Tagged with #reference-error
0 documentation articles | 0 announcements | 2 forum discussions


No posts found with the requested search criteria.
No posts found with the requested search criteria.
Comments (2)

Hi, I just have download the GATK, uncompress the file, and try to run the help. So, I type: java -jar GenomeAnalysisTK.jar -h, and it gives the following exception: Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/gatk/engine/CommandLineGATK : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:643) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:277) at java.net.URLClassLoader.access$000(URLClassLoader.java:73) at java.net.URLClassLoader$1.run(URLClassLoader.java:212) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:323) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:268) Could not find the main class: org.broadinstitute.gatk.engine.CommandLineGATK. Program will exit.

Comments (6)

Hi. I'm unable to use the IndelRealigner java jar. My previous steps were;

1) Convert Bowtie2 paired-end Illumina Reads .sam to .bam

2) Use bedtools to extract pairs that fall within the Hg19 exome.

3) Convert the new .bam to .sam

4) Sort the new .sam via SortSam.jar

5) Mark duplicates via MarkDuplicates.jar

6) Use AddOrReplaceReadGroups.jar

7 ) Use ReorderSam.jar

8) Use RealignerTargetCreator

Untill this far everything went well. Now I'm trying the following command; java -jar GenomeAnalysisTK.jar -T IndelRealigner -R [.fasta] -l [ReorderedSam.bam] -targetIntervals [aligner.intervals] -o output.bam (Also when applying -known and an .vcf file Im producing the same error):

ERROR MESSAGE: Unable to match: GATK_7-PicardReorderSam.bam to a logging level, make sure it's a valid level (DEBUG, INFO, WARN, ERROR, FATAL, OFF)

I hope you can help me, because I can't find anything related on google.