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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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Exception in thread "main" java.lang.NoSuchMethodError: java.nio.ByteBuffer.position(I)Ljava/nio/ByteBuffer; #162

Closed karthickbrlab closed 1 year ago

karthickbrlab commented 1 year ago

Hi im running pilon in a draft assembly from pacbio long reads. i'm gettin this error.

pilon --genome out3_JBAT.FINAL.fa --frags bwa.sorted.bam --output polished_assembly Pilon version [COMMIT] [DATE] Exception in thread "main" java.lang.NoSuchMethodError: java.nio.ByteBuffer.position(I)Ljava/nio/ByteBuffer; at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:124) 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.readBlock(BlockCompressedInputStream.java:458) at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196) at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331) at htsjdk.samtools.SamStreams.readBytes(SamStreams.java:26) at htsjdk.samtools.SamStreams.isBAMFile(SamStreams.java:61) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:384) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:209) at org.broadinstitute.pilon.BamFile.reader(BamFile.scala:51) at org.broadinstitute.pilon.BamFile.(BamFile.scala:57) at org.broadinstitute.pilon.Pilon$.optionParse(Pilon.scala:165) at org.broadinstitute.pilon.Pilon$.optionParse(Pilon.scala:172) at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:84) at org.broadinstitute.pilon.Pilon.main(Pilon.scala)