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A suite of tools for discovering and genotyping genome structural variation from sequencing data, including the Genome STRiP algorithm.

Project Members:

• Bob Handsaker (admin)

[syjandy]

Hi Bob,

When I run GenomeSTRiP CNVDiscoveryPipeline walker in SGE cluster system with '... -jobRunner Drmaa -gatkJobRunner Drmaa -jobNative "-q bc.q -P HUMxxxR" -jobNative "-l vf=2G" -run' and java 1.7 version, It reported errors as
Exception in thread "main" java.lang.ClassFormatError: org.broadinstitute.gatk.queue.QCommandLine (unrecognized class file version)
at java.lang.VMClassLoader.defineClass(libgcj.so.7rh)
at java.lang.ClassLoader.defineClass(libgcj.so.7rh)
at java.security.SecureClassLoader.defineClass(libgcj.so.7rh)
at java.net.URLClassLoader.findClass(libgcj.so.7rh)
at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
at gnu.java.lang.MainThread.run(libgcj.so.7rh)

But I set my env as below,
export JAVA_HOME=/usr/latest/jdk1.7.0_60
export PATH=$JAVA_HOME/bin:$PATH
export CLASSPATH=.:$JAVA_HOME/lib:$JAVA_HOME/jre/lib/rt.jar

I am sure that my java works well, can you help me handle this problem?

Thanks,
Andy

[Bob Handsaker]

It would be helpful to see your whole command line. I would guess you are picking up an older version of SVToolkit compiled for java 1.6. You should be able to test java version compatibility using "java -jar path/to/SVToolkit.jar".

[syjandy]

$cat myCNV.sh

export SV_DIR=/usr/bin/svtoolkit
export JAVA_HOME=/usr/latest/jdk1.7.0_60
export PATH=$JAVA_HOME/bin:$PATH
export CLASSPATH=.:$JAVA_HOME/lib:$JAVA_HOME/jre/lib/rt.jar
classpath=${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar

java -Xmx4G -Djava.io.tmpdir=/usr/bin/example/.queue/tmp
-cp ${classpath} org.broadinstitute.gatk.queue.QCommandLine
-S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q
-S ${SV_DIR}/qscript/SVQScript.q
-cp ${classpath}
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar
-R /usr/bin/ref/main.fa
-I /usr/bin//example/cnvdiscovery/discovery.bams.args.list
-genderMapFile /usr/bin//example/gender.map
-md /usr/bin//example/metadata
-configFile ${SV_DIR}/conf/genstrip_parameters.txt
-runDirectory /usr/bin/example/cnvdiscovery
-genomeMaskFile ${SV_DIR}/database/hg19_mask101.fasta
-intervalList chr1:1-4010001 -tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 -minimumRefinedLength 500
-jobRunner Drmaa -gatkJobRunner Drmaa -jobNative "-q bc.q -P HUMyddR" -jobNative "-l vf=2G" -run -jobLogDir /usr/bin//example/cnvdiscovery/logs

I run the shell in the command line as below, and found errors as above.

$ nohup sh myCNV.sh &

[Bob Handsaker]

Can you try these:

java -version
java -jar /usr/bin/svtoolkit/lib/SVToolkit.jar
unzip -v /usr/bin/svtoolkit/lib/gatk/gatk-queue-3.3.jar | grep QCommandLine

[syjandy]

$java -version
java version "1.7.0_60-ea"
Java(TM) SE Runtime Environment (build 1.7.0_60-ea-b10)
Java HotSpot(TM) 64-Bit Server VM (build 24.60-b09, mixed mode)

$java -jar /usr/bin/svtoolkit/lib/SVToolkit.jar
SVToolkit version 2.00 (build 1529)
Build date: 2015/01/25 21:14:07
Web site: http://www.broadinstitute.org/software/genomestrip

$unzip -v /usr/bin/svtoolkit/lib/gatk/gatk-queue-3.3.jar | grep QCommandLine
1335 Defl:N 620 54% 01-25-15 20:45 b0804cf1 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$7.class
19405 Defl:N 8602 56% 01-25-15 20:45 bb0019ea org/broadinstitute/gatk/queue/QCommandLine.class
1463 Defl:N 687 53% 01-25-15 20:45 f6aaf977 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$3.class
1619 Defl:N 677 58% 01-25-15 20:45 7caede7f org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$5$$anonfun$apply$1.class
994 Defl:N 511 49% 01-25-15 20:45 49aa1742 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$3.class
1434 Defl:N 608 58% 01-25-15 20:45 c61baf08 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$4.class
1939 Defl:N 792 59% 01-25-15 20:45 830b61ac org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$5$$anonfun$apply$2.class
1462 Defl:N 685 53% 01-25-15 20:45 71991897 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$1.class
2308 Defl:N 1058 54% 01-25-15 20:45 39ef2dc7 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$9.class
1483 Defl:N 617 58% 01-25-15 20:45 eb7a1826 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$qPluginType$1.class
2031 Defl:N 876 57% 01-25-15 20:45 fa91bc73 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$6.class
1786 Defl:N 748 58% 01-25-15 20:45 f5941ea3 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$6$$anonfun$4.class
1428 Defl:N 609 57% 01-25-15 20:45 5311547d org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$8$$anonfun$6.class
1162 Defl:N 544 53% 01-25-15 20:45 6b4b5fa9 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$qPluginType$2.class
2572 Defl:N 1064 59% 01-25-15 20:45 aa6ddef3 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$8.class
1049 Defl:N 553 47% 01-25-15 20:45 a69d6741 org/broadinstitute/gatk/queue/QCommandLine$$anon$1.class
1512 Defl:N 711 53% 01-25-15 20:45 d34bf7e5 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$1.class
4594 Defl:N 1917 58% 01-25-15 20:45 5af88904 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$5.class
1427 Defl:N 608 57% 01-25-15 20:45 dcde29b3 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$8$$anonfun$5.class
3781 Defl:N 1422 62% 01-25-15 20:45 c71d9759 org/broadinstitute/gatk/queue/QCommandLine$.class
1563 Defl:N 704 55% 01-25-15 20:45 af9ae043 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$execute$2.class
1435 Defl:N 609 58% 01-25-15 20:45 f579f2b0 org/broadinstitute/gatk/queue/QCommandLine$$anonfun$2.class

[Bob Handsaker]

I don't know. Maybe it's the "ea" version of java 7 (which I'm guessing stands for "early access"). I'm using 1.7.0_60-b19 with no problem.

The other thing you can try is to reduce the test case. For example, if I run

$ java -showversion -cp /humgen/cnp04/svtoolkit/stable/svtoolkit/lib/gatk/gatk-queue-3.3.jar org.broadinstitute.gatk.queue.QCommandLine
java version "1.7.0_60"
Java(TM) SE Runtime Environment (build 1.7.0_60-b19)
Java HotSpot(TM) 64-Bit Server VM (build 24.60-b09, mixed mode)

Exception in thread "main" java.lang.NoClassDefFoundError: org/broadinstitute/gatk/utils/commandline/CommandLineProgram
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Caused by: java.lang.ClassNotFoundException: org.broadinstitute.gatk.utils.commandline.CommandLineProgram
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
... 13 more

I get a ClassNotFound, but it does not complain about the class file version (which I suspect it might if I was having your issue).

[syjandy]