Building MuTect 1.1.7?

rontonronton USAMember
edited January 2015 in MuTect v1

I tried to build the latest MuTect according to the readme available at https://github.com/broadinstitute/mutect and I ran into an error. Specifically, there is an error building gatk-protected only if I include the git reset --hard 3.1.

cd gatk-protected

git reset --hard 3.1

(comment) build the GATK first and install it to the local mvn repo.

mvn -Ddisable.queue install

If I do not include the git reset --hard 3.1 then gatk-protected will build fine, but then

(comment) build MuTect

cd ../mutect

mvn verify

does not work and reports errors about needing gatk repository/dependencies.

Has something changed recently that interferes with building MuTect, or am I doing something wrong?

Thank you

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    What is the error you get when you use the git reset command?

  • rontonronton USAMember

    git reset --hard 3.1

    returns:

    HEAD is now at 72492bb Merge remote-tracking branch 'unstable/master'

    I was able to build gatk-protected without the 'git reset --hard 3.1' but then building MuTect gave errors about not finding its dependencies. When I follow (so this would actually be to build gatk-protected):

    git reset --hard 3.1

    mvn -Ddisable.queue install

    I receive the following error:

    Exception in thread "pool-1-thread-1" --------------------------------------------------- java.lang.NoClassDefFoundError: org/apache/commons/lang/StringUtils at org.apache.maven.wagon.providers.file.FileWagon.resolveDestinationPath(FileWagon.java:206) at org.apache.maven.wagon.providers.file.FileWagon.resourceExists(FileWagon.java:265) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$GetTask.run(WagonRepositoryConnector.java:577) at org.sonatype.aether.util.concurrency.RunnableErrorForwarder$1.run(RunnableErrorForwarder.java:60) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) constituent[0]: file:/usr/share/maven/lib/commons-httpclient.jar Caused by: java.lang.ClassNotFoundException: org.apache.commons.lang.StringUtils at org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50) at org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:259) at org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:235) at org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:227) ... 7 more constituent[1]: file:/usr/share/maven/lib/plexus-cipher.jar constituent[2]: file:/usr/share/maven/lib/maven-model-3.x.jar constituent[3]: file:/usr/share/maven/lib/maven-compat-3.x.jar constituent[4]: file:/usr/share/maven/lib/aether-spi.jar constituent[5]: file:/usr/share/maven/lib/wagon-provider-api.jar constituent[6]: file:/usr/share/maven/lib/wagon-http-shaded.jar constituent[7]: file:/usr/share/maven/lib/maven-repository-metadata-3.x.jar constituent[8]: file:/usr/share/maven/lib/maven-model-builder-3.x.jar constituent[9]: file:/usr/share/maven/lib/maven-settings-builder-3.x.jar constituent[10]: file:/usr/share/maven/lib/sisu-guice.jar constituent[11]: file:/usr/share/maven/lib/maven-core-3.x.jar constituent[12]: file:/usr/share/maven/lib/plexus-sec-dispatcher.jar constituent[13]: file:/usr/share/maven/lib/commons-codec.jar constituent[14]: file:/usr/share/maven/lib/aether-util.jar constituent[15]: file:/usr/share/maven/lib/maven-artifact-3.x.jar constituent[16]: file:/usr/share/maven/lib/guava.jar constituent[17]: file:/usr/share/maven/lib/sisu-inject-bean.jar constituent[18]: file:/usr/share/maven/lib/plexus-utils.jar constituent[19]: file:/usr/share/maven/lib/aether-api.jar constituent[20]: file:/usr/share/maven/lib/maven-embedder-3.x.jar constituent[21]: file:/usr/share/maven/lib/plexus-component-annotations.jar constituent[22]: file:/usr/share/maven/lib/commons-cli.jar constituent[23]: file:/usr/share/maven/lib/maven-plugin-api-3.x.jar constituent[24]: file:/usr/share/maven/lib/maven-aether-provider-3.x.jar constituent[25]: file:/usr/share/maven/lib/aether-connector-wagon.jar constituent[26]: file:/usr/share/maven/lib/sisu-inject-plexus.jar constituent[27]: file:/usr/share/maven/lib/maven-settings-3.x.jar constituent[28]: file:/usr/share/maven/lib/plexus-interpolation.jar constituent[29]: file:/usr/share/maven/lib/commons-logging.jar constituent[30]: file:/usr/share/maven/lib/aether-impl.jar
    constituent[31]: file:/usr/share/maven/lib/wagon-file.jar

    Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/lang/StringUtils at org.apache.maven.wagon.providers.file.FileWagon.resolveDestinationPath(FileWagon.java:206) at org.apache.maven.wagon.providers.file.FileWagon.resourceExists(FileWagon.java:265) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$GetTask.run(WagonRepositoryConnector.java:577) at org.sonatype.aether.util.concurrency.RunnableErrorForwarder$1.run(RunnableErrorForwarder.java:60) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) Caused by: java.lang.ClassNotFoundException: org.apache.commons.lang.StringUtils at org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50) at org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:259) at org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:235) at org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:227) ... 7 more

  • rontonronton USAMember

    Does this make sense? So, I can build gatk-protected without the git reset command no problem, but following the instructions in the MuTect readme and including the git reset command gives me this error when trying to build gatk-protected.

  • rontonronton USAMember
    edited January 2015

    If I try to proceed using the gatk-protected that was built without the git reset command, then building MuTect gives errors and will not build.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    You need to use the git reset command because the current MuTect is not yet compatible with changes that were made to the GATK codebase after version 3.1.

    I'll ask the developers to help figure out that build error. Can you give some info about your configuration, e.g. java and maven versions?

    In the meantime you can also try doing mvn clean before the install command.

  • rontonronton USAMember
    edited January 2015

    java version "1.7.0_65"

    Apache Maven 3.0.5

    ubuntu 14.04 LTS

    I tried mvn clean before the install command but no luck there, same error.

    Using (a previous version of) MuTect has yielded encouraging results, meaning that the reported # of variants per tumor/normal sample is closer to 10 than 10^2 or 10^3.

    I am looking for a straightforward way to compare the MuTect results across 5 or 10 samples. I tried simply searching for the same exact entry/line within the .vcf files, but that did not seem to work too well, considering the heterogeneity of mutations.

    The gene tally method that MutSig uses seems like an ideal approach. Reading through the publications for MuTect and MutSig, it looks like I may need to spend some more time with this. For example, setting up the .maf and covariate tables. If MuTect and/or Indelocator fed straight into MutSig that might be very useful. I am not quite sure how to try that yet.

    Thanks again so much.

  • rontonronton USAMember

    Got it! Thank you.

  • @Geraldine_VdAuwera said:
    OK, I couldn't figure out what's causing your build issues, so I added a compiled MuTect 1.1.7 jar to the GATK downloads page as a workaround. See http://www.broadinstitute.org/gatk/download

    Hi, the link on the download does not work.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Sorry, I broke the download over the weekend. Just put in a fix; should work now.

  • rafirafi NYCMember

    Hi Geraldine,

    I ran into very similar problems when trying to use the github install, and I eventually found my way to this page. I used your compiled MuTect jar on the GATK downloads page and I've put that on my server, but I don't see a readme anywhere. Where is a guide of some sort?

    Cheers!
    R

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @rafi We don't have much documentation for the original MuTect, largely because it was developed by a different group and we're just hosting it as a courtesy. There are some docs here: http://gatkforums.broadinstitute.org/gatk/categories/mutect-documentation

    We're putting all our effort into documenting MuTect2, which is a big revamp of the original MuTect program available in recent GATK versions. For that we have some documentation in our workshop presentations. We'll have more complete docs for the full somatic mutation discovery pipeline when the GATK4 general release happens next quarter.

  • rafirafi NYCMember

    Ok thank you so much for the quick repsonse!

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