Open mictadlo opened 2 years ago
Hi Michal,
does the problem persist? I see you opened a BRAKER2 issue 2 days ago so I wonder whether you were able to resolve it. If so, can you please share what the issue was?
If not, I will look into this.
Tomas
Hi, Yes, the error still persists. By any chance, do you know why I got the above error?
Because of the error, I was not able to use your tool yet to train Augustus, GlimmerHMM and SNAP. After all annotation tools are finished then I would like to merge them with EvidenceModeller. I found here how to train SNAP. They provide a script to convert GFF3 to SNAP's ZFF format (gff3_to_zff.pl). By any chance, do you know how to train GlimmerHMM?
Thank you in advance, Michal
Hi Michal,
sorry, I do not have any experience with training GlimmerHMM.
About the GeneMark error, did you try to run the check_install.bash
in GeneMark's directory? Does that work without errors? One common issue with GeneMark is a segmentation fault on new Linux systems. GeneMark now has a version (LINUX 64 kernel 4
) that solves this problem.
Best, Tomas
Hi, Thank you for your message. I got the following message:
$ uname -a
Linux appdev 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux
ProtHint-2.6.0/dependencies/GeneMarkES$ ./check_install.bash
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
What did I miss?
Thank you in advance,
Michal
Hi, this could be the error I mentioned (One common issue with GeneMark is a segmentation fault on new Linux systems).
Did you try downloading the LINUX 64 kernel 4
version from http://exon.gatech.edu/GeneMark/license_download.cgi?
Tomas
Hello,
What did I miss?
Thank you in advance,
Michal