Fastqc shows error message
0
0
Entering edit mode
4.1 years ago
Bioinfo ▴ 20

Hello everyone i hope you and your family and friends are doing fine

please i have question

i m remotely connected to the lab server , i want to check the quality of the my reads and i want to use fastqc for that . normaly it works well on the lab computer but what i tried to run on my computer it shows this error message

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)

fastqc works on my terminal ( in my computer ) but it dosen't work in server window on my computer ( i hope you undrestand me ) so i guess i have two solutions : either fix this error message ( but i don't know how ) or i transfer the data from the server to my computer so i can analyse them with fastqc in my computer Thank you very much

Assembly sequencing genome next-gen • 1.4k views
ADD COMMENT
0
Entering edit mode

If you want an interactive session on a remote server then you have to login via ssh -X (...) so the X11 starts up. That is what the error No X11 DISPLAY variable was set means. Did you try to run it interactively?

ADD REPLY
0
Entering edit mode

Please search for solutions before posting new questions.

Take a look at: A: FastQC Error Problem

You will need to have a X-Windows program available on your end to accept X11 output. MobaXterm (PC) and XQuartz (macOS) are two free options.

You can also run fastqc on command line by just providing a set of file names. You do not need to use the GUI.

ADD REPLY

Login before adding your answer.

Traffic: 2616 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6