Open kbrunnerLXG opened 11 months ago
Hello, I also meet this question. I think the reason may be the space from the name of remote disk, like "New\ Volume",but I don't know how to solve it. If you know it already, please tell me.
It looks like in this case, the space in "New\ Volume" was causing argument splitting, which can be fixed by putting double quotes around the entire path (i.e. "/media/aditya/New\ Volume/protein_database/"). I also came across the same error for another reason though. In lines 176-180 in run_alphafold.sh, if the which command is set to an alias on the user's computer (sometimes this can happen by accident), it returns an incorrect or missing argument instead of a database path. command
and type
tend to be more portable across systems. I've found that the following works more consistently - maybe it could be used instead of 'which'?:
# Binary path (change me if required)
hhblits_binary_path=$(command -v hhblits)
hhsearch_binary_path=$(command -v hhsearch)
jackhmmer_binary_path=$(command -v jackhmmer)
kalign_binary_path=$(command -v kalign)
So I was having issues with alphafold while builoding the docker image and decided to try this out i was able to follow all the steps but still can not run alphafold.
bash run_alphafold.sh -d /media/aditya/New\ Volume/protein_database/ -o ./dummy_test/ -f ./example/query.fasta -t 2020-05-14 Full AlphaFold protein structure prediction script. flags:
/home/aditya/alphafold-2.3.1/run_alphafold.py: --[no]benchmark: Run multiple JAX model evaluations to obtain a timing that excludes the compilation time, which should be more indicative of the time required for inferencing many proteins. (default: 'false') --bfd_database_path: Path to the BFD database for use by HHblits. --data_dir: Path to directory of supporting data. --db_preset: <full_dbs|reduced_dbs>: Choose preset MSA database configuration
Too many command-line arguments.
I have the alphafold database on a seperate NTSF formatted drive but i was in the past able to predict using this very same drive