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GeneMark-ES/ET/EP erro in run.cfg? #9

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DiegoSafian opened this issue Dec 31, 2022 · 1 comment
Open

GeneMark-ES/ET/EP erro in run.cfg? #9

DiegoSafian opened this issue Dec 31, 2022 · 1 comment

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@DiegoSafian
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Hi,

I have the following error when running GeneMark-ES/ET/EP ver 4.71_lic. Any help

error on call: /camp/lab/cardoso-moreiam/home/users/safiand/bin/gmes_linux_64_mod/parse_ET.pl --section EP_C --cfg /camp/lab/cardoso-moreiam/home/users/safiand/genome_annotation/turneri/turneri_braker1_2_tsebr/GeneMarkEP/run.cfg --v
finished Wed Dec 21 21:19:50 GMT 2022

The .log file indicate:
/camp/lab/cardoso-moreiam/home/users/safiand/bin/gmes_linux_64_mod/gmes_petap.pl : [Wed Dec 21 21:19:50 2022] /camp/lab/cardoso-moreiam/home/users/safiand/bin/gmes_linux_64_mod/parse_ET.pl --section EP_C --cfg /camp/lab/cardoso-moreiam/home/users/safiand/genome_annotation/turneri/turneri_braker1_2_tsebr/GeneMarkEP/run.cfg --v
/camp/lab/cardoso-moreiam/home/users/safiand/bin/gmes_linux_64_mod/gmes_petap.pl : [Wed Dec 21 21:19:50 2022] error

@DiegoSafian
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I run the check_install.bash script and I am getting the following error:

Checking GeneMark-ES installation
Checking Perl setup
All required Perl modules were found
Checking GeneMark.hmm setup
File gmhmme3 is not an executable or does not exist

The problem is that gmhmme3 does exist and it is executable.
-rwxrwx---+ 1 user domain users 1742336 Oct 23 04:18 gmhmme3

I just downloaded the last version GeneMark-ES/ET/EP ver 4.71_lic LINUX 64 kernel 2.6 - 4 from http://topaz.gatech.edu/GeneMark/license_download.cgi

I have also used the change_path_in_perl_scripts.pl as I am using an anaconda environment

Help please!

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