[maker-devel] EVM control file and est2genome

[Linnie Linnie]

Hi,

I am trying to run maker together with EVM. I want to annotate a genome for
which there is no evidence data, which is why I am using ESTs and protein
data from a closely related species. I am finding two unrelated issues.

The first one is the following:
I set up the control files passing alt_est with a fasta file of ESTs,
protein with protein from a closely related species as well as
uniprot-sprot.fa, es2genome=1 and prot2genome=1. I am getting the following
error:

>ERROR: You must provide some form of EST evidence to use est2genome as a
predictor.

Does this mean I can only use est2genome with ESTs from the species of
interest?

The second error relates to EVM:
I have passed in the file maker_opts.ctl the option run_evm=1. I have used
default parameters in the file maker_evm.ctl. I am getting the following
error:

>ERROR: You have failed to provide a value for 'evm' in the control files.

Does this error relate to the maker_opts.ctl file or the maker_evm.ctl one?
How could I fix it?


And lastly, a more general but fundamental question. Is my approach
sensible? My plan is to run this evidence-based annotation, then perhaps
train SNAP, Augustus and GeneMark, and use those output files to re-run
maker with ab-initio parameters.

I would appreciate any input on any of these issues.

Thank you!
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