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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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Error installing GeneMark-ESETEP #7

Closed Akinete closed 2 years ago

Akinete commented 2 years ago

Hi,

I installed the latest version of GeneMark-ESETEP，but when I run bash check_install.bash，I get the following error: Checking GeneMark-ES installation Checking Perl setup All required Perl modules were found Checking GeneMark.hmm setup GeneMark.hmm was found GeneMark.hmm is set Error, unexpected condition was detected

I checked the script, and found the following code： message=$($dir/gmhmme3 -v) if [[ $message != "gmhmme3 : error, sequence file's name is not provided" ]] then echo "Error, unexpected condition was detected" exit 1

I think there may be something wrong with gmhmme3，so I test gmhmme3 according to the README.md. It works normally. Here is the compared outputs 

$ ../../../compare_intervals_exact.pl  --f1 genemark.gff3  --f2 ../output/genemark.gff3  --v
# CDS in file genemark.gff3: 1531
# CDS in file ../output/genemark.gff3: 1527

#in     match   unique  %match  CDS

1531    1505    26      98.30   genemark.gff3
1527    1505    22      98.56   ../output/genemark.gff3

The resulting genemark.gff3 file in the test folder do not seem to be completely match the contents of the genemark.gff3 in the output folder.

Now I don't know what to do. could you please give me some suggestions？ Thank you very much for your time.