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I am running a program FASTQC in the command line(Ubuntu terminal on windows 10 PC) but got the error of the following. I am not sure how to solve this and I would appreciate it if some one already know the solutions.

Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
        at java.desktop/java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:208)
        at java.desktop/java.awt.Window.<init>(Window.java:548)
        at java.desktop/java.awt.Frame.<init>(Frame.java:423)
        at java.desktop/java.awt.Frame.<init>(Frame.java:388)
        at java.desktop/javax.swing.JFrame.<init>(JFrame.java:180)
        at uk.ac.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:63)
        at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:338)

Best, Amare

adR
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1 Answers1

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You don't say, but I suspect that you are running the program without any command line parameters. The help (fastqc -h) says:

If no files to process are specified on the command line then the program will start as an interactive graphical application. If files are provided on the command line then the program will run with no user interaction required. In this mode it is suitable for inclusion into a standardised analysis pipeline.

If you want to run it in non-interactive mode (which is how I always use it), just include the names of your FASTQ files on the command line.

Tom Morris
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  • thank you so much! Yes I have seen that and I was wonder to see how the interactive graphical application look like when typing fastqc on the command line. – adR Nov 26 '21 at 09:22
  • In that case, the generic Ubuntu answer applies https://stackoverflow.com/questions/662421/no-x11-display-variable-what-does-it-mean – Tom Morris Nov 26 '21 at 21:20