Hi all! I am trying to import the nt database into qiime2. I am doing this all on the university cluster. I am using qiime2 version 2023.9.
My code that I am using:
qiime tools import
--type 'BLASTDB'
--input-path /scratch/nt_database
--output-path full_blast_db.qza
My error message:
There was a problem importing /scratch/nt_database:
Unrecognized file (/scratch/nt_database/nt.095.nhi) for BLASTDBDirFmtV5.
I am not entirely sure what to do, I thought the file was the problem but I re-downloaded the nt database from NCBI, and no difference. Any assistance is greatly appreciated!
Hello @paperwolf, can you link to the exact database you're downloading? Just to make sure I'm looking at the same version of the database as you. It appears as though they may have added a file type that we don't support at some point.
Hi @Oddant1! Thank you for your help! So I used updateblast.pl via Blast+ to download the nt database, which can also be found here. It's files nt.000 through nt.142.
I previously didn't have the .njs file so it was giving me a different error message but with that fixed the code seems to find an issue with the nt.095.nhi file.
@paperwolf I downloaded a few of the files (I don't have space for all of them), and a less than optimal solution you might try for now at least is deleting the .nhi file(s) (back them up somewhere first!) then attempting to import again.
These databases produce a bit of a challenge for us when it comes to importing. We like to have a well speced out thing to import, but these tend to be full of different file extensions that may or may not be present, and they add new ones constantly as they see fit.
I'm talking to some members of the team with more knowledge about this specific data about what to do going forward.
I figured as much. There seem to be a number of unsupported file types in there at the moment. We just had a long weekend, but I'm going to try to discuss this with some other members of the team today and see if we can come up with a reasonable plan to deal with this.
Thank you for your help!! I have been removing the files that cause issues from the folder so see if that will help. So far I have removed files with the extensions
nhi
nni
nog
nhd
nt.nal
nt.nos
taxdb.bti
Appreciate the help! And I will keep trying with the advice from the error messages in the meantime.