Error: BLAT binary was not found

[charlie-durant]

Hello, similarly to #11 I also have an issue with a BLAT error.

I was not able to install successfully using conda install -c bioconda -c conda-forge pymlst, but pip install pymlst seemed to work fine.

I have also made sure the packages listed in requirements.txt are installed. Updating .bashrc did not solve the issue as in #10 .

claMLST
I seem to create the database from import fine with no errors:

claMLST import test.db

After selecting an option (staphylococcus aureus) from the presented list:

? (136) Results found staphylococcus aureus [INFO: 2023-11-08 11:09:05,973] One element found : mlst [INFO: 2023-11-08 11:09:05,974] Downloading mlst... [INFO: 2023-11-08 11:09:11,085] Database initialized

When trying to perform a search:
claMLST search test.db Staphylococcus_aureus_test.fa

I encounter an error BLAT binary was not found:

[INFO: 2023-11-08 11:13:29,404] Search ST from files: Staphylococcus_aureus_test.fa [INFO: 2023-11-08 11:13:29,404] Search coregene with BLAT for Staphylococcus_aureus_test Error: BLAT binary was not found

wgMLST
Similarly with wgMLST, I import the database without issues:

wgMLST import test.db

After selecting an option (Staphylococcus aureus) from the presented list:

[INFO: 2023-11-08 11:16:13,023] 30 elements found, please choose one: ? (30) Results found Staphylococcus aureus [INFO: 2023-11-08 11:16:18,038] Downloading the core genome... [INFO: 2023-11-08 11:16:36,188] Reverse-complemented genes: 961 [INFO: 2023-11-08 11:16:36,191] Database initialized

But when trying to add strains to the database:
wgMLST add test.db Staphylococcus_aureus_test.fa [INFO: 2023-11-08 11:18:24,130] Search coregene with BLAT Error: BLAT binary was not found

[bvalot]

Hi,

Very strange your are not able to install by conda. Can you give me more informations?

Nevertherless, you can specify the PATH for the other binary software using the command:
pyMLST configure -h

For BLAT, you can specify PATH like this:
pyMLST configure -b /path/to/blat

[charlie-durant]

Thank you! All working once mafft and blat were installed and configured correctly. As for the conda installation problem, here is what happens when trying to install into a new conda environment:

conda install -c bioconda -c conda-forge pymlst
Collecting package metadata (current_repodata.json): done
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: The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.31=0
  - feature:/linux-64::__unix==0=0
  - feature:|@/linux-64::__glibc==2.31=0
  - pymlst -> click[version='>=7.1'] -> __unix
  - pymlst -> click[version='>=7.1'] -> __win
  - pymlst -> mafft[version='>=7.3'] -> __glibc[version='>=2.17']

Your installed version is: 2.31

Note that strict channel priority may have removed packages required for satisfiability.```