Trouble downloading databases after re-installing foldseek

[farreve]

Expected Behavior

Current Behavior

I installed FoldSeek onto my local server (macOS M1) and have found that when I don't use it for a few days, it requires being uninstalled and then reinstalled to be used. This is no issue (and could easily be due to something on my end), however, after I reinstall I am unable to to run FoldSeek on previously downloaded databases nor redownload them.

Steps to Reproduce (for bugs)

1. To uninstall FoldSeek, I have simply deleted the directory and its associated tmp folder.
2. I then redownload using the OSX wget command: wget https://mmseqs.com/foldseek/foldseek-osx-universal.tar.gz; tar xvzf foldseek-osx-universal.tar.gz; export PATH=$(pwd)/foldseek/bin/:$PATH
3. I then try to either: a. redownload a previously downloaded database (eg: foldseek Alphafold/UniProt up tmp) b. run foldseek on a previously downloaded (or recently attempted to re-downloaded) database (eg: foldseek easy-search mypdb.pdb tmp)

   Foldssek Output (for bugs)

   Steps 1 and 2 run as expected. I get the following output when attempting step 3: a. Invalid Command: Alphafold/Swiss-Prot Did you mean "foldseek map"? or Invalid Command: ESMAtlas30 Did you mean "foldseek easy-cluster"? or Invalid Command: Alphafold/UniProt Did you mean "foldseek easy-search"? (depending on which database I am trying to download) b. foldseek easy-search mtpdb.pdb up output tmp

MMseqs Version: d8fab94f544fa5014274a376344c2cfd7d7530bd Seq. id. threshold 0 Coverage threshold 0 Coverage mode 0 Max reject 2147483647 Max accept 2147483647 Add backtrace false TMscore threshold 0 TMalign hit order 0 TMalign fast 1 Preload mode 0 Threads 8 Verbosity 3 LDDT threshold 0 Sort by structure bit score 1 Alignment type 2 Substitution matrix aa:3di.out,nucl:3di.out Alignment mode 3 Alignment mode 0 E-value threshold 10 Min alignment length 0 Seq. id. mode 0 Alternative alignments 0 Max sequence length 65535 Compositional bias 1 Compositional bias 1 Gap open cost aa:10,nucl:10 Gap extension cost aa:1,nucl:1 Compressed 0 Seed substitution matrix aa:3di.out,nucl:3di.out Sensitivity 9.5 k-mer length 6 Target search mode 0 k-score seq:2147483647,prof:2147483647 Max results per query 1000 Split database 0 Split mode 2 Split memory limit 0 Diagonal scoring true Exact k-mer matching 0 Mask residues 0 Mask residues probability 0.99995 Mask lower case residues 1 Minimum diagonal score 30 Selected taxa
Spaced k-mers 1 Spaced k-mer pattern
Local temporary path
Exhaustive search mode false Prefilter mode 0 Search iterations 1 Remove temporary files true MPI runner
Force restart with latest tmp false Cluster search 0 Chain name mode 0 Write mapping file 0 Mask b-factor threshold 0 Coord store mode 2 Write lookup file 1 Tar Inclusion Regex . Tar Exclusion Regex ^$ File Inclusion Regex . File Exclusion Regex ^$ Alignment format 0 Format alignment output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits Database output false Greedy best hits false

Input up does not exist

Context

Please let me know what you think might be happening and how I can address it! I greatly appreciate your feedback on this tool.

Your Environment

• Foldseek version: d8fab94f544fa5014274a376344c2cfd7d7530bd installed with wget for precompiled MacOS
• Operating system and version: Mac OS M1

[martin-steinegger]

It seems that you forgot to write a command Invalid Command: Alphafold/Swiss-Prot. Could you please try:

foldseek databases Alphafold/Swiss-Prot sp tmp 

[farreve]

Ah thank you! That was absolutely my issue. I appreciate the help!