BUSCO + miniprot fails with No such file or directory

usegalaxy.org support
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1

Hello,

Tested on UseGalaxy.org and UseGalaxy.ca. Running BUSCO (5.8.0+galaxy2) fails with

FileNotFoundError: [Errno 2] No such file or directory: '/cvmfs/data.galaxyproject.org/byhand/busco/v5/lineages/archaea_odb10/refseq_db.faa.gz'

The source archive file does not exists, but is instead extracted under /cvmfs/data.galaxyproject.org/byhand/busco/v5/lineages/archaea_odb10/

$ ls /cvmfs/data.galaxyproject.org/byhand/busco/v5/lineages/archaea_odb10/

ancestral  ancestral_variants  dataset.cfg  hmms  info  lengths_cutoff  links_to_ODB10.txt  scores_cutoff

Parameters used:

Cached database with lineage v5
Mode geno
Select a gene predictor miniprot
Auto-detect or select lineage? auto_detect
auto-lineage group All taxonomic groups (–auto-lineage)

and any sample fasta input will do, as the tool fails right away.

Note: it fails specifically with miniprot.

Thanks,

2

Hello @ccoulombe

Yes, your log messages are expected when attempting to combine Miniprot and an archaea lineage. Instead, toggle the first option back to the default to use MetaEuk.

at the UseGalaxy public servers, the computed indexes for prokaryotic genomes are only available for use with the MetaEuk option. This leads to Prodigal being used (technically!). Bacterial lineage index for miniprot are not available at this time.

How the indexes are organized is a bit complicated! Any server that uses the base public Galaxy pre-computed indexes will work this way, and that includes all UseGalaxy servers. Setting the form up this way routes the jobs to the clusters that can process the request (the tool, dependencies, and index data combinations). Please give this a try and let us know if it works for you!

Details if interested! :woman_scientist:

1 Like
3

Hi @jennaj ,

This is GREAT information! Thanks so much!

But the selected value is miniprot on .org and .ca :thinking: for genome assembly.

#if $busco_mode.mode == 'geno':
    #if $busco_mode.use_augustus.use_augustus_selector == 'miniprot':
        --miniprot
    #elif $busco_mode.use_augustus.use_augustus_selector == 'augustus':
        ${busco_mode.use_augustus.long}
        --augustus
        #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
            --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
        #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
            --augustus_species local
        #end if
    #else:
        --metaeuk
    #end if
#end if

Perhaps it is worth selecting metaeuk as the default selected value?

Thanks again for the help!

4

Updated End-user advice Feb 2026. Tool: Busco Assess genome assembly and annotation completeness (Galaxy Version 5.8.0+galaxy2) → To access Prokaryotic lineages: use MetaEuk + Select Lineage to access Prodigal. Important: avoid all Auto choices.

Example history: Galaxy

Thank you @ccoulombe for helping us to come up with recommended advice for the updated tool form.

You are right and I was mixed up about the default! The notation in the tool form is legacy from when the variables were original created and only human was supported! Later as the tool expanded, this was retained.

The option to select the specific lineages was available in prior releases, and some servers may still support this, but if a lineage seems to be missing, try Auto.

I’m going to message you directly to troubleshoot administrative issues you have questions about. :slight_smile: