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