GATK RUNTIME ERROR with BaseRecalibrator

vnkopardevnkoparde Posts: 3Member

INFO 17:40:38,765 ProgressMeter - chrX:147886444 3.21e+07 5.5 h 10.3 m 97.9% 5.6 h 7.1 m
INFO 17:41:08,775 ProgressMeter - chrX:151653849 3.21e+07 5.5 h 10.3 m 98.0% 5.6 h 6.7 m
INFO 17:41:38,785 ProgressMeter - chrX:153812787 3.22e+07 5.5 h 10.3 m 98.1% 5.6 h 6.5 m

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

java.lang.NoClassDefFoundError: net/sf/samtools/util/CloserUtil
at net.sf.picard.util.PeekableIterator.close(PeekableIterator.java:46)
at net.sf.picard.sam.MergingSamRecordIterator.addIfNotEmpty(MergingSamRecordIterator.java:169)
at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:125)
at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:39)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:1091)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:1057)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:105)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:81)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:41)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:24)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:12)
at org.broadinstitute.sting.utils.baq.ReadTransformingIterator.next(ReadTransformingIterator.java:36)
at org.broadinstitute.sting.utils.baq.ReadTransformingIterator.next(ReadTransformingIterator.java:15)
at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:71)
at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57)
at org.broadinstitute.sting.gatk.datasources.reads.ReadShard.fill(ReadShard.java:135)
at org.broadinstitute.sting.gatk.datasources.reads.ReadShardBalancer$1.advance(ReadShardBalancer.java:153)
at org.broadinstitute.sting.gatk.datasources.reads.ReadShardBalancer$1.next(ReadShardBalancer.java:116)
at org.broadinstitute.sting.gatk.datasources.reads.ReadShardBalancer$1.next(ReadShardBalancer.java:75)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:65)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
Caused by: java.lang.ClassNotFoundException: net.sf.samtools.util.CloserUtil
at java.net.URLClassLoader$1.run(URLClassLoader.java:199)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
... 29 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$1200(ZipFile.java:29)
at java.util.zip.ZipFile$ZipFileInputStream.read(ZipFile.java:447)
at java.util.zip.ZipFile$1.fill(ZipFile.java:230)
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:141)
at java.util.jar.Manifest$FastInputStream.fill(Manifest.java:422)
at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:358)
at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:390)
at java.util.jar.Attributes.read(Attributes.java:359)
at java.util.jar.Manifest.read(Manifest.java:182)
at java.util.jar.Manifest.(Manifest.java:52)
at java.util.jar.JarFile.getManifestFromReference(JarFile.java:167)
at java.util.jar.JarFile.getManifest(JarFile.java:148)
at sun.misc.URLClassPath$JarLoader$2.getManifest(URLClassPath.java:696)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:228)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
... 34 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-ge5ebf34):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, 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: net/sf/samtools/util/CloserUtil
ERROR ------------------------------------------------------------------------------------------

Any Idea what is the solution??

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,019Administrator, GATK Dev admin

    It looks like a problem with a bad BAM file. Please validate your input BAMs using ValidateSAMFile.

    Geraldine Van der Auwera, PhD

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