Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Clustering problem: the sequences length is less than 14 residues #346

Open
jiaweiguan opened this issue Sep 13, 2024 · 0 comments
Open

Comments

@jiaweiguan
Copy link

jiaweiguan commented Sep 13, 2024

Hi! foldseek team
I am using the clustering function of foldseek. It sometimes works and sometimes it doesn't
Here is example and question. The problem I see is that the number of amino acids is too small. In fact, the protein length I uploaded is long enough.

command

foldseek easy-cluster ./dataset/ ./res/ ./tmp/

dataset

dataset.zip

Foldssek Output (for bugs)

Query database size: 2 type: Aminoacid
Estimated memory consumption: 977M
Target database size: 2 type: Aminoacid
Index table k-mer threshold: 154 at k-mer size 6 
Index table: counting k-mers
[=================================================================] 2 0s 0ms
Index table: Masked residues: 0
No k-mer could be extracted for the database ./input_step_redundancy_ss.
Maybe the sequences length is less than 14 residues.
Error: Prefilter step 0 died
Error: Search died

Environment

foldseek Version: 9.427df8a

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant