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Picard SortVcf fail for no reason ?

alaabadrealaabadre FranceMember


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

  • Program console output and metrics files. Repetitive console output may be abbreviated
    This is the error:
    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.
    To get help, see
    Exception in thread "main" java.lang.NullPointerException
    at java.util.TimSort.countRunAndMakeAscending(
    at java.util.TimSort.sort(
    at java.util.Arrays.sort(
    at htsjdk.samtools.util.SortingCollection.spillToDisk(
    at htsjdk.samtools.util.SortingCollection.add(
    at picard.vcf.SortVcf.sortInputs(
    at picard.vcf.SortVcf.doWork(
    at picard.cmdline.CommandLineProgram.instanceMain(
    at picard.cmdline.PicardCommandLine.instanceMain(
    at picard.cmdline.PicardCommandLine.main(

  • 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: 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 !

Best Answer


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