I cannot run plmDCA

I could not run plmDCA with the latest docker environments. It kept crashing. I tried to resolve the issue, but I could not.

Following is the error message. [2019-11-12 15:06:28.109831] potts running. inserting gaps... Reformatted /data/1ubqA/1ubqA.a3m with 2018 sequences from a3m to a2m and written to file /data/1ubqA/1ubqA.a2m terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc /opt/entrypoint.sh: line 2: 6 Aborted (core dumped) /usr/bin/python3 /opt/prospr.py $@

And, I dug into the issue, and I found that hhblits.py could not import the plmDCA_asymmetric library with the following message. Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib64/python3.6/threading.py", line 916, in _bootstrap_inner self.run() File "/opt/prospr/hhblits.py", line 90, in run p = plmDCA_asymmetric.initialize() File "/usr/local/lib/python3.6/site-packages/plmDCA_asymmetric/__init__.py", line 305, in initialize return _pir.initialize_package() File "/usr/local/lib/python3.6/site-packages/plmDCA_asymmetric/__init__.py", line 253, in initialize_package package_handle.initialize() File "/usr/local/MATLAB/MATLAB_Runtime/v94/toolbox/compiler_sdk/pysdk_py/matlab_pysdk/runtime/deployablepackage.py", line 33, in initialize mcr_handle = self.__cppext_handle.startMatlabRuntimeInstance(self.__ctf_path) SystemError: CTF file '/usr/local/lib/python3.6/site-packages/plmDCA_asymmetric/plmDCA_asymmetric.ctf' failed to open for 'Read' access. Error message: 'Could not open source package'

[Lorenzo360]

https://files.physics.byu.edu/data/prospr/potts-code/ This has the whole python package and installer. You’ll need Matlab 2018a or Matlab redistributable (free) 2018a for it to work …

I would like to run prospr outside of docker, but failed with plmDCA_asymmetric. I used the .ctf file from https://files.physics.byu.edu/data/prospr/potts-code/ and get the following error message:

Index in position 3 exceeds array bounds.
Error in plmDCA_asymmetric (line 153)

Is this precompiled plmDCA version not patched yet? @YoshitakaMo seems to have found a solution. Unfortunately, I do not have a Matlab compiler, so I cannot apply the suggested changes. It would be great if you could share the patched .ctf file

[Tass0sm]

From what I remember, I compiled plmDCA asymmetric following the instructions in the readme at this repository: https://github.com/Urinx/alphafold_pytorch.

However, that repository does not use the modified version of plmDCA that this one does. All of the required modifications are described in src/potts.patch. That patch is unfortunately missing some modifications which results in a non-functional plmDCA file. The solution for me was using the code mentioned above in this issue by YoshitakaMo on Jan 9, 2020.

The instructions from alphafold_pytorch also fortunately use octave instead of MATLAB, so it can be done for free and without any proprietary code. It worked well for me.

I might be forgetting something so please respond if there is still something missing. I’m making a fork of this repository which will hopefully be more functional and well documented.