--singlestrand option does not work with prokaryotic species

[CarlosMenFer]

Hi,

I have had problems with the next Augustus run. Is the "--singlestrand" option compatible with prokaryotic models?

Command line:

augustus --species=sulfolobus_solfataricus --strand=both --singlestrand=true --genemodel=complete --protein=off --introns=on --start=on --stop=on --cds=on --UTR=off --noInFrameStop=false --stopCodonExcludedFromCDS=false --alternatives-from-sampling=true --sample=91 --minexonintronprob=0.08 --minmeanexonintronprob=1.0 --maxtracks=5 --temperature=2 --gff3=on --codingseq=on

Error message: Could not find the config file /root/augustus/config/model/states_singlestrand_bacterium.cfg. Looking for states_singlestrand_bacterium.cfg in the configuration directory instead ... not found.

[KatharinaHoff]

I think I never tried to run it for single strand in prokaryotes after we made it possible to run it on both strands simultaneously. This can with no doubt be improved but is an issue of low priority on our end. (Limited resources.)

[hmehlan]

possibly related:

$ bin/augustus --species=leishmania_tarentolae --singlestrand=true docs/tutorial/data/chr2R.fa
Could not find the config file config/model/states_singlestrand_intronless.cfg.
 Looking for states_singlestrand_intronless.cfg in the configuration directory instead ... not found.

bin/augustus: ERROR
	Properties::readFile: Could not open the this file!

[MarioStanke]

The combination of singlestrand and intronless is not implemented. I recommend to not use the singlestrand in this case and rather ignore the predicted genes on the other strand.