Hi,
I ran out of disk space while running our mapping pipeline. When running picard's ValidateSamFile tool on one of the bam files, it produced the Exception below. I'm not sure this is a bug per se, but I did expect ValidateSamFile to handle this more gracefully.
-G
[Thu Oct 20 08:53:01 CST 2016] picard.sam.ValidateSamFile INPUT=Bos_javanicus_lowi_HiSeq2000_DRR016397/collapsed.bam IGNORE=[MATE_NOT_FOUND, INVALID_QUALITY_FORMAT] MAX_OPEN_TEMP_FILES=7782 MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Thu Oct 20 08:53:01 CST 2016] Executing as me@host on Linux 2.6.32-504.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_20-b26; Picard version: 2.6.0-SNAPSHOT
[Thu Oct 20 08:53:10 CST 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=2075918336
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: BGZF file has invalid uncompressedLength: -477174215
at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:407)
at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:392)
at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127)
at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:260)
at java.io.DataInputStream.read(DataInputStream.java:149)
at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:404)
at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380)
at htsjdk.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:490)
at htsjdk.samtools.util.BinaryCodec.readInt(BinaryCodec.java:501)
at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:177)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:682)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:656)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:650)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:620)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:545)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:519)
at htsjdk.samtools.SamFileValidator.validateSamRecordsAndQualityFormat(SamFileValidator.java:269)
at htsjdk.samtools.SamFileValidator.validateSamFile(SamFileValidator.java:200)
at htsjdk.samtools.SamFileValidator.validateSamFileVerbose(SamFileValidator.java:160)
at picard.sam.ValidateSamFile.doWork(ValidateSamFile.java:199)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Caused by: java.lang.NegativeArraySizeException
at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:405)
... 22 more