soedinglab / MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite
https://mmseqs.com
MIT License
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Kalamari database link out of data #531

Closed Mattstorey closed 2 years ago

Mattstorey commented 2 years ago

Expected Behavior

mmseqs databases Kalamari kalamari tmp should grab the "Kalamari" sequences and produce a taxonomy database.

Current Behavior

Fails to download anything and database creation crashes. Inspection of the ../data/workflow/databases.sh script shows the link to download a .tsv file from the kalamari repo is no longer valid.

Steps to Reproduce (for bugs)

mmseqs databases Kalamari kalamari tmp

MMseqs Output (for bugs)

databases Kalamari kalamari tmp 

MMseqs Version:                 fcf52600801a73e95fd74068e1bb1afb437d719d
Force restart with latest tmp   false
Remove temporary files          false
Compressed                      0
Threads                         8
Verbosity                       3

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100    14  100    14    0     0     34      0 --:--:-- --:--:-- --:--:--    34
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100    32    0    32    0     0     24      0 --:--:--  0:00:01 --:--:--    24
createdb tmp/10928370746232574590/kalamari.fasta kalamari --compressed 0 -v 3 

Converting sequences

Time for merging to kalamari_h: 0h 0m 0s 3ms
Time for merging to kalamari: 0h 0m 0s 3ms
Database type: Nucleotide
The input files have no entry:  - tmp/10928370746232574590/kalamari.fasta
Please check your input files. Only files in fasta/fastq[.gz|bz2] are supported
Error: createdb died

Context

Updating the link might partially resolve the error. I have tried a manual download of the Kalamari database but can't get the final taxonomy database to be successfully produced.

Your Environment

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

martin-steinegger commented 2 years ago

I have changed the link pointing to a commit that contains the 3.7v tsv file.