fasta file not processed by colabfold_batch when using local mmseq2 server

[pannoniac]

Assumption: Databases not indexed correctly or naming mismatch. Input /apps/prod/COMPCHEM/colabfold/git/ColabFold/MsaServer/databases/uniref30_2103 does not exist -> ? Input /apps/prod/COMPCHEM/colabfold/git/ColabFold/MsaServer/databases/uniref30_2103.idx does not exist -> a file called "uniref30_2103_db.idx" exists

Expected Behavior

fasta input file processed by colabfold with locally installed msa server

Current Behavior

fasta input file not processed. Error: raise Exception(f'MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.') Exception: MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.

Steps to Reproduce (for bugs)

If running locally ypdate you local installation colabfold_batch to the newest version. Please provide your input if you can share it. Follow instructions from git:

• git clone https://github.com/sokrypton/ColabFold.git
• Adjust config.json for msa server to set host and port to local msa server
• Set symbolic link to manually prepared databases according to commands in setup-and-start-local.sh
• Execute setup-and-start-local.sh
• Local server is up and running
• Install collabfold via conda according to instructions
• From a different machine run:
• colabfold_batch --host-url=http://<local_server>:5444 <input_dir_with_fasta_file> <output_dir> Input fasta file taken from pdb. The same file is processed when using the "public" mmseq server (by omiitting the --host-url parameter)

ColabFold Output (for bugs)

See: https://gist.github.com/pannoniac/f1b38b169042d4c2e018d32348b65a94#file-colabfold_local_output-txt

Your Environment

Include as many relevant details about the environment you experienced the bug in.

• Git commit used Colabfold: 6e1d335 MMSEQS_COMMIT=${1:-92deb92fb46583b4c68932111303d12dfa121364} BACKEND_COMMIT=${2:-1d84d23ec1199a9e46df9a5cb3301f6d73f3530d}

• If you run it on a local system. Please add the server specifications

• Operating system and version: NAME="Red Hat Enterprise Linux Server" VERSION="7.9 (Maipo)"