GATK RUNTIME ERROR with BaseRecalibrator

vnkoparde

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??

Geraldine_VdAuwera

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