Problem on finding best augustus species

[444thLiao]

Hi, I am enjoy using the funannotate2
But recently, I want to annotate Gordionus_wolterstorffii genome and using this genome GCA_976986565.1

Ather clean step and I try to run

apptainer run funannotate2.sif funannotate2 train -f Gordionus_wolterstorffii_clean.fasta -s "Gordionus wolterstorffii" -o f2_trained --header-len 160 --cpus 20

It raised an error like the following

INFO:    underlay of /usr/local/bin/minimap2 required more than 50 (329) bind mounts
[May 07 11:44 AM] Python v3.12.13; funannotate2 v26.2.12; gfftk v26.2.12; buscolite v26.1.26; annorefine v2026.2.22
[May 07 11:44 AM] Loading genome assembly and running QC checks
[May 07 11:44 AM] Genome stats:
{
  "n_contigs": 8,
  "size": 210545467,
  "n50": 53486554,
  "n90": 48787178,
  "l50": 2,
  "l90": 4,
  "avg_length": 26318183
}
[May 07 11:45 AM] Filtered genome for training: kept 8 contigs (210,545,467 bp), filtered 0 contigs (0 bp) shorter than 10,000 bp
[May 07 11:45 AM] Getting taxonomy information
{
  "superkingdom": "Eukaryota",
  "kingdom": "Metazoa",
  "phylum": "Nematomorpha",
  "class": "Gordioida",
  "order": "Chordodea",
  "family": "Parachordodidae",
  "genus": "Gordionus",
  "species": "Gordionus wolterstorffii"
}
[May 07 11:45 AM] Choosing best augustus species based on taxonomy: elephant_shark
[May 07 11:45 AM] Choosing best busco species based on taxonomy: metazoa
[May 07 11:45 AM] Running buscolite to generate training set using filtered genome
[May 07 11:45 AM] metazoa_odb12 lineage contains 672 BUSCO models
[May 07 11:45 AM] Prefiltering predictions using miniprot of ancestral sequences
[May 07 11:45 AM] Found 15 complete models from miniprot, now launching 711 augustus/pyhmmer [species=elephant_shark] jobs for 412 BUSCO models
Traceback (most recent call last):
  File "/usr/local/bin/funannotate2", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/usr/local/lib/python3.12/site-packages/funannotate2/__main__.py", line 28, in main
    train(args)
  File "/usr/local/lib/python3.12/site-packages/funannotate2/train.py", line 183, in train
    buscolite(
  File "/usr/local/lib/python3.12/site-packages/funannotate2/train.py", line 428, in buscolite
    d, m, stats, cfg = runbusco(
                       ^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/buscolite/busco.py", line 485, in runbusco
    busco_id, results, jobs_submitted, jobs_skipped = future.result()
                                                      ^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/usr/local/lib/python3.12/concurrent/futures/thread.py", line 59, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/buscolite/busco.py", line 390, in process_busco_jobs
    result = predict_and_validate(
             ^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/buscolite/busco.py", line 156, in predict_and_validate
    aug_preds = proteinprofile(
                ^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/buscolite/augustus.py", line 94, in proteinprofile
    for line in execute_timeout(cmd):
                ^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/buscolite/utilities.py", line 273, in execute_timeout
    raise subprocess.CalledProcessError(return_code, cmd)
subprocess.CalledProcessError: Command '['augustus', '--species=elephant_shark', '--softmasking=1', '--gff3=on', '--UTR=off', '--genemodel=exactlyone', '--proteinprofile=/groups/burga/tianhua.liao/data/funannotate_db/metazoa_odb12/prfl/23294at33208.prfl', '--stopCodonExcludedFromCDS=False', '--strand=reverse', '--AUGUSTUS
_CONFIG_PATH=/usr/local/config/', '/tmp/tmpyuzoezh0.fasta']' returned non-zero exit status 1.

I think in some steps, it wrongly use a augustus species based on this taxonomy .