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mozack / abra

Assembly Based ReAligner
MIT License
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Error in Cadabra #28

Open GKerdivel opened 8 years ago

GKerdivel commented 8 years ago

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 commented 8 years ago

Sorted abra bams are the required input.

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

GKerdivel commented 8 years ago

Yes all the variables have values

mozack commented 8 years ago

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 commented 8 years ago

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