No X11 DISPLAY variable was set using FileZilla

Question

[ddurmus]

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!!!

[h.mon]

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

[GenoMax]

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.

[ddurmus]

Yes that's how I'm running it.

[GenoMax]

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?

[ddurmus]

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?

[GenoMax]

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.

[ddurmus]

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

[GenoMax]

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?

[ddurmus]

1. localhost:18.0
2. version number: 11.0 X.Org version: 1.18.4

[GenoMax]

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.

[ddurmus]

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