Having issues to create a NR db with taxonomy info

[ahof1704]

I would like to run the seq similarity search against the homo sapien samples in the NR dataset. For that I downloaded the dataset as follows:

mmseqs databases NR nr tmp

Then I attempted to filter for the tax I want

mmseqs filtertaxseqdb nr nr_human --taxon-list 9606

However, I am getting the following error:
nr_mapping is empty. Rerun createtaxdb to recreate taxonomy mapping.

It is unclear what this suggestion to recreate the taxonomy means or what this command should look like. I would appreciate any help with that.

Thanks
Antonio

[ahof1704]

Hi,

I have tried following the step described on the wiki to create the mapping for NR.

I have download and ensured I have the taxonomy folder

ls -lh /root/mmseqs2_db/taxonomy/
Permissions Size User Date Modified Name
drwxr-sr-x     - root 25 Mar 13:35  .ipynb_checkpoints/
.rw-rw-r--   20M 9019 12 Mar 21:27  citations.dmp
.rw-rw-r--  4.7M 9019 12 Mar 21:25  delnodes.dmp
.rw-rw-r--   452 9019 12 Mar 21:20  division.dmp
.rw-rw-r--   16k 9019 12 Mar 21:27  gc.prt
.rw-rw-r--  4.9k 9019 12 Mar 21:20  gencode.dmp
.rw-rw-r--  3.9M 9019 12 Mar 21:25  images.dmp
.rw-rw-r--  1.4M 9019 12 Mar 21:25  merged.dmp
.rw-rw-r--  244M 9019 12 Mar 21:27  names.dmp
.rw-rw-r--  194M 9019 12 Mar 21:27  nodes.dmp
.rw-rw----  3.1k 4544 27 Apr  2023  readme.txt
.rw-rw-r--   65M root 12 Mar 21:28  taxdump.tar.gz

But when attempting to extract the fasta and the tax id mapping, I get the following error:

cd /root/mmseqs2_db
blastdbcmd -db nr -entry all > nr.fna
BLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/root/mmseqs2_db::]

I have ensured that the files for nr are available in that path

ls -lh /root/mmseqs2_db/nr*
Permissions Size User Date Modified Name
.rw-rw-r--   13G root 15 Mar 16:54  /root/mmseqs2_db/nr
.rw-rw-r--     4 root 15 Mar 16:54  /root/mmseqs2_db/nr.dbtype
.rw-r--r--     0 root 25 Mar 13:46  /root/mmseqs2_db/nr.fna
.rw-rw-r--  779M root 15 Mar 16:54  /root/mmseqs2_db/nr.index
.rw-rw-r--  790M root 15 Mar 16:55  /root/mmseqs2_db/nr.lookup
.rw-rw-r--     8 root 15 Mar 16:52  /root/mmseqs2_db/nr.source
.rw-rw-r--    11 root 15 Mar 17:03  /root/mmseqs2_db/nr.version
.rw-rw-r--  4.0G root 15 Mar 16:52  /root/mmseqs2_db/nr_h
.rw-rw-r--     4 root 15 Mar 16:52  /root/mmseqs2_db/nr_h.dbtype
.rw-rw-r--  748M root 15 Mar 16:55  /root/mmseqs2_db/nr_h.index
.rw-rw-r--     0 root 15 Mar 16:55  /root/mmseqs2_db/nr_mapping
.rw-rw-r--  708M root 15 Mar 16:55  /root/mmseqs2_db/nr_taxonomy

nr.fna is still empty. Not sure if this is a required step in order to create the nr_mapping. I would appreciate any help in getting the tax info for the NR dataset.

Thanks!

[ahof1704]

Hi, I would really appreciate some help with this. Thanks!

[milot-mirdita]

I remember blastdbcmd having issues, however, I don't remember what was wrong.

We use a different workflow to assign taxids for the NR:

MMseqs2/data/workflow/databases.sh

Line 419 in 804bb2a

"NR")

The download part for the accession2taxid files:

MMseqs2/data/workflow/databases.sh

Line 120 in 804bb2a

downloadFile "https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz" "${TMP_PATH}/nr.gz"

[ahof1704]

Sorry, not sure if I follow. Am I supposed to do any differently from what I described above to filter NR by taxonomy info?