[maker-devel] GeneMarkES Installation

[Carson Holt]

Interesting.  The error message is similar to the bug I experienced, but may have a different cause.  Could you send me the fasta file you are using for GeneMark input.  If it's to big for e-mail, you can try sharing it with me using dropbox ( https://www.dropbox.com/ ).  They give you 2Gb of sharable storage for free.

Thanks,
Carson


On 11/17/09 5:00 PM, "Daniel Standage" <byuhobbes at gmail.com> wrote:

Carson,

I unpacked the tarball and confirmed that the original files were replaced. However, I am still getting the same problem.

Daniel


On Mon, Nov 16, 2009 at 11:17 AM, Carson Holt <carson.holt at genetics.utah.edu> wrote:
This is caused by a bug in GeneMark.  I submitted the same bug and a proposed fix to the GeneMark group some time ago, but it looks like they haven't updated the downloadable version yet.  I've attached my "fixed" version of two files that need to be replaced.  You should also submit a bug report to the GeneMark group as well, see their website on who to contact.  Seeing error reports from more people will help them with  their debugging.

Put the attached file in the same directory you downloaded the original GeneMark tar ball to.  Then extract the contents "tar -zxvf gm_es_bp_linux64_v2.3a_fix.tar.gz".  This should reach inside the directory created by GeneMark (gm_es_bp_linux64_v2.3a/) and replace the files get_bp_path_Pij.pl and get_single_multiple.pl <http://get_single_multiple.pl> .

You can then run gm_es.pl <http://gm_es.pl>  again.

Thanks,
Carson


On 11/16/09 7:34 AM, "Daniel Standage" <byuhobbes at gmail.com <http://byuhobbes@gmail.com> > wrote:

I'm trying to install GeneMarkES for use with Maker and I'm having trouble finding good documentation. I downloaded and unpacked gm_es_bp_linux64_v2.3a.tar.gz and genemark_hmm_euk.linux.tar.gz and followed the README instructions in each. When I run gm_es.pl <http://gm_es.pl>  <http://gm_es.pl>  in a test directory, I get the following error message.


cat: dna.fa_*: No such file or directory
Error on system: combine all training data

Any ideas where I could get more information about this message?

Thanks.

Daniel Standage
Plant Genetics Lab
Brigham Young University



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