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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-4.0.2.1/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] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants 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 java.net.URI.create(URI.java:852) at org.broadinstitute.hellbender.engine.FeatureInput.makeIntoAbsolutePath(FeatureInput.java:242) at org.broadinstitute.hellbender.engine.FeatureInput.toString(FeatureInput.java:314) at java.util.Formatter$FormatSpecifier.printString(Formatter.java:2886) at java.util.Formatter$FormatSpecifier.print(Formatter.java:2763) at java.util.Formatter.format(Formatter.java:2520) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broadinstitute.hellbender.engine.FeatureDataSource.close(FeatureDataSource.java:589) at org.broadinstitute.hellbender.engine.FeatureManager.lambda$close$9(FeatureManager.java:505) at java.util.LinkedHashMap$LinkedValues.forEach(LinkedHashMap.java:608) at org.broadinstitute.hellbender.engine.FeatureManager.close(FeatureManager.java:505) at org.broadinstitute.hellbender.engine.GATKTool.onShutdown(GATKTool.java:857) at org.broadinstitute.hellbender.engine.VariantWalker.onShutdown(VariantWalker.java:95) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:159) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:202) at org.broadinstitute.hellbender.Main.main(Main.java:288) Caused by: java.net.URISyntaxException: Illegal character in path at index 15: /media/yoshi/My Book/Aet_v4.0_ChrSeqSplit/HC.KU-2103.raw.snps.indels.g.vcf at java.net.URI$Parser.fail(URI.java:2848) at java.net.URI$Parser.checkChars(URI.java:3021) at java.net.URI$Parser.parseHierarchical(URI.java:3105) at java.net.URI$Parser.parse(URI.java:3063) at java.net.URI.<init>(URI.java:588) at java.net.URI.create(URI.java:850) ... 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.

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