search

rrwick / Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
http://rrwick.github.io/Bandage/
GNU General Public License v3.0
579 stars 96 forks source link

command line Bandage: --names --lengths --depth only draws black rectangels #97

Open sovp opened 4 years ago

sovp commented 4 years ago

I run: Bandage image assembly.gfa assembly.png and get: assembly-1

Then I run: Bandage image assembly.gfa assembly.png --names --lengths --depth and get: assembly-2

What went wrong?

rrwick commented 4 years ago

If you're running this on a remote server, then can you try connecting with ssh -X instead of just ssh? It's a strange issue that I don't really understand, but Qt seems to want X11 forwarding to render text.

sovp commented 4 years ago

Thank you very much for the answer @rrwick

I have checked that X11 forwarding is activated. It has been on all the time.

For background info to others is here some extra info on what I have tried:

I keep getting this error with command line Bandage with the labels “--names --lengths --depth”:

Bandage image assembly.gfa assembly_bandage_image_with_labels.png --names --lengths --depth

”QXcbConnection: Could not connect to display”

When I run command line Bandage without the labels, then I get the desired .png

Bandage image assembly.gfa assembly_bandage_image.png

I am on Ubuntu 16.04 LTS on a google webserver.

I have installed the depencies:

qt5-default

build-essential

git

qtbase5-dev

libqt5svg5-dev

I have tried installing both the static and dynamic Pre-built Bandage binaries.

I have built Bandage from source.

I have used the docker image nanozoo/bandage with the specified '--env="DISPLAY" --net=host'

All installs works without the labels parameters, but gives the ”QXcbConnection: Could not connect to display” error, when I specify “--names --lengths --depth”.