stack error when run muTect the first time

leiwangleiwang stanford universityMember

Hi, I ran into the following errors when I ran muTect the first time after I installed it on my Mac. I also downloaded GATK 3.4, it can run successfully. Can you help me to resolve this? Thanks.

Leis-MacBook-Pro:muTect leiwang$ java -jar muTect-1.1.4.jar

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.ExceptionInInitializerError
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.(GenomeAnalysisEngine.java:160)
at org.broadinstitute.sting.gatk.CommandLineExecutable.(CommandLineExecutable.java:53)
at org.broadinstitute.sting.gatk.CommandLineGATK.(CommandLineGATK.java:56)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)
Caused by: java.lang.NullPointerException
at org.reflections.Reflections.scan(Reflections.java:220)
at org.reflections.Reflections.scan(Reflections.java:166)
at org.reflections.Reflections.(Reflections.java:94)
at org.broadinstitute.sting.utils.classloader.PluginManager.(PluginManager.java:77)
... 4 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.2-25-g2a68eab):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

Leis-MacBook-Pro:muTect leiwang$ java -version
java version "1.8.0_31"
Java(TM) SE Runtime Environment (build 1.8.0_31-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.31-b07, mixed mode)
Leis-MacBook-Pro:muTect leiwang$ pwd
/Users/leiwang/software/muTect
Leis-MacBook-Pro:muTect leiwang$ ls -al
total 39328
drwxr-xr-x 6 leiwang staff 204 Aug 25 21:00 .
drwxr-xr-x 5 leiwang staff 170 Aug 25 21:35 ..
[email protected] 1 leiwang staff 83 Nov 8 2012 LICENSE.TXT
[email protected] 1 leiwang staff 9684017 Aug 25 20:36 muTect-1.1.4-bin.zip
[email protected] 1 leiwang staff 10438338 Nov 8 2012 muTect-1.1.4.jar
[email protected] 1 leiwang staff 54 Nov 8 2012 version.txt
Leis-MacBook-Pro:muTect leiwang$ pwd
/Users/leiwang/software/muTect

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Try using the more recent version of MuTect (1.1.7) from our downloads page, and use the supported version of java (1.7).

  • leiwangleiwang stanford universityMember

    when I login to the download page (https://www.broadinstitute.org/cancer/cga/mutect_download), there are only two versions, one is 1.1.4, and the other one is called "used in the Nature publication 1.1.1". There is no 1.1.7.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    It's on the GATK website Downloads page.

  • leiwangleiwang stanford universityMember

    there are three options from GATK website downloads page https://www.broadinstitute.org/gatk/download/ 1. GATK, 2. GATK+Queue (do not know that is), 3. Source code

    can you tell me which one is muTect? Or point me to the URL so I can download muTect 1.1.7? thanks

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    See "Download MuTect 1.1.7" at the bottom of that page.

  • leiwangleiwang stanford universityMember

    Thanks a lot and I was careless that did not see that. Now I have downloaded it and unjar it. Can you tell me how to build it from this step? The following is the ls -ltr command output:

    Leis-MacBook-Pro:muTect1.1.7 leiwang$ ls -ltr
    total 45200
    [email protected] 1 leiwang staff 11645558 Jan 21 2015 mutect-1.1.7.jar
    drwxr-xr-x 13 leiwang staff 442 Jan 21 2015 org
    drwxr-xr-x 4 leiwang staff 136 Jan 21 2015 net
    drwxr-xr-x 9 leiwang staff 306 Jan 21 2015 license
    drwxr-xr-x 4 leiwang staff 136 Jan 21 2015 javax
    drwxr-xr-x 60 leiwang staff 2040 Jan 21 2015 javassist
    drwxr-xr-x 3 leiwang staff 102 Jan 21 2015 it
    drwxr-xr-x 3 leiwang staff 102 Jan 21 2015 images
    drwxr-xr-x 3 leiwang staff 102 Jan 21 2015 hep
    drwxr-xr-x 5 leiwang staff 170 Jan 21 2015 freemarker
    -rw-r--r-- 1 leiwang staff 20 Jan 21 2015 exampleFASTA.fasta.fai
    -rw-r--r-- 1 leiwang staff 101673 Jan 21 2015 exampleFASTA.fasta
    -rw-r--r-- 1 leiwang staff 148 Jan 21 2015 exampleFASTA.dict
    -rw-r--r-- 1 leiwang staff 232 Jan 21 2015 exampleBAM.bam.bai
    -rw-r--r-- 1 leiwang staff 3635 Jan 21 2015 exampleBAM.bam
    drwxr-xr-x 3 leiwang staff 102 Jan 21 2015 corejava
    drwxr-xr-x 5 leiwang staff 170 Jan 21 2015 com
    drwxr-xr-x 5 leiwang staff 170 Jan 21 2015 cern
    -rw-r--r-- 1 leiwang staff 10364 Jan 21 2015 PrintReads.java
    -rw-r--r-- 1 leiwang staff 8121 Jan 21 2015 Pileup.java
    -rw-r--r-- 1 leiwang staff 24 Jan 21 2015 MuTectText.properties
    drwxr-xr-x 3 leiwang staff 102 Jan 21 2015 Jama
    -rw-r--r-- 1 leiwang staff 294 Jan 21 2015 GATK_public.key
    -rw-r--r-- 1 leiwang staff 2988 Jan 21 2015 CountReads.java
    -rw-r--r-- 1 leiwang staff 3277 Jan 21 2015 CountLoci.java
    -rw-r--r-- 1 leiwang staff 11844 Jan 21 2015 CheckPileup.java
    -rw-r--r-- 1 leiwang staff 771968 Jan 21 2015 StingText.properties
    [email protected] 1 leiwang staff 10547264 Aug 28 18:21 mutect-1.1.7.jar.zip
    drwxr-xr-x 17 leiwang staff 578 Aug 28 18:29 META-INF
    Leis-MacBook-Pro:muTect1.1.7 leiwang$

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    The jar you downloaded is the executable; no need to build anything.

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