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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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error message with Braker and gmes_petap.pl #764

Open LennWhy opened 4 months ago

LennWhy commented 4 months ago

Hi,

I am trying to run braker on a de novo masked vertebrate genome and I am encountering the following error message:

ERROR in file ~/miniconda3/envs/braker/bin/braker.pl at line 5323 Failed to execute: ~/miniconda3/envs/braker/bin/perl ../../gmes_linux_64/gmes_petap.pl

The code that I used is:

braker.pl --genome=$genome --bam=../../bam1.bam,../../bam2.bam --workingdir=braker_genome_masked/ --GENEMARK_PATH=../../gmes_linux_64

Can you please help?

Many thanks!

KatharinaHoff commented 4 months ago

Please use our container instead of a conda install. Or have a look at our Dockerfile on how we install separate components.

If the problem persists when you use the container, please let us know.

LennWhy commented 4 months ago

Thank you for your quick reply and suggestion.

My apologies but I am still a novice when it comes to using these different environments, i.e., conda/mamba, python, docker, singularity, which are all confusing (to me) and need their own dependencies somehow. I tried to download the container that you suggested (as I don't want the dependencies/software to conflict with other software versions on my computer), but I needed to install 'singularity', and unfortunately there are a lot of compatibilities/errors that creep up, which is beyond my knowledge as a linux user.

My experience with conda has been good so far for running most of my analyses (QC, mapping, de-nove assembly, busco etc...), which is why I was hoping that braker would work in it. I am mainly using RNA-seq data for the genome annotation, and was wondering if you might be able to suggest other 'user-friendly' ways to use braker for annotating my masked genome. Sorry, I realize it's asking a lot, but I would really appreciate the guidance.