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gatk-4.0.4.0 CombineGVCF

prasundutta87prasundutta87 EdinburghMember

On running CombineGVCF from gatk-4.0.4.0, nothing happens..even the help file does not come..java hangs..has anyone experienced this issue? This is the command I used:

java -jar gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar CombineGVCFs

Java version 1.8.0

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  • prasundutta87prasundutta87 EdinburghMember
    edited May 2018

    I don't know about others..but I am still using the jar file because I am running GATK on a grid engine and I can control java spawning multiple threads even though I assign only 1 core to a GATK job..it hampers other user's jobs sharing the node..

    Post edited by prasundutta87 on
  • SheilaSheila Broad InstituteMember, Broadie admin

    @prasundutta87
    Hi,

    What are your input GVCFs? Has anything happened in the progress meter?

    -Sheila

  • prasundutta87prasundutta87 EdinburghMember

    I just wanted to get the help file..when using -jar file, we do not need -h option, only the program's name is fine..anyway, I solved my problem..there was some issue with my university grid engine and it was not accepting any jobs due to some internal error..Now the -jar file is working fine..the grid engine issue lasted for a few days..thanks for the help..

  • prasundutta87prasundutta87 EdinburghMember

    Thanks a lot Geraldine..I was just following some old examples where -jar has been used extensively..and did not bother to change my scripts (except GATK versions) as it was working just fine..I may update my scripts in future to use the wrapper script..

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