Blast issue when trying to add species name

usegalaxy.org support
1

I’m running a blastn search to identify best hits for a large batch of sequences. I would like to return the scientific name for the best hit in the tabular data. I using the following command:

blastn  -query '/anvil/scratch/x-xcgalaxy/main/staging/70028283/inputs/dataset_921a7f8f-68ab-47c1-a502-b5de65826183.dat'   -db '"/cvmfs/data.galaxyproject.org/byhand/blastdb/nt/2023-09-01/nt"'  -task 'blastn' -evalue '1e-05' -out '/anvil/scratch/x-xcgalaxy/main/staging/70028283/outputs/dataset_eb92d3c7-bb52-43d1-b0bb-2ad4416fbb01.dat' -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore  staxids sscinames scomnames'  -num_threads "${GALAXY_SLOTS:-8}" -strand both -dust yes  -max_hsps '3'

This works as expected except that the final columns containing the species identifications (14 and 15) are empty (“N/A”).

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Upon closer inspection, I am getting the following warning:

Warning: [blastn] Taxonomy name lookup from taxid requires installation of taxdb database with ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz

How can the taxonomic database be added to the Galaxy servers?

Thanks!

Joel

2

Welcome @Joel_Brown

Yes, you are correct! The taxonomy functions are not wrapped into the BLAST+ functions directly. Instead, you can cut out the hits and run one of these tools to pull in the extra data you are interested in, then join columns as wanted.

  • Fetch taxonomic representation (find this at UseGalaxy.eu for now)
  • NCBI Datasets Gene download gene sequences and metadata

Placing all steps into a simple workflow is what most do. Then, that workflow functions in practical use as a “single custom tool” when you execute it.

For how to do this exactly, I’m guessing you already know about the our tabular data parsing tools but in case not or for anyone else reading later on: please try a search in the tool panel with common utility names, or see our tutorial here for a short tour.

Please give that a try and let us know if you have any follow up questions! :slight_smile: