Unable to run GCNovo locally

[BioGeek]

When building the GCNovo image (added in ad185ec) locally with ./build_apptainer_images.sh gcnovo (requires the changes from #35) and running with ./run.sh sample_data/9_species_human gcnovo, I get the error:

Running benchmark with gcnovo on dataset 9_species_human.
Recalculate all algorithm outputs: true
Processing dataset: 9_species_human (sample_data/9_species_human)
sample_data/9_species_human/mgf/151009_exo4_1.mgf
Output file: ./outputs/9_species_human/gcnovo_output.csv
Processing algorithm: gcnovo
RUN ALGORITHM gcnovo
/usr/bin/bash: line 1: ./make_predictions.sh: No such file or directory
EXPORT PREDICTIONS
cp: cannot stat '/algo/outputs.csv': No such file or directory
EVALUATE PREDICTIONS
/usr/local/lib/python3.10/site-packages/pyteomics/mass/unimod.py:373: SAWarning: relationship 'SpecificityToNeutralLoss.specificity' will copy column Specificity.id to column SpecificityToNeutralLoss.specificity_id, which conflicts with relationship(s): 'Specificity.neutral_losses' (copies Specificity.id to SpecificityToNeutralLoss.specificity_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards.   To silence this warning, add the parameter 'overlaps="neutral_losses"' to the 'SpecificityToNeutralLoss.specificity' relationship. (Background on this warning at: https://sqlalche.me/e/20/qzyx) (This warning originated from the `configure_mappers()` process, which was invoked automatically in response to a user-initiated operation.)
  inst = cls(
Evaluating results for 9_species_human.
Reference proteome length: 20420 proteins.