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Problem :

I am getting bellow error while running my program and unable to figure out what the solution would be
a fatal error has been detected by the java runtime environment:

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1 Answer

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Solution :

Please try setting it as:

export BCBIO_JAVA_HOME=/usr

It is meant to be the equivalent to JAVA_HOME, not a reference to the java executable. So bcbio does not use it in your case. If it is working correctly you should see the java referenced in the command as your locally installed version rather than the bcbio installed one. 

The command should also not have:

unset JAVA_HOME && export PATH=/mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/anaconda/bin:$PATH

which is bcbio referencing it is installed java rather than the system one. 

Hope this works for you.

by (20.3k points)  
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