FoldSeek freezes when Run when run in parallel

[Pooryamb]

Hi,

I have realized when I search against my target database in parallel mode, foldseek freezes. Yet, when I run it in single-threaded mode, it has no problem. The issue only arises with my attached target database. I could search my proteins against other databases without any problems.

Expected Behavior

Current Behavior

Steps to Reproduce (for bugs)

I have included the scripts for both single and multi-threaded runs in the attached file. Extract the attached file and run .sh files within the extracted directory.

Foldssek Output (for bugs)

When run in multi-threaded mode, FoldSeek freezes during the prefiltering.

Context

Providing context helps us come up with a solution and improve our documentation for the future.

The target database is a database of cut protein structures. I have made the _ss file by cutting the states sequence from full-length structures.

Your Environment

I used static installations and conda.

Link to the attachment (expires in 1 year) Attachment

[milot-mirdita]

Can you please post the terminal output too?

[Pooryamb]

Thanks for your reply! Here you are: log_multithread.txt log_singlethread.txt

[Pooryamb]

Hi again,

I just noticed even though the FoldSeek run proceeds without an error on a single thread, its output is lossy. As I said in the first message, I have modified by _ss file by cutting the 3Di sequence of the Full-Length structure and replacing the _ss files. When I repeat the search by using the original 3Di sequence (and not replacing it), the output size is nearly ten times more than using modified _ss sequences. However, when I use foldseek v4, the output sizes are comparable. I am resending the files. This time, I have also attached the database with the original 3Di sequences are there too. Scripts are also included in the tar file

Link to download attachment (expires in 1 year): link