Windows 10 Installation Problem

[rimelman]

.\mmseqs.bat --help

Expected Behavior

MMseqs2 (Many against Many sequence searching) is an open-source software suite
for very fast,
parallelized protein sequence searches and clustering of huge protein sequence d
ata sets.

Please cite: M. Steinegger and J. Soding. MMseqs2 enables sensitive protein sequ
ence searching for the analysis of massive data sets. Nature Biotechnology, doi:
10.1038/nbt.3988 (2017).

MMseqs2 Version: b0b8e85f3b8437c10a666e3ea35c78c0ad0d7ec2
© Martin Steinegger (martin.steinegger@snu.ac.kr)

usage: mmseqs <command> [<args>]

Easy workflows for plain text input/output
  easy-search           Sensitive homology search
  easy-linsearch        Fast, less sensitive homology search
  easy-cluster          Slower, sensitive clustering
  easy-linclust         Fast linear time cluster, less sensitive clustering
  easy-taxonomy         Taxonomic classification
  easy-rbh              Find reciprocal best hit
…

Current Behavior

no output

Steps to Reproduce (for bugs)

Please make sure to execute the reproduction steps with newly recreated and empty tmp folders. Zip file for respective download was extracted, and upon navigating to the mmseqs directory the '--help' help argument was input to test the installation, resulting in no output.

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 is the problem

  Context

  Providing context helps us come up with a solution and improve our documentation for the future. On this machine I have been having an ongoing issue in which cmd is unable to open in any scenario besides using another user account.

  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): none
• Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.): statically-compiled
• For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation: n/a
• Server specifications (especially CPU support for AVX2/SSE and amount of system memory): n/a
• Operating system and version: Windows 10 Home 21H1

[milot-mirdita]

I would recommend to install MMseqs2 on Windows through WSL2. See the official WSL guide for install instructions.

The mingw MMseqs2 version for Windows suffers from relatively poor memory performance in some modules. We tried to improve that, however its still slower than the Linux version.

I am not sure what your exact issue is. You might have to try to start MMseqs2 (mmseqs.bat) for the first time as administrator, so all links are setup correctly. Subsequent calls should then work without admin rights.