Running qualimap fails:

[SK-N-BE]

I tried to run qualimap: http://qualimap.bioinfo.cipf.es/.
When using the command ./qualimap, I am always getting the following error message:

./qualimap Java memory size is set to 1200M Launching application... OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1024m; support was removed in 8.0 QualiMap v.2.2.1 Built on 2016-10-03 18:14 java: symbol lookup error: /home/xxx/Softwares/miniconda3/jre/lib/amd64/../../../lib/libX11.so.6: undefined symbol: xcb_wait_for_reply64

What is the problem? Why doesn`t it work as it should? Is it a "java" problem or the file lixX11.so.6?

I got the following answer via researchgate:

"The symbol lookup error is a miniconda3 issue. The Java runtime environment (jre) therein has X11 libraries for managing windows to give a GUI when running a program from command line. Those libraries are looking for a specific set of libraries called XCB and not finding it. This tells me your miniconda3 environment is using Xlib instead of XCB, which makes sense (Xlib is a far more common and robust library than XCB, IMO).
To fix this you should just need to get the XCB libraries added/updated to your miniconda's jre build."

How may I do this?

[GenoMax]

I am not sure what the size of BAM file you are trying to use is but you could try adding the option "--java-mem-size=16G" to your qualimap command (Adjust RAM amount as needed). and see if that helps.