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bvalot / pyMLST

whole genome MLST analysis
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Error: BLAT binary was not found #18

Closed charlie-durant closed 9 months ago

charlie-durant commented 9 months ago

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 commented 9 months ago

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 commented 9 months ago

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.```