Error due to Sam to Bam and Indexing using picard

Error due to Sam to Bam and Indexing using picard


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 from jar:file:/home/mdrcubuntu/anaconda3/envs/smruti/share/picard-2.26.3-0/picard.jar!/com/intel/gkl/native/
[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.
To get help, see
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
    at htsjdk.samtools.BinaryTagCodec.readTags(
    at htsjdk.samtools.BAMRecord.decodeAttributes(
    at htsjdk.samtools.BAMRecord.getAttribute(
    at htsjdk.samtools.SAMRecord.getAttribute(
    at htsjdk.samtools.SAMRecord.isValid(
    at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(
    at htsjdk.samtools.BAMFileReader$
    at htsjdk.samtools.BAMFileReader$
    at htsjdk.samtools.SamReader$
    at htsjdk.samtools.SamReader$
    at picard.sam.SortSam.doWork(
    at picard.cmdline.CommandLineProgram.instanceMain(
    at picard.cmdline.PicardCommandLine.instanceMain(
    at picard.cmdline.PicardCommandLine.main(

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



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