Error: BLAT binary was not found/KMA binary was not found

[sunx0766]

Hi Benoit,

Thanks for your quick response regarding issue #9, however, another problem has arose when I tried to add my strains to the database. My input was: wgMLST add strep.db seq_of_interest.fna where strep.db was creating following your instruction on issue #9, and seq_of_interest.fna is my genome fasta file. The error message I got was: Error: BLAT binary was not found.

I also tried using raw reads files with the wgMLST add2 option. My input was: wgMLST add2 strep.db raw_R1_fastq.gz raw_R2_fastq.gz where the fastq files are raw illumina reads. I then got this error: Error: KMA binary was not found Could you kindly point me to where could have gone wrong?

Thanks, Erica

[bvalot]

Hello Erika,

You need to install other tools that depends pyMLST. https://github.com/bvalot/pyMLST#dependancy

If you have conda, you can install pyMLST and dependancy directly: https://github.com/bvalot/pyMLST#automatic-installation

[sunx0766]

Hi Benoit,

The problem is solved now, and I have successfully ran wgMLST :) Thank you again for such a great tool!

I wasn't able to do conda install and kept getting the errors like this:

Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.                                       
failed
UnsatisfiableError:

I ended up having to update my .bashrc and .condarc files. Hope this may help whoever encounter the same problem in the future!

[bvalot]

Thx for the reply.

In fact, I forgot a dependency of channel for this installation. The correct command line was: conda install -c bioconda -c conda-forge pymlst