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No X11 DISPLAY variable was set using FileZilla

Hello, I am trying to run fastqc on my sequencing files. However after the first file is completed, I get this error and a corrupted .zip file:

 A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f67c16af009, pid=15527, tid=15559
#
# JRE version: OpenJDK Runtime Environment (9.0) (build 9-internal+0-2016-04-14-195246.buildd.src)
# Java VM: OpenJDK 64-Bit Server VM (9-internal+0-2016-04-14-195246.buildd.src, mixed mode, tiered, compressed oops, g1 gc, linux-amd64)
# Problematic frame:
# C  [libjava.so+0x1d009]  JNU_GetEnv+0x19
#
# No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home3/ddurmus/Sb_Pilot_Exp_5_30/hs_err_pid15527.log

and when I enter just the fastqc command on my terminal I get this error:

No X11 DISPLAY variable was set, but this program performed an operation which requires it

I saw couple of posts online how to fix this issue in Putty, I was wondering if anyone can help me to fix this in FileZilla? Thanks!!!

rna-seq next-gen rna-seq software error sequencing
• 4,361 views • link
written by ddurmus • ddurmus

You can directly run fastqc on command line with input/output options to avoid having to use graphical user interface.

$ fastqc seqfile1 seqfile2 .. seqfileN -o /path_to_where_you_want_output

If you want the output to go to local directory with data files then leave -o option out. Is this how you are running your analysis?

You can then download the html result files for viewing on the local computer using filezilla.

• 0 views • link
written by GenoMax GenoMax

Yes that's how I'm running it.

• 0 views • link
written by ddurmus • ddurmus

Can you try logging in with ssh -Y username@server? That should set the $DISPLAY variable (check by echo $DISPLAY after you log in. Since you mention putty, this is a PC?

• 0 views • link
written by GenoMax GenoMax

No it's Mac. After I logged in with ssh -Y username@server and entered echo $DISPLAY, I got nothing. Does this mean the display variable is not set?

• 0 views • link
written by ddurmus • ddurmus

No it is not set. You would normally see something like Name/IP_address_of_server:11.0. That number 11 will vary.

Just to be sure. You are logging in to a remote server using terminal on your Mac or are you running fastqc on your mac locally?

Can you install XQuartz (https://www.xquartz.org/ ) on your mac to make sure you have X11 available locally.

• 0 views • link
written by GenoMax GenoMax

I'm logging into a remote server using terminal. I've downloaded XQuartz.

• 0 views • link
written by ddurmus • ddurmus

Log in using the terminal built into XQuartz using ssh -Y instead of PuTTY.

  1. Check echo $DISPLAY after you log in.

  2. What does xdpyinfo | grep version produce?

• 0 views • link
written by GenoMax GenoMax
  1. localhost:18.0
  2. version number: 11.0 X.Org version: 1.18.4
• 0 views • link
written by ddurmus • ddurmus

All that looks good. DISPLAY variable is set. Your server does have X11 installed.

Try running fastqc command now. Let us know what happens. You could also just run fastqc , have the GUI interface come up and run your files by choosing File --> Open.

• 0 views • link
written by GenoMax GenoMax

It worked!! Thank you so much for your help and time!

• 0 views • link
written by ddurmus • ddurmus

Hello ddurmus!

We believe that this post does not fit the main topic of this site.

This is not a bioinformatics question.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

[ATpoint]: See moderator slack please :)

• 0 views • link
updated by ATpoint ATpoint • written by GouthamAtla GouthamAtla

How are you running FastQC in FileZilla? Isn't FileZilla a FTP client? Does it have a shell?

• 0 views • link
written by h.mon h.mon

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