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EBI-Metagenomics / EukCC

Tool to estimate genome quality of microbial eukaryotes
GNU General Public License v3.0
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FileNotFoundError: [Errno 2] No such file or directory: 'hmmsearch' #8

Closed openpaul closed 4 years ago

openpaul commented 4 years ago

With the current version 0.2 in bioconda pplacer and hmmer are not getting installed. This will be fixed soon, but in case you get this error please make sure to install hmmer and pplacer manually in the conda environment:

conda install -c bioconda hmmer pplacer

Hope to have this fixed soon.

openpaul commented 4 years ago

This should be fixed now

OnlineArts commented 3 years ago

I've installed it today following you guide on readthedocs and it failed by: pplacer is not installed 09/23/2020 12:36:53: Placing proteins in tree Pplacer failed with unkown reason

Even your suggested conda install command above does not help. What can I do? I'm using Ubuntu 18.04 LTS.

openpaul commented 3 years ago

It seems pplacer was not installed or loaded by conda. Pplacer needs to be availiable in your path.

Can you do a 

which pplacer

And 

which hmmsearch

Both should give something like /home/paul/.miniconda3/bin/pplacer. If they result in pplacer not found, you dont have them installed correctly.

OnlineArts commented 3 years ago

Hey Paul, thank you very much. Indeed, it was a problem by conda :-) I've solved that. Conda did not load correctful the environment. Thank you for your response.