[ERR 0104][ERR XTSE0010] during ant build of mutect

Hi,

I have tried:

ant -v -Dexternal.dir=pwd/../mutect-src -Dexecutable=mutect package

using apache-ant-1.8.4 and apache-ant-1.9.1. I believe the crucial error is:

[xslt] /local/opt-local/mutect/mutect-compile/gatk/public/packages/CreatePackager.xsl:14:31: Error! [ERR 0104][ERR XTSE0010] cannot contain as a child.

cat /etc/SuSE-release

SUSE Linux Enterprise Server 11 (x86_64)
VERSION = 11
PATCHLEVEL = 2

java -version

java version "1.7.0"
Java(TM) SE Runtime Environment (build pxa6470sr4fp2-20130426_01(SR4 FP2))
IBM J9 VM (build 2.6, JRE 1.7.0 Linux amd64-64 Compressed References 20130422_146026 (JIT enabled, AOT enabled)
J9VM - R26_Java726_SR4_FP2_20130422_1320_B146026
JIT - r11.b03_20130131_32403ifx4
GC - R26_Java726_SR4_FP2_20130422_1320_B146026_CMPRSS
J9CL - 20130422_146026)
JCL - 20130425_01 based on Oracle 7u21-b09

I can provide more details as requested. Does anybody have any ideas on how to get the build to complete?

Thanks,
Susan

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Answers

  • kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭

    Hi

    First -- I would try to see if you can successfully compile just the GATK by just running "ant". If that doesn't work, that would be the first task.

    Also -- what tags/version of the MuTect and GATK codebase are you using?

  • smwilsonsmwilson Member

    Hi and thanks,

    I followed the Readme.txt from nbt.2514-S3.zip. (Sort of):

    git clone https://github.com:broadgsa/gatk.git gatk
    git reset --hard ae5b339d274a18419559b140816fe8b0c954fd4b

    Since I posted, I changed the java version to:

    java -version

    java version "1.7.0_21"
    Java(TM) SE Runtime Environment (build 1.7.0_21-b11)
    Java HotSpot(TM) 64-Bit Server VM (build 23.21-b01, mixed mode)

    and got further. Now my error is:
    Property "additional.jars" has not been set
    dropping /local/opt-local/mutect/mutect-compile/gatk/${additional.jars} from path as it doesn't exist
    [available] Found: staging/StingText.properties
    [mkdir] Created dir: /local/opt-local/mutect/mutect-compile/gatk/dist/packages/muTect-2.2-25-gae5b339
    [jar] No Implementation-Title set.No Implementation-Version set.No Implementation-Vendor set.
    [jar] Location: /local/opt-local/mutect/mutect-compile/gatk/dist/packages/mutect.xml:13:
    [ant] Exiting /local/opt-local/mutect/mutect-compile/gatk/dist/packages/mutect.xml.

    BUILD FAILED

    Susan

  • smwilsonsmwilson Member

    Sorry about the bold. I see it's my root prompt.

  • kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭

    That specific version of the GATK requires Java 1.6 -- can you try using that?

  • smwilsonsmwilson Member

    Is there a GATK version I can use with 1.7?

  • smwilsonsmwilson Member

    I'm sorry, but I just tried the build with:

    $ env | grep JAVA
    JAVA_HOME=/opt/local/jdk-6u45-linux-x64/jdk1.6.0_45/

    $ which java
    /opt/local/jdk-6u45-linux-x64/jdk1.6.0_45/bin/java

    but I get the same error about "additional.jars".

  • smwilsonsmwilson Member

    If I simply issue:

    $ ant -v

    the build completes.

    Thanks,
    Susan

  • smwilsonsmwilson Member

    Still looking for an answer to this. Using java1.6.0. ant -v runs to completion, but when I add the external.dir and executable parameters I get:

    package:
    Property "additional.jars" has not been set
    dropping /local/opt-local/mutect/mutect-compile/gatk/${additional.jars} from path as it doesn't exist
    [available] Found: staging/StingText.properties
    [mkdir] Created dir: /local/opt-local/mutect/mutect-compile/gatk/dist/packages/muTect-2.2-25-gae5b339
    [jar] No Implementation-Title set.No Implementation-Version set.No Implementation-Vendor set.
    [jar] Location: /local/opt-local/mutect/mutect-compile/gatk/dist/packages/mutect.xml:14:
    [ant] Exiting /local/opt-local/mutect/mutect-compile/gatk/dist/packages/mutect.xml.

    BUILD FAILED

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