taxidlist doesn't work

[JochenSchaefergmxde]

genevalidator -b "-taxidlist 47466_taxid.txt" -d /mnt/nvme0n1p5/blast_db/nr -s -n 32 --force -o ./47466_Borrelia_miyamotoi_nr_gv --output_formats "all" -m 32 47466_Borrelia_miyamotoi.fna
==> Analysing input arguments
*** Error: Couldn't find the BLAST tabular file: axidlist 47466_taxid.txt.

The "-t" from -taxidlist get deleted ?

I want to restrict the blast search to the genus or to the lineages

cat 47466_taxid.txt
47466
1292392
1302858
If i made it like the docu with "-gilist gi_list.txt" it doesnt accept these.

blastx: 2.15.0+
Package: blast 2.15.0, build Oct 19 2023 13:35:57
./blastn -version
blastn: 2.15.0+
Package: blast 2.15.0, build Oct 19 2023 13:35:57
./blastp -version
blastp: 2.15.0+
Package: blast 2.15.0, build Oct 19 2023 13:35:57

[IsmailM]

Hi @JochenSchaefergmxde,

Apologies for this.

I have identified the underlying issue and will try and release a fix over this coming week.

[IsmailM]

As a quick solution, the following should work:

genevalidator -b " -taxidlist 47466_taxid.txt" -d /mnt/nvme0n1p5/blast_db/nr -s -n 32 --force -o ./47466_Borrelia_miyamotoi_nr_gv --output_formats "all" -m 32 47466_Borrelia_miyamotoi.fna

Specifically, add a space at the beginning of the -b argument.

(The issue was that the Command line parser was attempting to assign -taxidlist 47466_taxid.txt to GV's -t argument)