I’m trying to run igblast from NCBI in windows powershell. When following the documentation and trying to run the following code:

bin/igblastn -germline_db_V database/mouse_gl_V -germline_db_J database/mouse_gl_J -germline_db_D database/mouse_gl_D -organism mouse -query myseq -auxiliary_data optional_file/mouse_gl.aux -show_translation -outfmt 3

and

bin/igblastn -germline_db_V database/V.fasta -germline_db_J database/J.fasta -germline_db_D database/D.fasta -organism rhesus_monkey -query myseq -auxiliary_data optional_file/rhesus_monkey_gl.aux -show_translation -outfmt 3

I get the following error:

BLAST query/options error: Germline annotation database C:Program FilesNCBIigblast-1.22.0internal_datarhesus_monkeyrhesus_monkey_V could not be found in [internal_data] directory
Please refer to the BLAST+ user manual.

Additionally, I’m having issues running NCBI/igblast’s and unable to create my own database references:
bin/edit_imgt_file.pl imgt_file > my_seq_file creates an empty my_seq_file and open notepad with the code or prompt to choose a program to open the .pl

I’ve tried using different os: Windows 10, 11, and on a virtual machine (Windows 11). On the virtual machine it doesn’t return the error but it doesn’t run either.

Setting environment variables or designating a path hasn’t helped.