htsjdk.samtools.util.RuntimeIOException: {bqsr_bam_file} has invalid uncompressed Length: -196200583

Hi!

I'm using GATK4.0.7.0 and best practice workflow, where I first applied Base reacalibrator on my RNASeq bam-files. These seems to work fine (files are not truncated). Those bqsr-bam files now used to work with Haplotypecaller but I always get the error htsjdk.samtools.util.RuntimeIOException: {bqsr_bam_file} has invalid uncompressed Length: -196200583

Using GATK jar /gatk-4.0.7.0/gatk-package-4.0.7.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx30G -jar /gatk-4.0.7.0/gatk-package-4.0.7.0-local.jar HaplotypeCaller -R /ref_info/HG19.karyo.fasta -I /raw_vcf_new/sample_bqsr.recal.bam -O /media/big_hd/Cosima/raw_vcf_new/sample_haplocaller0017-17.recal.bam.g.vcf.gz -L /media/big_hd/Cosima/ref_info/Exom_V6.interval_list

16:45:18.831 INFO HaplotypeCaller - Shutting down engine
[March 7, 2019 4:45:18 PM CET] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 13.07 minutes.
Runtime.totalMemory()=2069364736
htsjdk.samtools.util.RuntimeIOException: /media/big_hd/Cosima/raw_vcf_new/sample_bqsr0017-17.recal.bam has invalid uncompressedLength: -196200583
at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:543)
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 java.io.DataInputStream.read(DataInputStream.java:149)
at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:418)
at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:394)
at htsjdk.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:504)
at htsjdk.samtools.util.BinaryCodec.readInt(BinaryCodec.java:515)
at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:263)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:829)
at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:981)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:803)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:797)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:765)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:1034)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:1024)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:988)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:576)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:548)
at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.loadNextRecord(SamReaderQueryingIterator.java:114)
at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.next(SamReaderQueryingIterator.java:151)
at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.next(SamReaderQueryingIterator.java:29)
at org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator.next(SAMRecordToReadIterator.java:27)
at org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator.next(SAMRecordToReadIterator.java:13)
at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42)
at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14)
at org.broadinstitute.hellbender.utils.iterators.ReadFilteringIterator.loadNextRead(ReadFilteringIterator.java:53)
at org.broadinstitute.hellbender.utils.iterators.ReadFilteringIterator.next(ReadFilteringIterator.java:47)
at org.broadinstitute.hellbender.utils.iterators.ReadFilteringIterator.next(ReadFilteringIterator.java:13)
at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42)
at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14)
at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69)
at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55)
at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49)
at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16)
at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42)
at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17)
at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71)
at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57)
at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160)
at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315)
at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252)
at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104)
at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99)
at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69)
at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21)
at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143)
at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135)
at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201)
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)


Do you have an idea what is going wrong?
Thanks a lot!
Cosima