Problem in running Java JAR of contEst and Indelocator

Question

[Chetan Joshi]

http://www.broadinstitute.org/cancer/cga/contest

and

http://www.broadinstitute.org/cancer/cga/indelocator

Java and Javac version

$ java -version java version "1.8.0_05" Java(TM) SE Runtime Environment (build 1.8.0_05-b13) Java HotSpot(TM) 64-Bit Server VM (build 25.5-b02, mixed mode)

$ javac -version javac 1.8.0_05

My Input command:

$ java -Xmx9g -jar   /media/storage1/softwares/contEst/contest-1.0.24530-bin/ContEst.jar \
    -I chr20_sites.bam \
    -R human_g1k_v37.fasta \
    -B:pop,vcf hg19_population_stratified_af_hapmap_3.3.vcf \
    -T Contamination \
    -B:genotypes,vcf hg00142.vcf \
    -BTI genotypes \
    -o contamination_results_chr20.3-6-14.cj.txt

---

Exception in thread "main" java.lang.ExceptionInInitializerError
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.<init>(GenomeAnalysisEngine.java:150)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.<init>(CommandLineExecutable.java:60)
    at org.broadinstitute.sting.gatk.CommandLineGATK.<init>(CommandLineGATK.java:50)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:86)
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException:
java.lang.RuntimeException: could not create class file from NativeString.class
    at org.reflections.Reflections.scan(Reflections.java:166)
    at org.reflections.Reflections.<init>(Reflections.java:91)
    at org.broadinstitute.sting.utils.classloader.PluginManager.<clinit>(PluginManager.java:60)
    ... 4 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: could not create class file from NativeString.class
    at java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.util.concurrent.FutureTask.get(FutureTask.java:192)
    at org.reflections.Reflections.scan(Reflections.java:162)
    ... 6 more
Caused by: java.lang.RuntimeException: could not create class file from NativeString.class
    at org.reflections.scanners.AbstractScanner.scan(AbstractScanner.java:41)
    at org.reflections.Reflections$2.run(Reflections.java:149)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: invalid constant type: 15
    at javassist.bytecode.ConstPool.readOne(ConstPool.java:1023)
    at javassist.bytecode.ConstPool.read(ConstPool.java:966)
    at javassist.bytecode.ConstPool.<init>(ConstPool.java:127)
    at javassist.bytecode.ClassFile.read(ClassFile.java:693)
    at javassist.bytecode.ClassFile.<init>(ClassFile.java:85)
    at org.reflections.adapters.JavassistAdapter.createClassObject(JavassistAdapter.java:86)
    at org.reflections.adapters.JavassistAdapter.createClassObject(JavassistAdapter.java:22)
    at org.reflections.scanners.AbstractScanner.scan(AbstractScanner.java:38)
    ... 6 more

Answer 1

[Chetan Joshi]

I have removed all oracle jdk and installed openjdk with jre and its started working.

mainly I have removed jdk's configuration, then openjdk was working fine. Hence both java tools are working.

[MAPK]

Hi Chetan, Could you explain a bit more on this please. I am really stuck on the same issue.

> INFO  18:37:11,177 HelpFormatter -
> -----------------------------------------------------------------------------------  INFO  18:37:11,179 HelpFormatter - The Genome Analysis Toolkit (GATK)
> v1.0-6228-gdf95121, Compiled 2011/07/14 11:09:43  INFO  18:37:11,179
> HelpFormatter - Copyright (c) 2010 The Broad Institute  INFO 
> 18:37:11,179 HelpFormatter - Please view our documentation at
> http://www.broadinstitute.org/gsa/wiki  INFO  18:37:11,179
> HelpFormatter - For support, please view our support site at
> http://getsatisfaction.com/gsa  INFO  18:37:11,179 HelpFormatter -
> Program Args: -T Contamination -I
> ../contest/ContEst_example_data/chr20_sites.bam -R ../contest/hg19.fa
> -B:pop,vcf ../contest/hg19_population_stratified_af_hapmap_3.3.vcf -B:genotypes, ../contest/ContEst_example_data/hg00142.vcf -BTI genotypes -o Sample1.out.txt   INFO  18:37:11,179 HelpFormatter -
> Date/Time: 2016/04/28 18:37:11  INFO  18:37:11,180 HelpFormatter -
> -----------------------------------------------------------------------------------  INFO  18:37:11,180 HelpFormatter -
> -----------------------------------------------------------------------------------  INFO  18:37:11,186 GenomeAnalysisEngine - Strictness is SILENT  INFO 
> 18:37:11,319 RMDTrackBuilder - Creating Tribble index in memory for
> file ../contest/hg19_population_stratified_af_hapmap_3.3.vcf  WARN 
> 18:37:42,058 RestStorageService - Error Response: PUT
> '/GATK_Run_Reports/WQ0yQ7iYPGr6ZYYoWr2NxwpLmkEBWbuI.report.xml.gz' --
> ResponseCode: 403, ResponseStatus: Forbidden, Request Headers:
> [Content-Length: 1851, Content-MD5: vU5aKZtRa8ssFYGy2XD89Q==,
> Content-Type: application/octet-stream, x-amz-meta-md5-hash:
> bd4e5a299b516bcb2c1581b2d970fcf5, Date: Thu, 28 Apr 2016 08:37:40 GMT,
> Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:xT8NnPhf2W9O2TM1dNWi+ajZ8yY=,
> User-Agent: JetS3t/0.8.0 (Linux/3.13.0-71-generic; amd64; en; JVM
> 1.7.0_91), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 9C1EA2ED6B034436, x-amz-id-2:
> lMuQF1CtY4zHeR0Qgt59vfl7fS6Ro0hY07dlBuWGEH1qLfbAzuQcANDrNMtZd4GIF9Uk7IE1xFY=,
> Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu,
> 28 Apr 2016 08:37:41 GMT, Connection: close, Server: AmazonS3] 
> ##### ERROR ------------------------------------------------------------------------------------------
> ##### ERROR A USER ERROR has occurred (version 1.0-6228-gdf95121): 
> ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
> ##### ERROR Please do not post this error to the GATK forum
> ##### ERROR
> ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
> ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
> ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
> ##### ERROR
> ##### ERROR MESSAGE: Input files /mypath/contest/../contest/hg19_population_stratified_af_hapmap_3.3.vcf and reference have incompatible contigs: No overlapping contigs found.
> ##### ERROR   /mypath/contest/../contest/hg19_population_stratified_af_hapmap_3.3.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
> 18, 19, 20, 21, 22, X]
> ##### ERROR   reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chrX, chr8, chr9, chr10, chr11, chr12]

Answer 2

[Pierre Lindenbaum]

Hum... java 1.8 is a really new java virtual machine.

I would try to use the previous java (1.7 / 7)