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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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How to fix the --busco_lineage argument issue in braker3? #817

Closed RezwanCAAS closed 4 months ago

RezwanCAAS commented 5 months ago

Hi braker team, I am running this code for braker3 but having this issue regarding

Unknown option: busco_lineage Error in command line arguments

I have also download the eudicotes lineage as "mb_downloads"

module load braker/3.0.3/singularity
export AUGUSTUS_CONFIG_PATH=/Augustus/config/ \

singularity exec -B $PWD,/ibex,/sw /ibex/scratch/projects/ibex_cs_temp/47882/braker3.sif braker.pl \
 --workingdir=~path/braker1/ \
 --genome=genome.fasta.masked \
 --prot_seq=ghb_db_cg_os_le.fa \
 --bam=$RNA_seq
 --crf --busco_lineage=eudicots_odb10 --threads=32 --AUGUSTUS_CONFIG_PATH=/Augustus/config/ \
 --filterOutShort

Could you please guide how to fix this busco issue. moreover, please suggest what more arguments I can add in command as per your expertise.

Regards Rezwan

KatharinaHoff commented 5 months ago

Are you sure you are running the latest container? Just rebuild and confirm.

Rezwan Tariq @.***> schrieb am Do. 2. Mai 2024 um 12:43:

Hi braker team, I am running this code for braker3 but having this issue regarding

Unknown option: busco_lineage Error in command line arguments

I have also download the eudicotes lineage as "mb_downloads"

module load braker/3.0.3/singularity export AUGUSTUS_CONFIG_PATH=/Augustus/config/ \

singularity exec -B $PWD,/ibex,/sw /ibex/scratch/projects/ibex_cs_temp/47882/braker3.sif braker.pl \ --workingdir=~path/braker1/ \ --genome=genome.fasta.masked \ --prot_seq=ghb_db_cg_os_le.fa \ --bam=$RNA_seq --crf --busco_lineage=eudicots_odb10 --threads=32 --AUGUSTUS_CONFIG_PATH=/Augustus/config/ \ --filterOutShort

Could you please guide how to fix this busco issue. moreover, please suggest what more arguments I can add in command as per your expertise.

Regards Rezwan

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RezwanCAAS commented 5 months ago

the server admin team installed the latest one as per their information. Just now, I change the command like

eudicots_odb10=~path/mb_downloads/

--busco_lineage=$eudicots_odb10

its working now Actaully, I installed the new compleasm version 0.2.6 and download the eudicots lineage as mb_downloads. Do you suggest some good arguments in order to have more better results.

Regards Rezwan

RezwanCAAS commented 5 months ago

sorry again, It again shows the same error like Unknown option: busco_lineage Error in command line arguments

KatharinaHoff commented 5 months ago

I don't trust that information because it says braker3.0.3 in your initial post. that version did indeed not know that argument. We are now at 3.0.8. You need to rebuild the container image with the latest sources.

On Thu, May 2, 2024 at 2:35 PM Rezwan Tariq @.***> wrote:

sorry again, It again shows the same error like

Unknown option: busco_lineage Error in command line arguments

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/817#issuecomment-2090389530, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JG2SJBKSF5PWTUIS6DZAIXJJAVCNFSM6AAAAABHDO46EOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJQGM4DSNJTGA . You are receiving this because you commented.Message ID: @.***>

RezwanCAAS commented 4 months ago

Yes, thank you @KatharinaHoff . It makes sense and admin team has installed the latest one. Now the compleasm is working under braker3.