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## Expected Behavior
I am trying to cluster based on similarity (`--similarity-type 1`) instead of the default identity (`--similarity-type 2`)
## Current Behavior
Using either parameter gives t…
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Since cluster module needs too much memory. (I have 2 million nucleotide seqs, about 30G, and 1T memory, and segment fault occurred).
I try to use LINCLUST instead. But I also want a better perf…
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## Expected Behavior
Running a cluster analysis in all 128 cores.
## Current Behavior
I'm running a clustering analysis to leave out redundant sequences in a big dataset of approximately 10 m…
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Hi
Is mmseqs deterministic? When running linclust on a large FASTA file of proteins, one would expect to get very similar clusters when rerunning the same command on the same fasta file (with defau…
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Hi, I'm encountering an issue while trying to download AlphaFold 3 databases.
During the download process, I received the following error message:
```shell
Fetching databases to ../af3_require_…
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I tried to run `mmseqs easy-linclust` on the MERC dataset (from http://gwdu111.gwdg.de/~compbiol/plass/2018_08/) but got a segmentation fault.
## Expected Behavior
Normal output of `mmseqs easy-li…
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Hi, I think there is some inconsistency in `extractalignedregion` module to generate database with regions.
I'm trying to cluster aligned regions belonging to a db.
```
mmseqs search id_0.3cov_…
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My command:
```
mmseqs createdb 1831648_seqs.fasta 1831648_seqs.mmseqs2db
mmseqs cluster 1831648_seqs.mmseqs2db 1831648_seqs.mmseqs2clu tmp --cov-mode 0 -c 0.85 --min-seq-id 0.95 --threads 112
```…
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I'm currently testing linclust using the easy-linclust workflow with very small datasets (100 / 1000 sequences). Each sequence is a nucleotide sequence, on average, 3000 basepairs long. So using 20 …
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## Expected Behavior
I'm trying to cluster my large protein sequence file (1400412352 entries, wc -l all.mmseqDB.index) with:
## Current Behavior
`mmseqs cluster all.mmseqDB all.95.clu tmp -s 7.5…