attempting to run jalview with -nodisplay

Jalview Discussion
1

Hello

I would like to run the stand alone Jalview without the user interface in order to create a png file of the alignment I’m interested in on the command line as follows:

Jalview -props /home/alignment.fa -nodisplay -png test.png

However, the png file is not created and I get this error printed in output.txt

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.

No files to open!

And the alignment file is ‘corrupted’ with extra text as follows:

#—JalviewX Properties File—
#Wed Mar 03 15:29:36 GMT 2010
FGAGGDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYP…DGLRTTVQPGPL.AAELEGGPRPTHFAGV=

1mopA01=
1ihoA01=
LTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVP…=
FGPGEDYHRYPRDLERDRALLQEAGVDLLFAPGVEEMYPEG…FATRVQVEGPLTALWEGAVRPGHFQGV=
CTVVTKLFNIVKPHRAYFGQKDAQQFRVLRRMVRDLNMDVEMIECPIVR=
LATEST_VERSION=2.4.0.b2
FDRPEDLARYPRTLQEDCEKLNKRKVDLVFAPSVKEIYPNGTETHTYVDVPG.LSTMLEGASRPGHFRGV=
…RIIETIEEMKKFSEEMREKKKTIGFVPTMGYLHEGHLSLVRRARAEND.VVVVSIFVNPTQ=

etc.

Originally, the alignment file was just a standard alignment file in Fasta format.

I’m running the nov 2009 development version. Do you know what might be going on, or whether I’m not running the program correctly?

Thank you in advance!

2

Hi there, Al.

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