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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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No start value for parameter in config file error #544

Open aswathyseb opened 1 year ago

aswathyseb commented 1 year ago

Hi,

I am trying to run braker2 using pfalciparum models and my RNASeq dataset for additional evidence.

However at the optimization step, optimize_augustus.pl is throwing out an error

The error message is


No start value for parameter /UtrModel/prob_polya found in file ~/miniconda3/envs/braker2/config/species/pfalciparum/pfalciparum_parameters.cfg.

Maybe you misspelled this parameter in ~/miniconda3/envs/braker2/config//species/pfalciparum/pfalciparum_metapars.utr.cfg

The command I ran is braker.pl --genome=chr1.fa --species=pfalciparum --bam=consensus/bam/illum_fwd.bam,consensus/bam/illum_rev.bam,consensus/bam/ont_fwd.bam,consensus/bam/ont_rev.bam --stranded=+,-,+,- --cores=22 --gff3 --workingdir=consensus/braker2_hybrid --UTR=on --softmasking --alternatives-from-evidence=true --useexisting

Could you please help with this? I would really appreciate your comments/suggestions.

Thank you,

thdurand4 commented 5 months ago

Hello i have the same problem any one know how to fix this bug ?

Thanks you