This is a test version of Biostars. For the public version, visit https://www.biostars.org.
GeneMark-ES command line errors while executing program

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:

  1. ~/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

  1. ~/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

  1. ~/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

genemark genemark-es annotation fungus
• 4,188 views • link
updated by alexpersa77 • alexpersa77 • written by likoo27 • likoo27

sudo ./gmes_petap.pl

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?

• 0 views • link
written by h.mon h.mon

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

• 0 views • link
written by likoo27 • likoo27

Have you figured out what is going wrong with "../../InsideOut.pm line 1953 during global destruction" ?

• 0 views • link
written by alexpersa77 • alexpersa77

0 answers

No answers yet.

Log in to answer this question.

More posts like this