Problem with `create-index` command

[fjell-dev]

Hi,
I have a directory containing all of the final.cif files from PDB-REDO:

But when I tried to run the create-index command like alphafill create-index --pdb-dir /media/datastore/Databases/pdb-redo/final_cif/ --pdb-fasta pdb-redo.fasta, the pdb-redo.fasta file was empty.
I tried also to use the config file alphafill create-index --config alphafill.conf with the correct path to the PDB-REDO final cif files but it did not work either.
Could you help me figure out what I could have done wrong?
Thanks a lot.

[drlemmus]

This has likely to do with the directory structure. The indexer expects the same structure as the pdb_redo databank.

[fjell-dev]

Thank you. I managed to copy the final_cif files with the folder structure like the one from pdb_redo database. It worked with the alphafill create-index command and I got an index FASTA file of the size around 92 M.
When I tried to run alphafill process with an example CIF file like alphafill process --config alphafill.conf cif/8DQ2_A.cif filled/8DQ2.filled.cif -v, the command stopped at "Found 87 hits":
(The ligands in the input file, La, have been removed)

Adding mandatory item id to category entity
The asym ID's of ndb_poly_seq_scheme and pdbx_poly_seq_scheme are not equal, dropping ndb_poly_seq_scheme
Blasting:
ASGADALKALNKDNDDSLEIAEVIHAGATTFTAINPDGDTTLESGETKGRLTEKDWARANKDGDQTLEMDEWLKILRTRFKRADANKDGKLTAAELDSKAGQGVLVMIMK

Found 87 hits

Both the JSON and filled CIF output files did not show the expected filled La as when I tried with the AlphaFill webserver.
Do you know what could be the issue here?

[drlemmus]

Did you use exactly the same file as input for the command-line and server version?

[fjell-dev]

Yes, it is the same. You can find the Alphafill server result here: https://alphafill.eu/model?id=CS-1c4ba9ffaee88f8c2d1348f4dcdfcd6546134d64.
Not sure if it helps but I installed alphafill using mamba together with libcifpp, libzeep, libmcfp as I had a lot of troubles installed them using the instructions on the repos. Attached is the packages in the mamba environment.
env.txt
The output JSON file is also included:
8DQ2.filled.json
And the file components.cif exists in the environment: