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

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sovp opened this issue Aug 19, 2020 · 2 comments
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@sovp
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sovp commented Aug 19, 2020

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
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rrwick commented Aug 26, 2020

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
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sovp commented Aug 26, 2020

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”.

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