Error due to Sam to Bam and Indexing using picard
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5 weeks ago

Hii all, I ran the following command:

picard SortSam -I 10100123749_NIKEC.bam -O 10100123749.bam --SORT_ORDER coordinate --MAX_RECORDS_IN_RAM 1500000 --VALIDATION_STRINGENCY LENIENT

But I am getting this error:

18:09:18.048 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/mdrcubuntu/anaconda3/envs/smruti/share/picard-2.26.3-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Oct 18 18:09:18 IST 2021] SortSam --INPUT 10100135488_Sunita.bam --OUTPUT 10100135488.bam --SORT_ORDER coordinate --VALIDATION_STRINGENCY LENIENT --MAX_RECORDS_IN_RAM 1500000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Oct 18 18:09:18 IST 2021] Executing as mdrcubuntu@mdrcubuntu-H110M-H on Linux 5.13.0-19-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_302-b08; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.26.3
INFO    2021-10-18 18:09:18 SortSam Seen many non-increasing record positions. Printing Read-names as well.
[Mon Oct 18 18:10:20 IST 2021] picard.sam.SortSam done. Elapsed time: 1.03 minutes.
Runtime.totalMemory()=1261436928
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
    at htsjdk.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:282)
    at htsjdk.samtools.BAMRecord.decodeAttributes(BAMRecord.java:412)
    at htsjdk.samtools.BAMRecord.getAttribute(BAMRecord.java:391)
    at htsjdk.samtools.SAMRecord.getAttribute(SAMRecord.java:1182)
    at htsjdk.samtools.SAMRecord.isValid(SAMRecord.java:2164)
    at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:848)
    at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:834)
    at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:802)
    at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:591)
    at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:570)
    at picard.sam.SortSam.doWork(SortSam.java:162)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

I tried it several times but failed. Did anyone have idea what to do to rectify this error?

WES • 292 views
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Looks like you are running out of memory. You can try specifying java temp io directory as shown here: Setting temporary directory for GATK4 SortSam .

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Still I am not getting the result. Runtime.totalMemory()=3722969088 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp htsjdk.samtools.SAMFormatException: Did not inflate expected amount at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:147) 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 java.io.DataInputStream.read(DataInputStream.java:149) at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:421) at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:394) at htsjdk.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:507) at htsjdk.samtools.util.BinaryCodec.readInt(BinaryCodec.java:518) at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:261) at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:866) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:840) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:834) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:802) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:591) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:570) at picard.sam.SortSam.doWork(SortSam.java:160) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308) at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37) 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)

Please tell me how to clear memory

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Assuming you used a temp IO directory we seem to have returned to the old problem you were having before SAMFormatException: Did not inflate expected amount error

htsjdk.samtools.SAMFormatException: Did not inflate expected amount

Your input BAM file must be corrupt.

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I have again created the bam file but it is giving the same error. To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded at htsjdk.samtools.SAMUtils.getAlignmentBlocks(SAMUtils.java:717) at htsjdk.samtools.SAMRecord.getAlignmentBlocks(SAMRecord.java:1919) at htsjdk.samtools.SAMRecord.validateCigar(SAMRecord.java:1937) at htsjdk.samtools.BAMRecord.getCigar(BAMRecord.java:284) at htsjdk.samtools.SAMRecord.isValid(SAMRecord.java:2233) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:848) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:834) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:802) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:591) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:570) at picard.sam.SortSam.doWork(SortSam.java:162) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

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