databases

[CaroleBelliardo]

Expected Behavior

I try to do download database but the commande line give in the manual doesn't work

Current Behavior

error message : ' Invalid Command: databases Did you mean "mmseqs clusterupdate"? '

Steps to Reproduce (for bugs)

Please make sure to execute the reproduction steps with newly recreated and empty tmp folders. i use this line : 'mmseqs databases UniProtKB/Swiss-Prot testdb/swissprot tmp'

MMseqs Output (for bugs)

Please make sure to also post the complete output of MMseqs. You can use gist.github.com for large output. no output, just error message

Context

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

Your Environment

Include as many relevant details about the environment you experienced the bug in.

• Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters):
• Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.):
• For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation:
• Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
• Operating system and version:

[milot-mirdita]

The databases module is new, the documentation refers to the latest git version. It will be included in the next MMseqs2 release we are preparing and hopefully release in the next few days.

You can already install MMseqs2 from git or download precompiled static binaries to try out the latest features.

[CaroleBelliardo]

Thanks but i already use the version 10.6d92c. Is it the lastest, no ?

[milot-mirdita]

10.6d92c is the latest release, however we have been working on the next release. The databases module will be included in the next release. If you want to try it out already please refer to the install static or compile from source sections of the user guide:

For Linux: https://github.com/soedinglab/MMseqs2/wiki#install-static-linux-version https://github.com/soedinglab/MMseqs2/wiki#compile-from-source-under-linux For macOS: https://github.com/soedinglab/MMseqs2/wiki#install-static-macos-version

[CaroleBelliardo]

Ok! thanks for all these informations. Last question, is it also envisaged to have a refseq genomic database ? Thanks a lot for your help

[milot-mirdita]

I didn't add the RefSeq yet, since it's kind of annoying to work with (no single FASTA download available) and I thought that the NR, NT or Uniprot would cover most use-cases already. I might take another look at the RefSeq in the next few days. No promises though for now.

By the way, if you want a set of stickers (see https://twitter.com/thesteinegger/status/1201076220957315074), send me your address to milot at mirdita de.

[CaroleBelliardo]

OK, thanks

[cespos]

Hi! I have tried to use the databases module but it is still not available. Is the new MMseqs version not released yet or have you decided to not add this module?

[milot-mirdita]

It's available since a while. Are you running the latest release?