gatk: Invalid lookback distance found

Question

[rk.khayami94]

I tried to run the FilterVariantTranches tool from GATK 4.2.4.1 docker image and encountered the following error:

java.lang.RuntimeException: Invalid lookback distance found.
        at com.intel.gkl.compression.IntelInflater.inflateNative(Native Method)
        at com.intel.gkl.compression.IntelInflater.inflate(IntelInflater.java:174)
        at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:145)
        at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
        at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
        at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
        at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
        at htsjdk.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:380)
        at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:427)
        at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:46)
        at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:170)
        at htsjdk.tribble.TabixFeatureReader$FeatureIterator.<init>(TabixFeatureReader.java:159)
        at htsjdk.tribble.TabixFeatureReader.query(TabixFeatureReader.java:133)
        at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:622)
        at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:591)
        at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:357)
        at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:173)
        at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:125)
        at org.broadinstitute.hellbender.tools.walkers.vqsr.FilterVariantTranches.firstPassApply(FilterVariantTranches.java:184)
        at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.nthPassApply(TwoPassVariantWalker.java:17)
        at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.lambda$traverse$0(MultiplePassVariantWalker.java:40)
        at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.lambda$traverseVariants$1(MultiplePassVariantWalker.java:77)
        at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
        at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
        at java.util.Iterator.forEachRemaining(Iterator.java:116)
        at java.util.Spliterators$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.MultiplePassVariantWalker.traverseVariants(MultiplePassVariantWalker.java:75)
        at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:40)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
        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)

I wanted to know what it means and how to solve it. Thanks

ps: This is the command that I used:

gatk FilterVariantTranches \
--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' \
-V /gatk/data/RK/Analysis/Variants/CNN.X.vcf \
-O /gatk/data/RK/Analysis/Variants/CNN.X.GIAB.vcf  \
--info-key CNN_2D \
-resource /gatk/data/RK/databases/1000G_phase1_SNP/NCBI_1000G_phase1.snps.high_confidence.hg38.vcf.gz \
-resource /gatk/data/RK/databases/1000Gomni2.5/NCBI_1000G_omni2.5.hg38.vcf.gz \
-resource /gatk/data/RK/databases/Hapmap3.3/NCBI_hapmap_3.3.hg38.vcf.gz \
-resource /gatk/data/RK/databases/mills/NCBI_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
-resource /gatk/data/RK/databases/dbsnp/GCF_000001405.39.gz \
--tmp-dir /gatk/data/RK/tmp \
-L /gatk/data/RK/databases/Gencode/list.interval_list \
   -ip 100 \

Answer 1

[Pierre Lindenbaum]

this is a problem with a file that should be compressed with bgzip. Try to test all your files with tabix.

for example:

tabix  /gatk/data/RK/databases/Hapmap3.3/NCBI_hapmap_3.3.hg38.vcf.gz  "chr22" | tail

[rk.khayami94]

Thank you very much. It was the HapMap one.

Answer 2

[arifbicakcii]

i am not sure about docker image but i got a similar error when building gatk myself. try using java-jdk 8 manually

[rk.khayami94]

the HapMap database I used had a problem. I uncompressed it and indexed it again and this solved my problem