Error due to Sam to Bam and Indexing using picard

Error due to Sam to Bam and Indexing using picard

0

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

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