run_get_good_pae.sh crashes in homo-oligomeric mode when monomers are present

[jkosinski]

Command:

singularity exec --no-home --bind /scratch/kosinski/Giardia/interactome/Group1/homooligomers:/mnt     
/g/kosinski/kosinski/devel/AlphaPulldown/alpha-analysis.sif run_get_good_pae.sh --output_dir=/mnt --cutoff=5

Error:

Traceback (most recent call last):
  File "/app/programme_notebook/get_good_inter_pae.py", line 136, in <module>
    app.run(main)
  File "/opt/conda/lib/python3.9/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/opt/conda/lib/python3.9/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/app/programme_notebook/get_good_inter_pae.py", line 110, in main
    iptm_ptm_score = json.load(open(os.path.join(result_subdir,"ranking_debug.json"),'rb'))['iptm+ptm'][best_model]
KeyError: 'iptm+ptm'

[dingquanyu]

I think this is because at least one of the homooligomers is a monomer?

I haven't updated the image yet but will avoid the crash if there is monomer

[jkosinski]

OK!

…

On Sat, Jul 16, 2022 at 6:44 PM Dingquan Yu ***@***.***> wrote: I think this is because at least one of the homooligomers is a monomer? I haven't updated the image yet but will avoid the crash if there is monomer — Reply to this email directly, view it on GitHub <#25 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAMDPOL2PZOGNIS5TOFLQFTVULRH5ANCNFSM53YKRCUQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[dingquanyu]

Is there any monomer in the directory btw?

[jkosinski]

yes, exactly, there are some, you can test on this one.

…

On Sat, Jul 16, 2022 at 7:41 PM Dingquan Yu ***@***.***> wrote: Is there any monomer in the directory btw? — Reply to this email directly, view it on GitHub <#25 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAMDPOKQ4G2D6D6CF6L2TX3VULX55ANCNFSM53YKRCUQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[dingquanyu]

Just to check if that ModuleNotFoundError: No module named 'jax' error still exists? I tried the display_pae_plots() on the same directory after activating the env with the latest alphapulldown and it finished without any error.

[jkosinski]

Yeah, am getting "ModuleNotFoundError: No module named 'jax' error" on mac but because the AlphaPulldown installation instruction does work on mac .... - can't install jax because of some version conflicts. It worked with previous versions of AP.

(AlphaPulldown) hinox:~ kosinski$ pip install -q "jax[cuda]>=0.3.8,<0.4" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
ERROR: Cannot install jax[cuda]==0.3.10, jax[cuda]==0.3.11, jax[cuda]==0.3.12, jax[cuda]==0.3.13, jax[cuda]==0.3.14, jax[cuda]==0.3.8 and jax[cuda]==0.3.9 because these package versions have conflicting dependencies.
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts

[dingquanyu]

Now the new image is uploaded here https://oc.embl.de/index.php/s/cDYsOOdXA1YmInk