sokrypton / sokrypton/ColabFold
'Nan' or Not-a-number issue with running ColabFold
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Description
Just this afternoon (Mon Feb 27), my ColabFold AF2.3.1 multimer runs suddenly started exhibiting odd "Nan" (which = Not-a-number) values for the pLDDT, pTM and ipTM metrics, and accordingly, the program crashes (see error msgs below) at the end of the Model1 run. I've repeated this with a number of different sequences, rebooted the Colab with no changes, etc. Thx in advance for your expert help and advice.
023-02-27 21:11:34,081 Setting max_seq=508, max_extra_seq=2048
2023-02-27 21:12:16,142 alphafold2_multimer_v3_model_1_seed_000 recycle=0 pLDDT=nan pTM=nan ipTM=nan
2023-02-27 21:12:22,278 alphafold2_multimer_v3_model_1_seed_000 recycle=1 pLDDT=nan pTM=nan ipTM=nan tol=nan
2023-02-27 21:12:28,461 alphafold2_multimer_v3_model_1_seed_000 recycle=2 pLDDT=nan pTM=nan ipTM=nan tol=nan
2023-02-27 21:12:34,688 alphafold2_multimer_v3_model_1_seed_000 recycle=3 pLDDT=nan pTM=nan ipTM=nan tol=nan
2023-02-27 21:12:40,963 alphafold2_multimer_v3_model_1_seed_000 recycle=4 pLDDT=nan pTM=nan ipTM=nan tol=nan
2023-02-27 21:12:47,300 alphafold2_multimer_v3_model_1_seed_000 recycle=5 pLDDT=nan pTM=nan ipTM=nan tol=nan
2023-02-27 21:12:53,677 alphafold2_multimer_v3_model_1_seed_000 recycle=6 pLDDT=nan pTM=nan ipTM=nan tol=nan
2023-02-27 21:13:00,076 alphafold2_multimer_v3_model_1_seed_000 recycle=7 pLDDT=nan pTM=nan ipTM=nan tol=nan
2023-02-27 21:13:06,486 alphafold2_multimer_v3_model_1_seed_000 recycle=8 pLDDT=nan pTM=nan ipTM=nan tol=nan
2023-02-27 21:13:12,943 alphafold2_multimer_v3_model_1_seed_000 recycle=9 pLDDT=nan pTM=nan ipTM=nan tol=nan
2023-02-27 21:13:19,443 alphafold2_multimer_v3_model_1_seed_000 recycle=10 pLDDT=nan pTM=nan ipTM=nan tol=nan
2023-02-27 21:13:25,990 alphafold2_multimer_v3_model_1_seed_000 recycle=11 pLDDT=nan pTM=nan ipTM=nan tol=nan
2023-02-27 21:13:32,512 alphafold2_multimer_v3_model_1_seed_000 recycle=12 pLDDT=nan pTM=nan ipTM=nan tol=nan
2023-02-27 21:13:32,514 alphafold2_multimer_v3_model_1_seed_000 took 113.3s (12 recycles)
LinAlgError Traceback (most recent call last)
in
64
65 download_alphafold_params(model_type, Path("."))
---> 66 results = run(
67 queries=queries,
68 result_dir=result_dir,
8 frames
/usr/local/lib/python3.8/dist-packages/numpy/linalg/linalg.py in _raise_linalgerror_svd_nonconvergence(err, flag)
95
96 def _raise_linalgerror_svd_nonconvergence(err, flag):
---> 97 raise LinAlgError("SVD did not converge")
98
99 def _raise_linalgerror_lstsq(err, flag):
LinAlgError: SVD did not converge
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
The report identifies a Colab notebook entry point calling run(...) and a NumPy SVD traceback, but no repository file or test. Start by reproducing the NaN metrics and tracing them from run(...) to the failing SVD; done means identifying the cause and verifying a fix for the reported multimer run.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, numpy, python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100