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An error I met.

cymcym ChinaMember
edited December 2015 in Ask the GATK team

I use the picard to create the reference.The command line is right. But error. The information shows that it is connected with Java.
I tried some way to solve it, but failed. I want to know why and how to solve ir.

Post edited by cym on

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Answers

  • cymcym ChinaMember

    @Sheila said:
    @cym
    Hi,

    Can you tell me what version of Picard you are using and the exact command you ran? Also, please post the full error message you get.

    Thanks,
    Sheila

    Thanks for your reply. I installed version of Picard is "picard-tools-2.0.1". And the command I used was :

    java -jar /my_path_to/picard-tools-2.0.1/picard.jar CreateSequenceDictionary REFERENCE=/home/my/data/reference/P.heterocycla-v1.0.Scaffolds.fa OUTPUT=/home/my/data/reference/P.heterocycla-v1.0.Scaffolds.dic

    And the error file is:

    A fatal error has been detected by the Java Runtime Environment:

    #

    SIGFPE (0x8) at pc=0x00002b7d0bee168f, pid=29310, tid=1074792768

    #

    JRE version: Java(TM) SE Runtime Environment (8.0_25-b17) (build 1.8.0_25-b17)

    Java VM: Java HotSpot(TM) 64-Bit Server VM (25.25-b02 mixed mode linux-amd64 compressed oops)

    Problematic frame:

    C [ld-linux-x86-64.so.2+0x868f] do_lookup_x+0xcf

    #

    Core dump written. Default location: /home/SCE/chenyunmei/data/reference/core or core.29310

    #

    If you would like to submit a bug report, please visit:

    http://bugreport.sun.com/bugreport/crash.jsp

    The crash happened outside the Java Virtual Machine in native code.

    See problematic frame for where to report the bug.

  • cymcym ChinaMember

    @Sheila said:
    @cym
    Hi,

    Can you tell me what version of Picard you are using and the exact command you ran? Also, please post the full error message you get.

    Thanks,
    Sheila

    This problem has been solved! The cause is the memory of server. I have completed it successully.
    Thank you very much.

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