unable to create png image from alignment

Jalview Discussion
1

I’m currently investigating how to run Jalview on the command line. I’m opening up a fasta alignment, connecting to a couple of das servers and then trying to output the alignment as a png file.

This is what I’m adding to the command line

Jalview -open /my_dir/myfile…fa -dasserver das1=http://mydas1url -dasserver das2=http://mydas2url -png myalignment.png

But the .png file s not being created. The alignment itself opens up fine as do the DAS connections.

The output.txt says:

Java version: 1.6.0_13
amd64 Linux 2.6.18-128.1.6.el5
Jalview Version: Automated Build

INFO: Setting default net timeout to 30 seconds.

INFO - Not enabling Google Tracking.

I’m running the InstallAnywhere installation from October last year.

Any help much appreciated!!!

2

Hello there, Ali.

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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
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