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Old 09-26-2018, 02:38 AM   #1
Location: Germany

Join Date: Apr 2018
Posts: 11
Default Running qualimap fails:

I tried to run qualimap:
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/ 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

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?
SK-N-BE is offline   Reply With Quote
Old 09-26-2018, 03:07 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,795

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.
GenoMax is offline   Reply With Quote

java, miniconda, qualimap

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