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?
From what I'm reading the first output is jsut a warning, and not actually an error. Your virtual machine is running at least java 8.0, which has dropped support for an option being passed by to set a max memory size to 1GB.
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. I don't use miniconda, unfortunately, so I have no idea how you would go about updating that.
Hei Seth,
thank you for your answer!
Now, I have to find out how to update miniconda. Unfortunately, I have no idea.
Hi Sarah,
If I'm right, you are running a binary version of Qualimap, which is 2 years old. This binary has been compiled and linked to the versions of the libraries that were available at that time.
Several workarounds can be tested:
1) Upgrade miniconda to the latest version : "conda update conda"
2) If this does'nt work, create a soft link (ln -s) /home/xxx/Softwares/miniconda3/jre/lib/amd64/../../../lib/libX11.so.6 to the latest libX11.so.xxx found on your system
3) Compile qualimap by yourself from sources : https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1_src.zip
Hope this helps
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