EVM control file and est2genome

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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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Re: EVM control file and est2genome

Carson Holt-2
est2genome only works with the data given to est=.

For the second error, you must provide the path of the evm executable in maker_exe.ctl. It apparently was not in your PATH, so it didn’t get automatically filled out.

Here is an example from the wiki of using est2genome and protein2genome to train SNAP for the next MAKER run —> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#Training_ab_initio_Gene_Predictors

—Carson


On Oct 24, 2018, at 3:28 AM, Linnie Linnie <[hidden email]> wrote:

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!


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org