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Picard SortVcf fail for no reason ?

alaabadrealaabadre FranceMember

Hello,

  • Command line(s) you ran:
    java -jar picard.jar SortVcf I=cosmic/cosmic.vcf O=cosmic/cosmic.srt.vcf SD=reference/GRCh38.d1.vd1.dict

  • Program console output and metrics files. Repetitive console output may be abbreviated
    This is the error:
    INFO...
    INFO 2017-05-29 14:06:07 SortVcf read 18,475,000 records. Elapsed time: 00:00:49s. Time for last 25,000: 0s. Last read position: chrX:31,147,476
    INFO 2017-05-29 14:06:07 SortVcf read 18,500,000 records. Elapsed time: 00:00:49s. Time for last 25,000: 0s. Last read position: chrX:34,703,820
    [Mon May 29 14:06:07 CEST 2017] picard.vcf.SortVcf done. Elapsed time: 0.83 minutes.
    Runtime.totalMemory()=2360868864
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    Exception in thread "main" java.lang.NullPointerException
    at htsjdk.variant.variantcontext.VariantContextComparator.compare(VariantContextComparator.java:87)
    at htsjdk.variant.variantcontext.VariantContextComparator.compare(VariantContextComparator.java:22)
    at java.util.TimSort.countRunAndMakeAscending(TimSort.java:360)
    at java.util.TimSort.sort(TimSort.java:234)
    at java.util.Arrays.sort(Arrays.java:1512)
    at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:219)
    at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:166)
    at picard.vcf.SortVcf.sortInputs(SortVcf.java:168)
    at picard.vcf.SortVcf.doWork(SortVcf.java:101)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)

  • Version of JVM you are using (obtained by running 'java -version'):
    openjdk version "1.8.0_121"
    OpenJDK Runtime Environment (build 1.8.0_121-8u121-b13-0ubuntu1.16.04.2-b13)
    OpenJDK 64-Bit Server VM (build 25.121-b13, mixed mode)

I am using the reference from TCGA: https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files but because COSMIC and that reference have different contigs, I had to use picard SortVcf so that I can, hopefully, resolve this problem.

I have no idea why the SortVcf is suddenly stopping without giving any reasonable errors. Can you guys help me figure it out ?

Thanks a bunch !

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