I am new to ROOT and am trying to use it within another genomics based application called cnvnator that calls ROOT.
The basic command to run cnvnator is:
./cnvnator -root NA12878.root -chrom chr8 -tree NA12878.bam
-root specifies the name of the output file.
I have never run this application (i.e. cnvnator) before and am also new to ROOT.
I installed ROOT and it seems successfully installed as calling root from the shell gives the expected output.
When I run this command {./cnvnator -root NA12878.root -chrom chr8 -tree NA12878.bam} the only output is:
Segmentation fault 11.
I’ve had this error after running other genomics based apps and I recall the issue was with the size of the stack that had to be increased due to the memory demands. However, I also wonder if this error could be related to running ROOT on my macbook that is running OS X El Capitan 11.5. Are there any known issues with running ROOT on OS X El Capitan 11.5?
Yes, you can debug it (explained, for example, here en.wikipedia.org/wiki/Debugging).
Or you can ask authors of this very well-known ‘cnvnator’ for help.
“Yes, sure, it’s a well-known issue - El Capitan 11.5 does not exist”.
Is is because I left out the first two digits in the version OS X El Capitan 10.11.5?
or possibly because ROOT is not specifically compatible with OS X El Capitan 10.11.5?
To be clear, as far as we know ROOT itself works fine on MacOS 10.11.5. I suspect the ‘error’ comes from the code added by ‘cnvnator’ and short of more information (stack trace or small self contained reproducers), we have no clue what might specifically go wrong.
As Timur suggested, contacting the author of ‘cnvnator’ is probably your best approach (alternative you would have to build this tool in debug mode and try to debug the problem).
Ok, next time I’ll add hints, tool-tips and annotations everywhere so that jokes are more obvious.