Closed kimdn closed 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
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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
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.
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.
I solved HMMER and other library issues by using
export HMMER=$HOME
My bin has jackhmmer, hmmbuild and hmmsearch
I could generate features.
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