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gatech-genemark / GeneMark-EP-plus

GeneMark-EP and -EP+: automatic eukaryotic gene prediction supported by spliced aligned proteins
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GeneMark-ES/ET/EP erro in run.cfg? #9

Open DiegoSafian opened 1 year ago

DiegoSafian commented 1 year ago

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 commented 1 year ago

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!