uniprotKB database setup error

[mhyleung]

Dear all

I have been creating multiple github issue posts here, mainly trying to set up SLURM capabilities on AWS (recent thread here). We have since then returned back in trying to set up HPC in our local server, which means that agnostos had to be set up again.

Having said that, while I was trying to download/setup the UniProtKB database with MMSEQS, I encounter the following messages:

"${MMSEQS}" databases "UniProtKB" uniprotKB tmp --remove-tmp-files 1 -v 0
databases UniProtKB uniprotKB tmp --remove-tmp-files 1 -v 0

MMseqs Version:                 2f1db01c5109b07db23dc06df9d232e82b1b4b99-MPI
Force restart with latest tmp   false
Remove temporary files          true
Compressed                      0
Threads                         96
Verbosity                       0

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   151  100   151    0     0   1129      0 --:--:-- --:--:-- --:--:--  1135
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 86.6M  100 86.6M    0     0  7105k      0  0:00:12  0:00:12 --:--:--  9.7M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 52.7G  100 52.7G    0     0  5136k      0  2:59:28  2:59:28 --:--:-- 5332k
createdb tmp/9145239893181210742/uniprot_sprot.fasta.gz tmp/9145239893181210742/uniprot_trembl.fasta.gz uniprotKB --compressed 0 -v 0

Converting sequences
[230895596] 23m 20s 481ms
Time for merging to uniprotKB_h: 0h 2m 34s 996ms
Time for merging to uniprotKB: 0h 3m 30s 766ms
Database type: Aminoacid
Time for processing: 0h 33m 17s 737ms
prefixid uniprotKB_h tmp/9145239893181210742/header_pref.tsv --tsv --threads 96 -v 0

[=================================================================] 100.00% 230.90M 19s 822ms
Time for merging to header_pref.tsv: 0h 2m 45s 511ms
Time for processing: 0h 3m 33s 500ms
Tmp tmp/9145239893181210742/taxonomy folder does not exist or is not a directory.
Create dir tmp/9145239893181210742/taxonomy
createtaxdb uniprotKB tmp/9145239893181210742/taxonomy --threads 96 -v 0

Download taxdump.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 55.2M  100 55.2M    0     0  2563k      0  0:00:22  0:00:22 --:--:-- 1738k
Database created
tmp/9145239893181210742/taxonomy/createindex.sh: 90: [: Illegal number:

I am not sure what the "illegal number" error means, and whether it is related mmseqs not recognizing my tmp/9145239893181210742/taxonomy directory...any help would be greatly appreciated.

Thank you very much

Marcus

[genomewalker]

Hi @mhyleung did you solve this? This seems an error related to MMseqs2 when creating the taxonomy files. Check if there's something in https://github.com/soedinglab/MMseqs2/issues

[mhyleung]

Hi Antonio

I just re downloaded the Uniprot KB database yesterday, and the error seems to have disappeared. Thanks!

Marcus