# BUSCO + miniprot fails with No such file or directory

**URL:** <https://help.galaxyproject.org/t/busco-miniprot-fails-with-no-such-file-or-directory/17495>\
**Category:** usegalaxy.org support\
**Tags:** usegalaxyorg, busco, usegalaxy-ca\
**Created:** [February 24, 2026, 1:43pm UTC](https://help.galaxyproject.org/t/busco-miniprot-fails-with-no-such-file-or-directory/17495 "2026-02-24T13:43:39Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![ccoulombe](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/ccoulombe/32/7328_2.png) [@ccoulombe](https://help.galaxyproject.org/u/ccoulombe)\
**Post date:** [February 24, 2026, 1:43pm UTC](https://help.galaxyproject.org/t/busco-miniprot-fails-with-no-such-file-or-directory/17495/1 "2026-02-24T13:43:39Z")

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Hello,

Tested on [UseGalaxy.org](http://UseGalaxy.org) and UseGalaxy.ca. Running BUSCO (`5.8.0+galaxy2`) fails with

```auto
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/`

```auto
$ 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,

---

<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [February 24, 2026, 5:57pm UTC](https://help.galaxyproject.org/t/busco-miniprot-fails-with-no-such-file-or-directory/17495/2 "2026-02-24T17:57:37Z")

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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! 👩‍🔬

> [@BUSCO error: refseq db not found](https://help.galaxyproject.org/t/busco-error-refseq-db-not-found/16328/8):
>
> I just checked the data at [UseGalaxy.org](http://UseGalaxy.org) and everything was working as expected. The [UseGalaxy.org.au](http://UseGalaxy.org.au) server should be using this same data through a shared CVMFS repository.
> 
> Shared history: [Galaxy](https://usegalaxy.org/u/jen-galaxyproject/h/test-busco-2025-01)
> 
> Screenshot of some of the test jobs with parameters tagged (you can explore the shared history for exact details).
> 
> Important keys: please notice how the **Select a gene predictor** must be set to **metaeuk** to allow the selection of the **bacterial** lineage. All prokaryotic lineages will require this same gene predictor.
> 
> For eukaryotic, you can use either of the predictors.
> 
> ![test-busco-2025-1-dataset-14-metaeuk-for-bacterial](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/3640607a46f719d91e4d5643f975d25dedd1d480.jpeg)
> 
> This is a good question so I’m glad you asked again, and I understand your point about suspecting that the gene predictor setting is unexpectedly specific!
> 
> But this is known and intentional for now – 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.
> 
> ![busco-5.8.0-galaxy1-tool-form-gene-predictor-parameter](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/c/c45addb69687a24e5214fdce66aec8251ad5cb62.png)
> 
> The tool is a bit complicated with all of the options and the comprehensive indexes! Hopefully this explains what is going on.. but does this actually help?

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<div class="post-metadata">

**Author:** ![ccoulombe](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/ccoulombe/32/7328_2.png) [@ccoulombe](https://help.galaxyproject.org/u/ccoulombe)\
**Post date:** [February 24, 2026, 6:34pm UTC](https://help.galaxyproject.org/t/busco-miniprot-fails-with-no-such-file-or-directory/17495/3 "2026-02-24T18:34:51Z")

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Hi @jennaj ,

This is GREAT information! Thanks so much!

> [@jennaj](#):
>
> Instead, toggle the first option back to the default to use **MetaEuk**.

But the selected value is `miniprot` on `.org` and `.ca` 🤔 for genome assembly.

```xml
#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!

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [February 24, 2026, 8:09pm UTC](https://help.galaxyproject.org/t/busco-miniprot-fails-with-no-such-file-or-directory/17495/4 "2026-02-24T20:09:56Z")

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**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](https://usegalaxy.org/u/jen-galaxyproject/h/test-busco-2025-01)

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**.

- [Busco: The option to download lineage data has been removed, but there are missing files for many lineages in CVMFS data · Issue #7462 · galaxyproject/tools-iuc · GitHub](https://github.com/galaxyproject/tools-iuc/issues/7462)

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

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [May 18, 2026, 4:25pm UTC](https://help.galaxyproject.org/t/busco-miniprot-fails-with-no-such-file-or-directory/17495/5 "2026-05-18T16:25:01Z")

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