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FreshAirTonight / af2complex

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
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Error with run_fea_gen.sh #17

Closed kimdn closed 1 year ago

kimdn commented 1 year ago

I installed all requirements with pip install -r requirements.txt (also I installed AF2 already).

However, when I ran run_fea_gen.sh single_pair_of_RBD_NA.fasta I see

Screen Shot 2023-04-08 at 9 22 21 PM
FreshAirTonight commented 1 year ago

Which AF2 version are you using? AF2Complex v1.4 works with AF v2.3.x environment after you add one additional python module networkx by pip3 install networkx==2.5.

It seems that you have installed a higher version of jaxlib, try this: pip3 install jax==0.3.25 jaxlib==0.3.25+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

kimdn commented 1 year ago

I use 2.3.0 (singularity /share/apps/alphafold/2.3.0/alphafold).

pip3 install jax==0.3.25 jaxlib==0.3.25+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html solved my issue. Thank you.

I updated some paths of your run_fea_gen.sh

Now I need to solve FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-10.3.0/hmmer-3.3.2-y25u7humnxtqnaf7yc2il3misyze6pac/bin/jackhmmer'

So you specified export HMMER=/usr/local/pace-apps/spack/packages/linux-rhel7-xj6_64/gcc-10.3.0/hmmer-3.3.2-y25u7humnxtqnaf7yc2il3misyze6pac

But I don't know where my HMMER path is. Did you download it from somewhere?

For me, I don't need to specify hmmer path to run alphafold and alphafold-multimer.

FreshAirTonight commented 1 year ago

I use 2.3.0 (singularity /share/apps/alphafold/2.3.0/alphafold).

pip3 install jax==0.3.25 jaxlib==0.3.25+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html solved my issue. Thank you.

I updated some paths of your run_fea_gen.sh

Now I need to solve FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-10.3.0/hmmer-3.3.2-y25u7humnxtqnaf7yc2il3misyze6pac/bin/jackhmmer'

So you specified export HMMER=/usr/local/pace-apps/spack/packages/linux-rhel7-xj6_64/gcc-10.3.0/hmmer-3.3.2-y25u7humnxtqnaf7yc2il3misyze6pac

But I don't know where my HMMER path is. Did you download it from somewhere?

For me, I don't need to specify hmmer path to run alphafold and alphafold-multimer.

The AF2 container you used has third party tools installed within. To install them independent of the container, you need to follow this Dockerfile to install hmm, hh-suite and kalign for MSA searches.

Alternatively, when you build the container, add an additional python module networkx. Then, you should be able to use this container to run both AF2Complex and AF2.

kimdn commented 1 year ago

I solved HMMER and other library issues by using export HMMER=$HOME

My bin has jackhmmer, hmmbuild and hmmsearch

I could generate features.