Open Lcornet opened 3 years ago
The license needs to be found by GeneMark, please have a look on http://exon.gatech.edu/GeneMark to find out exactly where to place the license.
In the versions I used it was always $HOME/.gm_key, but considering you are using singularity I am not sure where you would have to place the license exactly, as this depends on your mount paths.
For debugging I would suggest starting an interactive singularity shell.
Dear all,
I would like to use EukCC, installed in a singularity (ubuntu), but I have an error with GeneMark-ES license
singularity exec --bind ${PWD}:/mnt eukcc.sif eukcc --db /mnt/eukccdb --ncores 4 --ncorespplacer 1 --outdir eukcc_testgenome /mnt/metabat/bin.19.fa 04/14/2021 15:33:11: Starting EukCC 04/14/2021 15:33:12: Running GeneMark-ES 04/14/2021 15:33:12: I could not find the license of GeneMark-ES. Make sure you have a valid license in your home directory with the name '.gm_key'. Will try to run GeneMark-ES regardless, but it will likely fail 04/14/2021 15:45:45: GeneMark-ES failed on this bin 04/14/2021 15:45:45: No estimates were written
The license key is the home (root) directory: singularity exec --bind ${PWD}:/mnt eukcc.sif ls /root/.gm_key /root/.gm_key
Di I need to place the license somewhere else ? This is how EukCC is installed :
eukcc