Open Imogen-D opened 2 years ago
So it did parse genemark models
[12/13/21 18:31:13]: Summary of gene models: {'total': 30708, 'Augustus': 6351, 'HiQ': 43, 'GeneMark': 8207, 'GlimmerHMM': 12111, 'snap': 3996}
However, because it turned the weights to 0 for genemark because it is not in your PATH nor is GENEMARK_PATH set, those models did not get passed to EVM.
[12/13/21 18:31:13]: EVM Weights: {'Augustus': 1, 'HiQ': 2, 'GeneMark': 0, 'GlimmerHMM': 1, 'snap': 1, 'proteins': 1}
So you just need to have gmes_petap.pl
in your PATH, or you can export the envinromental variable GENEMARK_PATH, ie
export GENEMARK_PATH=/the/actual/path/to/dir/containing-genemark
Also, it seems like snap
might be broken on your install -- if it is installed through conda on debian systems it is a known bug. You can delete the one from conda, ie conda uninstall -n your_env snap --force
and then install with apt-get package manager, sudo apt-get install snap
.
Thanks! Didn't realise I still needed the GENEMARK_PATH exported. I also fixed the SNAP issue, I'd used a file with different fasta headers for the genemark input originally.
Hi, I'm parsing a genemark_gtf into funannotate predict as utilising genemark_path isn't working (through various rounds of trial and error, I'm not sure why as gmes_petap.pl works as a stand alone script and I've read through previous issues regarding it). How do I know if this genemark_gtf file has been used? In addition, SNAP shows multiple errors (exon out_of_bounds) which, looking through other documentation appears to occur if there are multiple different input files but this is not the case here. Since snap found 3966 genes and 450 of them have the error is this a major concern? Here is my output, I have removed most of the SNAP errors for clarity