Running IgBlast Mac / Error

Question

[cneha]

I am new to Ig repertoire analysis and mac usage. I am trying to run standalone IgBlast. When I try to run IgBlast it gives an error :

BLAST query/options error: Germline annotation database mouse/mouse_V could not be found in [internal_data] directory

Please refer to the BLAST+ user manual.

I checked the internal_data directory and it has the mouse_V file.

I did not need to add path to igBlast as it was added during installation.

How can I fix it?

Thanks!

[R.T. Canterbury]

I have this same question and observed the same error but for Windows. I also performed the exporting of the database directory as IGDATA to no avail. It seems like nobody has the specific answer to this question and you posted two years ago. Any luck?

Answer 1

[camole]

I had the same issue and was able to solve it. The Germline annotation database cannot be found or the internal_data cannot be found issues were both probably caused by an improper value of the IGDATA variable. Maybe try these below:

1. Make sure you have the correct directory structure.

2. Need to export IGDATA=path/to/bin/folder. Note that the IGDATA should point to the bin folder and not the internal_data folder. If you're running Conda (or an virtual environment), do NOT add IGDATA as the virtual environment variable, like what you do with conda env config vars. Directly export it.

3. For IGDATA, supply an absolute path (from the root) instead of a relative path (from a certain folder)

4. Your absolute path should not contain spaces (might as well avoid _ and - in the directory names as well). For step-by-step guide on database setup, this might be helpful: https://github.com/xinyu-dev/igblast