qualimap reported java.awt.AWTError: Can't connect to X11 window server

Question

[Yingzi Zhang]

Hi biostars!

I was using qualimap to evaluate bam files. The code I used was qualimap --java-mem-size=700G multi-bamqc -r -d <mapfile1> -gff <genomic.gff> -outdir <multi_bamqc> -outformat PDF:HTML The error reported like this: Exception in thread "main" java.awt.AWTError: Can't connect to X11 window server using 'localhost:10.0' as the value of the DISPLAY variable.

I guessed it was because that our server was not with X11 installed. So I removed the HTML choice. The code changed into qualimap --java-mem-size=700G multi-bamqc -r -d <mapfile1> -gff <genomic.gff> -outdir <multi_bamqc> -outformat PDF However, it still reported the same error. what should be the reason please? If it was because of the absence of X11, is it necessary for me to install X11? (I try to avoid this situation for some reason...) Thank you.

Yingzi

[GenoMax]

Set -Djava.awt.headless=true (or System.setProperty("java.awt.headless", "true");

[Yingzi Zhang]

thank you. I learned that your code is to guide the server in a headless mode. I tried them and it reported either "command not found" or “syntax error near unexpected token `"java.awt.headless"'. I am still trying.

Answer 1

[GenoMax]

You can find detailed instructions to address this here.

Edit: Link updated based on response from opplatek below.

[Yingzi Zhang]

Problem solved with the guide of instructions. Thank you biostars. Thank you all.

[opplatek]

The link is no longer active. Here is an updated link for the same thing.