sgt_constructor.py "Could not create conda environment from /opt/anaconda3/envs/fisher/bin/bmge.yaml"

TheBrownLab / PhyloFisher

PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of eukaryotic protein sequences.

MIT License

31 stars 15 forks source link

sgt_constructor.py "Could not create conda environment from /opt/anaconda3/envs/fisher/bin/bmge.yaml" #105

Closed AlexGalvez closed 11 months ago

AlexGalvez commented 11 months ago

Hello!

First of all thank you for such an amazing tool!

At the moment I am running Phylofisher v1.2.13 and I am encountering the following error messages (command: sgt_constructor.py -i working_dataset_constructor_out_Oct.24.2023/):

error_sgt_constructor.txt

Do you have any idea of what can be causing this issue? How could I solve it?

Thanks again for your work!

Cheers,

Àlex.

atice commented 11 months ago

Hi Alex,

Thank you for contacting us. It will be Monday before Robert and I can sit down to look at this error. I apologize for the inconvenience and the delay. Thank you for choosing PhyloFisher for your work.

Alex

AlexGalvez commented 11 months ago

Hi!

No rush at all! Thanks for the support!

Àlex.

atice commented 11 months ago

Hi Alex,

If the working nodes on the cluster you are using cannot connect to the internet you may need to submit this first job to the head node just long enough for the dependencies to be installed in the conda env. Once they install just kill the job and submit your real run to the queue. Then from there you should always be able to submit directly to the queue. Sorry for this "hack" suggestion but it should keep you going until we find a longer term solution. Let us know if this does indeed solve the issue.

Alex and Robert

AlexGalvez commented 11 months ago

Hi! I think there has been a confusion. I am running Phylofisher in a personal computer with internet access!

Àlex

atice commented 11 months ago

Hi Àlex,

Thank you for this information and sorry for the confusion. Could you provide us some information about the specifications of your local machine? Regardless we would highly recommend running this step of the PhyloFisher on a large remote HPCC type resource due to the computational demands it takes to construct that many gene trees with hundreds of sequences under the LG4X model.

Alex and Robert

AlexGalvez commented 11 months ago

Hi Alex,

I erased conda and tried a fresh install (miniforge3), which seems to solve the problem. Sorry for bothering and thanks for the support!