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
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 errorNo X11 DISPLAY variable was set
means. Did you try to run it interactively?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.