Hello, I tried to use Gene-Mark-ES but for some reason errors keep showing up and since I have zero knowleadge of Perl I'm lost what to do.
We tried the following commands with such results:
- ~/Programs/genemark-es/linux_32$ ./gmes_petap.pl --ES --fungus --sequence Canu_Pilon.fna (same for linux_64)
OIO::Method error: Can't locate object method "write_error" via package "Logger::Simple" Package: Logger::Simple File: /usr/local/share/perl/5.26.1/Logger/Simple.pm Line: 45
Trace begun at /usr/local/share/perl/5.26.1/Logger/Simple.pm line 45 Logger::Simple::open_log('Logger::Simple=SCALAR(0x55f6e6458320)') called at /usr/local/share/perl/5.26.1/Logger/Simple.pm line 37 Object::InsideOut::new('Logger::Simple', 'HASH(0x55f6e6eaf0a0)') called at gmes_petap.pl line 1053 main::SetLogger at gmes_petap.pl line 1032 main::ReadParameters at gmes_petap.pl line 98
- ~/Programs/genemark-es/linux_64$ sudo ./gmes_petap.pl --ES --fungus --sequence Canu_Pilon.fna
readdir() attempted on invalid dirhandle DIR at ./gmes_petap.pl line 908.
closedir() attempted on invalid dirhandle DIR at ./gmes_petap.pl line 914. error, file not found: info/training.fna
(in cleanup) (in cleanup) at /usr/local/share/perl/5.26.1/Object/InsideOut.pm line 1953 during global destruction
- ~/Programs/genemark-es/linux_32$ sudo ./gmes_petap.pl --ES --fungus --sequence Canu_Pilon.fna
Can't exec "/home/damian/Programs/genemark-es/linux_32/probuild": No such file or directory at ./gmes_petap.pl line 1000.
error on call: /home/damian/Programs/genemark-es/linux_32/probuild --seq data/dna.fna --allowx --stat info/dna.general
(in cleanup) (in cleanup) at /usr/local/share/perl/5.26.1/Object/InsideOut.pm line 1953 during global destruction
Never, ever, run analyses as root or using sudo.
How did you install GeneMark? Did you install the mentioned Perl modules? What is your operating system?
downloaded it from their site, copied gm_key to Home and installed all modules that are written in README. Operating system is Ubuntu 18.10
Have you figured out what is going wrong with "../../InsideOut.pm line 1953 during global destruction" ?