Parameters for annotation with maker

Question

[san96]

Hi everyone, I'm starting with plant annotation and I'm using maker for the first time, however I have some doubts on how to configure my maker_opts.ctl file for my first round. I intend to do this first round with my previously masked genome (RepeatModeler and RepeatMasker), RNA-seq and proteins. My doubt is mainly in the masking section, I don't know what would be the correct way to set these parameters if I'm already providing a softmask genome:

#-----Repeat Masking (leave values blank to skip repeat masking)
model_org=all #select a model organism for RepBase masking in RepeatMasker
rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker
repeat_protein=
rm_gff= #pre-identified repeat elements from an external GFF3 file
prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no
softmask= #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)

When I set it as follows:

#-----Repeat Masking (leave values blank to skip repeat masking)
model_org=all #select a model organism for RepBase masking in RepeatMasker
rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker
repeat_protein=/NFS/LUSTRE/storage/data/software/maker-2.31/maker/data/te_proteins.fasta #provide a fasta file of transposable eleme$rm_gff= #pre-identified repeat elements from an external GFF3 file
prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no
softmask=0 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)

or softmask=1

I get the following error in all my scaffolds:

Processing run.log file...
MAKER WARNING: The file Plant_aura_var.Colimex.maker.output/Plant_aura_var.Colimex_datastore/B4/1C/scaffold_268//theVoid.scaffold_268/0/scaffold_268.0.all.rb.out
did not finish on the last run and must be erased
examining contents of the fasta file and run log

I would greatly appreciate your response.

Answer 1

[colindaven]

I don't know what the error is here , but check all paths and try this

#add quotes
repeat_protein="/NFS/LUSTRE/storage/data/software/maker-2.31/maker/data/te_proteins.fasta"

Did you delete the following line ?

rm_gff= #pre-identified repeat elements from an external GFF3 file

Also try to find and list the actual error so we can help.

[san96]

Hi colindaven ,

Thanks for your reply, the problem I have is actually about how to configure my make_opts file for my first round. My plan is to run a first round with RNA-seq and proteins, a second with training with SNAP and Augustus and the previous gff and the third using the above. My doubts are about masking, is it better to use a softmask genome at the beginning and disable the masking options in maker? or maybe put a non-mask genome and a gff file of repetitions? Do you have any recommendations? I have many conflicts in the

#-----Repeat Masking section

Thank you very much.