Error in Cadabra

[GKerdivel]

Hi
I realigned my reads using abra and wants to do somatic calling using Cadabra but keep having a problem and I do not understand why.

Here is my command:
java -Xmx24G -cp /home/gwenneg/bin/abra-0.95-SNAPSHOT-jar-with-dependencies.jar abra.cadabra.Cadabra $REF $INNORM $INTUM > $OUTPUT

And my error:
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 2
at abra.cadabra.Cadabra.main(Cadabra.java:508)
Command exited with non-zero status 1

I used the bam files output from abra and the same hg19.fa file that was used with abra. I also tried with bam and sorted bam but with the same result.

Thanks for helping

Regards

Gwenneg Kerdivel

[mozack]

Sorted abra bams are the required input.

Please confirm that all of your script variables have values:
$REF $INNORM $INTUM $OUTPUT

[GKerdivel]

Yes all the variables have values

[mozack]

So, the error you posted can only occur if an input parameter is missing. I'd suggest printing out your variables in your script prior to the call. I'll add better input checking in the next release.

[GKerdivel]

Thank you for you answer. I 'll see what I can do.