search

klebgenomics / Kleborate

GNU General Public License v3.0
117 stars 49 forks source link

could not find makeblastdb #71

Closed revaoleg closed 10 months ago

revaoleg commented 1 year ago

Hello! The program was properly installed on Windows (Python 3.11.4) and Linux (Python 3.9) with the latest Biopython installation. Any attempts to run the program caused the following error:

kleborate -o results.txt -a *.fasta ... BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( Error: could not find makeblastdb

Is it because a Biopython version mismatch? Are there any solutions? Have a good day! Oleg

revaoleg commented 1 year ago

The problem was solved. It should be noted in the requirements that ncbi-blast+ and mash must be installed in advance.

katholt commented 10 months ago

thanks, this is indeed noted in the install instructions https://github.com/klebgenomics/Kleborate/wiki/Installation