Reduced database setup

[drames29]

I am having an issue with executing alphalink2 searches. Due to the storage space on my computer I have downloaded the smaller database for MSA generation:

bash scripts/download/download_all_data.sh /path/to/database/directory reduced_dbs

The issue is that, amongst other file types, a file titled "small_bfd\bfd-first_non_consensus_sequences.fasta" is saved instead of the expected "bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt" file. This stops AlphaLink2 from running. Is there a way of using the reduced database? Or do I need to purchase a hard drive to download the full database for alphalink to work?

Thanks.

[lhatsk]

Hi,
How do you run homo_search.py? You need to at least add --small_bfd_database_path=PATH and set --db_preset=reduced_dbs in your call to homo_search.py or in run_alphalink.sh.