Greetings,
I am attempting to use the HaplotypeCaller using GATK version 3.6 and received a Runtime Error.
The command I used was:
Java –jar GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R $chicken.fa \
-I $chickenmerged.bam \
--genotyping_mode DISCOVERY \
-stand_emit_conf 10 \
-stand_call_conf 30 \
-o $chicken_raw_variants5.vcf
The error I received was:
ERROR --
ERROR stack trace
java.lang.NoClassDefFoundError: org/broadinstitute/gatk/utils/help/HelpConstants
at org.broadinstitute.gatk.utils.exceptions.UserException.(UserException.java:53)
at org.broadinstitute.gatk.engine.iterators.MalformedBAMErrorReformatingIterator.next(MalformedBAMErrorReformatingIterator.java:59)
at org.broadinstitute.gatk.engine.iterators.MalformedBAMErrorReformatingIterator.next(MalformedBAMErrorReformatingIterator.java:38)
at org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIterator.advance(IntervalOverlapFilteringIterator.java:139)
at org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIterator.next(IntervalOverlapFilteringIterator.java:120)
at org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIterator.next(IntervalOverlapFilteringIterator.java:52)
at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:68)
at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:54)
at htsjdk.samtools.MergingSamRecordIterator.next(MergingSamRecordIterator.java:126)
at htsjdk.samtools.MergingSamRecordIterator.next(MergingSamRecordIterator.java:38)
at org.broadinstitute.gatk.utils.iterators.PrivateStringSAMCloseableIterator.next(GATKSAMIteratorAdapter.java:125)
at org.broadinstitute.gatk.utils.iterators.PrivateStringSAMCloseableIterator.next(GATKSAMIteratorAdapter.java:109)
at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:1181)
at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:1147)
at org.broadinstitute.gatk.engine.iterators.ReadFormattingIterator.next(ReadFormattingIterator.java:107)
at org.broadinstitute.gatk.engine.iterators.ReadFormattingIterator.next(ReadFormattingIterator.java:40)
at org.broadinstitute.gatk.engine.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:131)
at org.broadinstitute.gatk.engine.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:102)
at org.broadinstitute.gatk.engine.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:41)
at org.broadinstitute.gatk.utils.iterators.PrivateStringSAMCloseableIterator.next(GATKSAMIteratorAdapter.java:125)
at org.broadinstitute.gatk.utils.iterators.PrivateStringSAMCloseableIterator.next(GATKSAMIteratorAdapter.java:109)
at org.broadinstitute.gatk.engine.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:60)
at org.broadinstitute.gatk.engine.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:39)
at org.broadinstitute.gatk.utils.sam.GATKSAMRecordIterator.next(GATKSAMRecordIterator.java:54)
at org.broadinstitute.gatk.utils.sam.GATKSAMRecordIterator.next(GATKSAMRecordIterator.java:41)
at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:68)
at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:54)
at org.broadinstitute.gatk.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:180)
at org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:295)
at org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:236)
at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:67)
at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:54)
at org.broadinstitute.gatk.engine.executive.WindowMaker$WindowMakerIterator.advance(WindowMaker.java:201)
at org.broadinstitute.gatk.engine.executive.WindowMaker$WindowMakerIterator.hasNext(WindowMaker.java:170)
at org.broadinstitute.gatk.engine.datasources.providers.LocusView.advance(LocusView.java:179)
at org.broadinstitute.gatk.engine.datasources.providers.LocusView.hasNextLocus(LocusView.java:147)
at org.broadinstitute.gatk.engine.datasources.providers.AllLocusView.advance(AllLocusView.java:127)
at org.broadinstitute.gatk.engine.datasources.providers.AllLocusView.hasNext(AllLocusView.java:85)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$ActiveRegionIterator.hasNext(TraverseActiveRegions.java:338)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:268)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:274)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
Caused by: java.lang.ClassNotFoundException: org.broadinstitute.gatk.utils.help.HelpConstants
at java.net.URLClassLoader$1.run(URLClassLoader.java:370)
at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 49 more
Caused by: java.util.zip.ZipException: error reading zip file
at java.util.zip.ZipFile.read(Native Method)
at java.util.zip.ZipFile.access$1400(ZipFile.java:60)
at java.util.zip.ZipFile$ZipFileInputStream.read(ZipFile.java:717)
at java.util.zip.ZipFile$ZipFileInflaterInputStream.fill(ZipFile.java:419)
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
at java.util.jar.Manifest$FastInputStream.fill(Manifest.java:441)
at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:375)
at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:409)
at java.util.jar.Attributes.read(Attributes.java:376)
at java.util.jar.Manifest.read(Manifest.java:199)
at java.util.jar.Manifest.(Manifest.java:69)
at java.util.jar.JarFile.getManifestFromReference(JarFile.java:199)
at java.util.jar.JarFile.getManifest(JarFile.java:180)
at sun.misc.URLClassPath$JarLoader$2.getManifest(URLClassPath.java:944)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:450)
at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
... 55 more
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
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 https://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: org/broadinstitute/gatk/utils/help/HelpConstants
ERROR ------------------------------------------------------------------------------------------
I verified that there were no errors in the BAM files using Picard’s ValidateSamFile, and that my BAM index was not corrupted by regenerating the index using samtools index. Also, I’ve submitted the same command previously and received the runtime error at different positions in the genome, so it is not consistent.
Any assistance would be greatly appreciated.