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Problem with g++ not being detected when GATK germlineCNVCaller is running

Matthieu_MMatthieu_M Santiago, ChileMember

Hello Team,

I am trying to run GATK germlineCNVCaller on a local cluster and getting this warning:

'WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.'

...and indeed the program is running at such slow speeds that the one time I accidentally let it running for weeks it still was nowhere near completion.

g++ is available on the system though, if I type 'g++ --version', the first line is: 'g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)'

I'm a bit at a loss here as to what is going on.


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