@Jose Espinosa-Carrasco I'm getting weird strings in the

cp

and

mv

operations, empty lists, quoted values etc. Have you seen these before (

dev

)?

fix_obsolete.py pdb_mmcif/obsolete.dat > clean_obsolete.dat

## Handles multiple versions of mgnify database and selects the latest version
mgnify_db_path=$(ls -v ./mgnify/mgy_clusters*.fa | tail -n 1)

python3 /app/alphafold/run_alphafold.py         --fasta_paths=T1026.1.fasta         --model_preset=monomer_ptm --pdb70_database_path=./pdb70/pdb70          --db_preset=reduced_dbs --small_bfd_database_path=./small_bfd/bfd-first_non_consensus_sequences.fasta         --output_dir=$PWD         --data_dir=$PWD         --uniref90_database_path=./uniref90/uniref90.fasta         --mgnify_database_path=$mgnify_db_path         --template_mmcif_dir=./pdb_mmcif/mmcif_files         --obsolete_pdbs_path=./clean_obsolete.dat         --use_gpu_relax=true --max_template_date 2038-01-19

cp "T1026.1"/ranked_0.pdb ./"[]"_alphafold2.pdb

extract_metrics.py --name [] \
    --pkls T1026.1/features.pkl T1026.1/*.pkl \
    --structs T1026.1/ranked*.pdb

mv "[]_msa.tsv" "[]_alphafold2_msa.tsv"

# Can't use fasta.baseName to batch outputs in publishDir
mv "T1026.1" raw/

cat <<-END_VERSIONS > versions.yml
"NFCORE_PROTEINFOLD:ALPHAFOLD2:RUN_ALPHAFOLD2":
    python: $(python3 --version | sed 's/Python //g')
    alphafold2: $(cd /app/alphafold && git rev-parse HEAD 2>/dev/null || echo "unknown")
    jax: $(python3 -c "import jax; print(jax.__version__)" 2>/dev/null || echo "unknown")
    jaxlib: $(python3 -c "import jaxlib; print(jaxlib.__version__)" 2>/dev/null || echo "unknown")
    numpy: $(python3 -c "import numpy; print(numpy.__version__)" 2>/dev/null || echo "unknown")
    biopython: $(python3 -c "import Bio; print(Bio.__version__)" 2>/dev/null || echo "unknown")
END_VERSIONS

Nope Seems that the

meta.id

is empty 🤔 How are your running the pipeline? seems that you are using the test dataset, so it is strange

Got it, I was using the v1.0 test data samplesheet

Good question, we discussed to maintain some backwards compatibility but if it is silently not working it might be worth getting rid of it

Better to error early than fail with weird error messages

yep, but was not aware of this issue, thought it was working