[maker-devel] GeneMark HMM

[Cook, Malcolm]

Xavier,

I've experienced the same (I think with fgenesh output) and my workaroud was to use symbolic links to the long path from shorter paths.


Malcolm Cook
Stowers Institute for Medical Research - Kansas City, Missouri




________________________________
From: maker-devel-bounces at yandell-lab.org [mailto:maker-devel-bounces at yandell-lab.org] On Behalf Of Xavier Watkins
Sent: Thursday, July 16, 2009 8:29 AM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] GeneMark HMM

Hi there,

I've recently started using Maker and it's great!
I've got RepeatMasker, Snap and Blastall working fine but I'm having problems with GeneMark HMM. I think the problem comes from the fact it doesn't seem to like output file paths longer than about 90 characters...
When I run it from the command line I get "ehmm: error in command line" but when I reduce the length of the -o path it runs fine. As the path generated by maker is quite long, I was wondering if you had come across this problem and found a workaround? I'm running GeneMark.hmm eukaryotic on LINUX 64.

Many thanks,
Xavier

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