Question: qualimap reported java.awt.AWTError: Can't connect to X11 window server
0
gravatar for Yingzi Zhang
13 months ago by
Yingzi Zhang60
Beijing
Yingzi Zhang60 wrote:

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

software error • 993 views
ADD COMMENTlink modified 13 months ago by genomax70k • written 13 months ago by Yingzi Zhang60
1

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

ADD REPLYlink written 13 months ago by genomax70k

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.

ADD REPLYlink written 13 months ago by Yingzi Zhang60
3
gravatar for genomax
13 months ago by
genomax70k
United States
genomax70k wrote:

You can find detailed instructions to address this here.

ADD COMMENTlink written 13 months ago by genomax70k

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

ADD REPLYlink written 13 months ago by Yingzi Zhang60
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