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:
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://:5444
Input fasta file taken from pdb. The same file is processed when using the "public" mmseq server (by omiitting the --host-url parameter)
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: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)"