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HaplotypeCaller haploid GVCF format error?

Hi all,

I prepared a clean Bam file following GATK Best Practice and used GATK4 HaplotypeCaller to create a gvcf with ploidy1 option:

gatk- HaplotypeCaller --native-pair-hmm-threads 24 -I KU_filtered_sorted_mdup.bam -O HC.KU.raw.snps.indels.g.vcf -R ref.fasta -ploidy 1 --emit-ref-confidence GVCF

When I validated the gvcf, ValidateVariants threw errors at the end:

11:27:55.681 INFO ProgressMeter - Traversal complete. Processed 124689522 total variants in 3.8 minutes. 11:27:55.681 INFO ValidateVariants - Shutting down engine [April 10, 2018 11:27:55 AM JST] done. Elapsed time: 3.82 minutes. Runtime.totalMemory()=4682940416 java.lang.IllegalArgumentException: Illegal character in path at index 15:HC.KU.raw.snps.indels.g.vcf at at org.broadinstitute.hellbender.engine.FeatureInput.makeIntoAbsolutePath( at org.broadinstitute.hellbender.engine.FeatureInput.toString( at java.util.Formatter$FormatSpecifier.printString( at java.util.Formatter$FormatSpecifier.print( at java.util.Formatter.format( at java.util.Formatter.format( at java.lang.String.format( at org.broadinstitute.hellbender.engine.FeatureDataSource.close( at org.broadinstitute.hellbender.engine.FeatureManager.lambda$close$9( at java.util.LinkedHashMap$LinkedValues.forEach( at org.broadinstitute.hellbender.engine.FeatureManager.close( at org.broadinstitute.hellbender.engine.GATKTool.onShutdown( at org.broadinstitute.hellbender.engine.VariantWalker.onShutdown( at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool( at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs( at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain( at org.broadinstitute.hellbender.Main.runCommandLineProgram( at org.broadinstitute.hellbender.Main.mainEntry( at org.broadinstitute.hellbender.Main.main( Caused by: Illegal character in path at index 15: /media/yoshi/My Book/Aet_v4.0_ChrSeqSplit/HC.KU-2103.raw.snps.indels.g.vcf at$ at$Parser.checkChars( at$Parser.parseHierarchical( at$Parser.parse( at<init>( at ... 19 more

When I ran GenotypeGVCFs using the gvcf, it ran to completion, but threw the same "java.lang.IllegalArgumentException" errors at the end.

My java is Java runtime: OpenJDK 64-Bit Server VM v1.8.0_162-8u162-b12-0ubuntu0.16.04.2-b12.

Could you please help me with this problem?
Many thanks.

Best Answer


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