eborobert

Thanks for the clarification and suggestions. I am now running `colabfold_search` with the precompiled binary [mmseqs-linux-gpu.tar.gz](https://mmseqs.com/latest/mmseqs-linux-gpu.tar.gz) with db-load-mode omitted. I am also not starting the gpuserver. I will let you...

Also, have there been reported cases where the MSAs from the colabfold msa server is substantially different from the ones a user computes on their local machines? If so, does...

I just completed the running with the precompiled binary with db-load-mode not set. I have attached the log file. [colabfold_github_issue_v2.txt](https://github.com/user-attachments/files/20847512/colabfold_github_issue_v2.txt) The fallouts are: 1. It took 4.5hrs to complete the...

Hi, here's the fasta file. [proteins.zip](https://github.com/user-attachments/files/20852632/proteins.zip) I realized that both the CPU and GPU version returned the MSAs for only **99/147** queries – meaning it there may be an issue...

Please forgive my ignorance. Is there a way to run mmseqs with only one fasta file containing a of proteins, but that each of them is an independent protein and...

The CPU database was set up using `MMSEQS_NO_INDEX=1`.

> Have you test colabfold_search gpu version benchmark, or how it should be fast ? I meet colabfold_search speed issue too, I query a fasta about 10 min using colabfold_search...

@yank666 Okay, thanks for the information. Can you share the number of sequences you queried and some stats like the min, max and average sequence lengths? Thanks.

I have re-setup my GPU database using the precompiled binary available at [mmseqs-linux-gpu.tar.gz](https://mmseqs.com/latest/mmseqs-linux-gpu.tar.gz). This time around, I was lucky to get a 1TB machine on my instution's HPC and decided...

> I think you are using a GPU database with MMseqs2-CPU. > > If you remove `--index-subset 2` from this script: > > [ColabFold/setup_databases.sh](https://github.com/sokrypton/ColabFold/blob/747aa90a5bac8b12c58292142dc445354bd3c36a/setup_databases.sh#L94) > > Line 94 in [747aa90](/sokrypton/ColabFold/commit/747aa90a5bac8b12c58292142dc445354bd3c36a)...