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soedinglab / metaeuk

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
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Error using `--add-orf-stop` #88

Closed berkelem closed 5 months ago

berkelem commented 7 months ago

Hi, I am encountering an error when I add the --add-orf-stop option to a metaeuk easy-predict run.

Here's my command: 

metaeuk easy-predict --threads 12 GCA_000192795.1_Vavr_culi_floridensis_V1_genomic.fna busco_downloads/lineages/fungi_odb10/refseq_db.faa test_output.fna tmp/ --max-intron 60000 --max-seq-len 70000 --min-exon-aa 15 --max-overlap 15 --min-intron 5 --overlap 1 --add-orf-stop -s 4.5

This works fine without the --add-orf-stop option, but once I add it in I get

ERROR: strand is MINUS but the contig coordinates are positive. Soemthing is wrong.

The relevant line in the code base is https://github.com/soedinglab/metaeuk/blob/master/src/exonpredictor/unitesetstofasta.cpp#L61

Might this be a bug?

elileka commented 5 months ago

Hi,

Hmm. Thank you, this needs checking...

Thank you

elileka commented 5 months ago

Hi,

I was able to reproduce your problem. The parameter you set is an MMseqs2 parameter, which should be blocked from MetaEuk because it messes it up. But I think you can actually get the info you need about stop codons by setting the MetaEuk param instead: --write-frag-coords 1.

Thank you for reporting this!

Best, Eli

elileka commented 5 months ago

The MMseqs2 parameter was blocked in the latest commit (6643). Please use --write-frag-coords 1 for information about stop codon positions.

berkelem commented 5 months ago

Thanks!

elileka commented 5 months ago

and sorry for your inconvenience... :-/

On Fri, Apr 19, 2024 at 2:04 PM Matthew Berkeley @.***> wrote:

Thanks!

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