
INFO 10:42:20,808 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 10:42:20,808 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 10:42:20,831 HelpFormatter - Program Args: --num_threads 8 -R /home/duceppemo/gbs/Gmax_ref_genome/Gma1.01.20140304.fasta -V /home/duceppemo/gbs/MADmat/snp/snp_filtered_sorted_chr_NoLD1.vcf.gz -T RegenotypeVariants -o /home/duceppemo/gbs/MADmat/snp/snp_filtered_sorted_chr_NoLD1_regenotyped.vcf
INFO 10:42:20,837 HelpFormatter - Executing as [email protected] on Linux 3.16.0-43-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_60-b27.
INFO 10:42:20,837 HelpFormatter - Date/Time: 2015/09/08 10:42:20
INFO 10:42:20,838 HelpFormatter - ---------------------------------------------------------------------------------
INFO 10:42:20,838 HelpFormatter - ---------------------------------------------------------------------------------
INFO 10:42:21,276 GenomeAnalysisEngine - Strictness is SILENT
INFO 10:42:21,459 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
WARN 10:42:21,591 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
INFO 10:42:21,617 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 1 CPU thread(s) for each of 8 data thread(s), of 8 processors available on this machine
INFO 10:42:21,898 GenomeAnalysisEngine - Preparing for traversal
INFO 10:42:21,902 GenomeAnalysisEngine - Done preparing for traversal
INFO 10:42:21,903 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 10:42:21,903 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 10:42:21,903 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 10:42:23,158 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.IllegalStateException: Key AF found in VariantContext field INFO at Gm01:93302 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:176)
at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:115)
at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:222)
at org.broadinstitute.gatk.engine.io.storage.VariantContextWriterStorage.add(VariantContextWriterStorage.java:182)
at org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub.add(VariantContextWriterStub.java:271)
at org.broadinstitute.gatk.tools.walkers.variantutils.RegenotypeVariants.map(RegenotypeVariants.java:179)
at org.broadinstitute.gatk.tools.walkers.variantutils.RegenotypeVariants.map(RegenotypeVariants.java:117)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.4-46-gbc02625):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Key AF found in VariantContext field INFO at Gm01:93302 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
ERROR ------------------------------------------------------------------------------------------

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