Entering edit mode
4.8 years ago
ddurmus
•
0
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!!!
How are you running FastQC in FileZilla? Isn't FileZilla a FTP client? Does it have a shell?
You can directly run fastqc on command line with input/output options to avoid having to use graphical user interface.
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.
Yes that's how I'm running it.
Can you try logging in with
ssh -Y username@server
? That should set the$DISPLAY
variable (check byecho $DISPLAY
after you log in. Since you mentionputty
, this is a PC?No it's Mac. After I logged in with
ssh -Y username@server
and enteredecho $DISPLAY
, I got nothing. Does this mean the display variable is not set?No it is not set. You would normally see something like
Name/IP_address_of_server:11.0
. That number11
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.
I'm logging into a remote server using terminal. I've downloaded XQuartz.
Log in using the
terminal
built intoXQuartz
usingssh -Y
instead ofPuTTY
.Check
echo $DISPLAY
after you log in.What does
xdpyinfo | grep version
produce?localhost:18.0
version number: 11.0 X.Org version: 1.18.4
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 runfastqc
, have the GUI interface come up and run your files by choosing File --> Open.It worked!! Thank you so much for your help and time!