[maker-devel] error: training genemodel with SNAP and GeneMark & run time to generate AUGUTUS species file

[Kudtarkar, Parul V.]

Dear Maker developers,

1. We use assembled RNAseq(from same species) and protein evidence(from evolutionary close species) to generate training gene structure(1st iteration, est2genome=1,protein2genome=1 ).

2. This is than used to train abinito gene predictors, SNAP and AUGUSTUS.

3. GeneMarkES( version: GeneMark-ES / ET v.4.32) is used to produce training data-set with the command

gmes_petap.pl --sequence pmin_jelly.fa

4. We would be predicting genes using results from SNAP, Genemark and AUGUSTUS(2nd iteration, est2genome=0, protein2genome=0)

I have couple of questions relating to Genemark and AUGUSTUS

1. AUGUSTUS

We do not have a species file for species file of our interest or evolutionary closer species

following command is used to generate species file

/autoAug.pl --genome=pmin_jelly.fa --species=pminiata --cdna=pmin_transcripts.fa --trainingset=genome.gff3 --singleCPU -v --useexisting
AUGUSTUS is taking too long to compute species file, is there a solution for this issue. Using species file from other organism might generate false positives. Is it advised in such situations to not used AUGUSTUS model?

2. Genemark

I used the gmhmm file generated in the genemark output directory, however I encounter following error

-------------------------

STATUS: Parsing control files...
ERROR: You have failed to provide a value for 'gmhmme3' in the control files.
ERROR: You have failed to provide a value for 'probuild' in the control files.
---------------------
FYI

-----

maker_opts.ctl

#-----Gene Prediction
snaphmm=/home/parul/Pmin_new/maker_snap/pmin1.hmm #SNAP HMM file
gmhmm=/home/parul/Pmin_new/maker_snap/gmhmm.mod #GeneMark HMM file

-----

Using SNAP for training gene model yields over 6000-7000 additional gene. The model has good cumulative AED value.

I was hoping in addition to SNAP, if I could use AUGUSTUS and GeneMark to train the gene model to fuse dispersed models so that the gene count is within the expected range.


Thanks and regards,

Parul


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