bioconda jalview : png export fails

Jalview Developers
1

Hi all,

with the recent bioconda jalview installation I get for a call like this

   jalview -nodisplay -open mRNA.fasta -feature mRNA_feature.txt -annotation mRNA_annotation.txt -png mRNA.png

an output like that

···

#########################
Java version: 1.8.0_121
amd64 Linux 2.6.32-696.18.7.el6.x86_64
Jalview Version: 2.10.3-1 (bioconda git-commit: [])
CMD [-open 462_aroL_ct_367_mRNA.fasta] executed successfully!
File format identified as Fasta
Feb 20, 2018 11:49:38 AM jalview.util.MessageManager <clinit>
INFO: Getting messages for lang: en_US
java.awt.HeadlessException
CMD [-annotations mRNA_annotation.txt] executed successfully!
Written alignment in Fasta format to mRNA_feature.txt
Error creating PNG file.
Creating PNG image: evo_align_img/mRNA.png
#########################

an no PNG output file is created.

Can you please check if you can confirm this? Maybe a dependency issue?

Thanks and best,
Martin

--
Dr. Martin Raden, nee Mann, Postdoc

Bioinformatics - Prof. Dr. R. Backofen
Department of Computer Science
Albert-Ludwigs-University Freiburg
Add: Georges-Koehler-Allee 106, room 02012, 79110 Freiburg, Germany
Tel: ++49-761-203-8254 (Monday-Wednesday)
Fax: ++49-761-203-7462
http://www.bioinf.uni-freiburg.de/~mmann/

Forest Growth and Dendroecology
Institute of Forest Sciences
Albert-Ludwigs-University Freiburg
Add: Tennenbacher Str. 4, room 02062, 79106 Freiburg, Germany
Tel: ++49-761-203-3733 (Thursday+Friday)
Fax: ++49-761-203-3740
http://www.iww.uni-freiburg.de

2

Hi Martin.

with the recent bioconda jalview installation I get for a call like this

   jalview -nodisplay -open mRNA.fasta -feature mRNA_feature.txt 
-annotation mRNA_annotation.txt -png mRNA.png

OK…

an output like that

#########################
Java version: 1.8.0_121
amd64 Linux 2.6.32-696.18.7.el6.x86_64
Jalview Version: 2.10.3-1 (bioconda git-commit: [])
CMD [-open 462_aroL_ct_367_mRNA.fasta] executed successfully!
File format identified as Fasta
Feb 20, 2018 11:49:38 AM jalview.util.MessageManager <clinit>
INFO: Getting messages for lang: en_US
java.awt.HeadlessException
CMD [-annotations mRNA_annotation.txt] executed successfully!
Written alignment in Fasta format to mRNA_feature.txt

^ this looks wrong - ‘-feature’ should be ‘-features’ and ‘-annotation’ should be ‘-annotations’. We need to fix our args parsing to spot this issue (it’s really rather dumb right now!).

Error creating PNG file.
Creating PNG image: evo_align_img/mRNA.png

not good. I wasn’t able to recreate the problem on OSX however. My guess is that your running out of memory, but that should have raised an error saying as such (and since the wrapper tries to max out the heap allocation is less likely).

Is this for all alignments ? Can you send us some data to try ?
Jim.

The University of Dundee is a registered Scottish Charity, No: SC015096

···

On 20/02/2018 12:11, Martin Raden wrote: