MMseqs2

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Error: indexdb died on a server with 256 CPUs

3

## Current Behavior I did `mmseqs createdb` for [nt.gz database](https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/), and now try to index it using the following command: `/usr/bin/time -f "%P %M" mmseqs createindex --threads 8 --search-type 3...

OlgaChechekina

Unexpectedly short alignment lengths using alignall

2

## Expected Behavior Workflow: cluster -> alignall -> createtsv I noticed there are cluster members in my output with very short alignment lengths. I was expecting the aligned length to...

knishiura3

`easy-search` with `--cov-mode 1 -c 1 --greedy-best-hits` drops exact matches

4

I've bumped into what appears to be a bug when using `easy-search` with the `--greedy-best-hits` flag and `--cov-mode 1 -c 1`, where hits containing targets that fully cover the query...

milenkodespotovic

Hi, I use mmseqs2 to align genome sequences, but I found that the alignment length are always smaller than 10kb. Here are the steps describle how I use mmseqs2 1)...

xiekunwhy

mmseqs databases GTDB setup fails

8

## Expected Behavior Completes databases workflow, creating GTDB database. ## Current Behavior Error occurs near the end of the workflow. Files created: ```gtdb gtdb.dbtype gtdb_h gtdb_h.dbtype gtdb_h.index gtdb.index gtdb.source tmp```...

AroneyS

[Question] Would clusters of proteins from MMSEQS2 be considered orthologs?

1

Let's say you had 100 strains of a particular species. If you did an all-vs-all clustering of proteins, would those resulting clusters be considered orthologs?

jolespin

## Expected Behavior ## Current Behavior ## Steps to Reproduce (for bugs) Please make sure to execute the reproduction steps with newly recreated and empty tmp folders. ## MMseqs Output...

farhanquadir

Creating index for ColabDB failed on cluster.

4

Hello, I've been encountering an issue for creating index of ColabDB. It looks like it is a memory consumption issue. Could you help me with this matter please? Thank you...

IlyesAbdelhamid

Getting PSSMs from the msa output of mmseqs

2

Dear all, Does MMSeqs2 provide a way (a command) to generate PSSM profiles from the MMSeqs2 multiple sequence alignment (msa) output file out.mm_msa? I think providing such a functionality can...

rezahay

hello, I want to ask which algorithm is suitable 2blca or top-hit(mmseqs aggregatetax), when assigning taxonomy to metagenomics contigs.

zzsunday