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sokrypton / ColabFold

Making Protein folding accessible to all!
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ColabFold multimer breaks down with SVD error #408

Closed TobiasMadl closed 1 year ago

TobiasMadl commented 1 year ago

Expected Behavior

Successful completion of multimer calculation, e.g.

MVWDRQTKMEYEWKPDEQGLQQILQLLKESQSPDTTIQRTVQQKLEQLNQYPDFNNYLIF VLTKLKSEDEPTRSLSGLILKNNVKAHFQNFPNGVTDFIKSECLNNIGDSSPLIRATVGI LITTIASKGELQNWPDLLPKLCSLLDSEDYNTCEGAFGALQKICEDSAEILDSDVLDRPL NIMIPKFLQFFKHSSPKIRSHAVACVNQFIISRTQALMLHIDSFIENLFALAGDEEPEVR KNVCRALVMLLEVRMDRLLPHMHNIVEYMLQRTQDQDENVALEACEFWLTLAEQPICKDV LVRHLPKLIPVLVNGMKYSDIDIILLKGDVEEDETIPDSEQDIRPRFHRSRTVAQQHDED GIEEEDDDDDEIDDDDTISDWNLRKCSAAALDVLANVYRDELLPHILPLLKELLFHHEWV VKESGILVLGAIAEGCMQGMIPYLPELIPHLIQCLSDKKALVRSITCWTLSRYAHWVVSQ PPDTYLKPLMTELLKRILDSNKRVQEAACSAFATLEEEACTELVPYLAYILDTLVFAFSK YQHKNLLILYDAIGTLADSVGHHLNKPEYIQMLMPPLIQKWNMLKDEDKDLFPLLECLSS VATALQSGFLPYCEPVYQRCVNLVQKTLAQAMLNNAQPDQYEAPDKDFMIVALDLLSGLA EGLGGNIEQLVARSNILTLMYQCMQDKMPEVRQSSFALLGDLTKACFQHVKPCIADFMPI LGTNLNPEFISVCNNATWAIGEISIQMGIEMQPYIPMVLHQLVEIINRPNTPKTLLENTA ITIGRLGYVCPQEVAPMLQQFIRPWCTSLRNIRDNEEKDSAFRGICTMISVNPSGVIQDF IFFCDAVASWINPKDDLRDMFCKILHGFKNQVGDENWRRFSDQFPLPLKERLAAFYGV : MDPGNENSATEAAAIIDLDPDFEPQSRPRSCTWPLPRPEIANQPSEPPEVEPDLGEKVHT

Current Behavior

ColabFold breaks down with SVD error for multimer calculations

Steps to Reproduce (for bugs)

Please make sure to reproduce the issue after a "Factory Reset" in Colab. If running locally ypdate you local installation colabfold_batch to the newest version. Please provide your input if you can share it.

ColabFold Output (for bugs)

Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.

2023-03-09 07:24:12,197 Setting max_seq=508, max_extra_seq=2048 2023-03-09 07:25:16,915 alphafold2_multimer_v3_model_1_seed_000 recycle=0 pLDDT=nan pTM=nan ipTM=nan 2023-03-09 07:25:46,748 alphafold2_multimer_v3_model_1_seed_000 recycle=1 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:26:16,570 alphafold2_multimer_v3_model_1_seed_000 recycle=2 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:26:46,397 alphafold2_multimer_v3_model_1_seed_000 recycle=3 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:27:16,221 alphafold2_multimer_v3_model_1_seed_000 recycle=4 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:27:46,056 alphafold2_multimer_v3_model_1_seed_000 recycle=5 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:28:15,880 alphafold2_multimer_v3_model_1_seed_000 recycle=6 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:28:45,720 alphafold2_multimer_v3_model_1_seed_000 recycle=7 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:29:15,542 alphafold2_multimer_v3_model_1_seed_000 recycle=8 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:29:45,374 alphafold2_multimer_v3_model_1_seed_000 recycle=9 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:30:15,198 alphafold2_multimer_v3_model_1_seed_000 recycle=10 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:30:45,022 alphafold2_multimer_v3_model_1_seed_000 recycle=11 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:31:14,843 alphafold2_multimer_v3_model_1_seed_000 recycle=12 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:31:44,661 alphafold2_multimer_v3_model_1_seed_000 recycle=13 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:32:14,496 alphafold2_multimer_v3_model_1_seed_000 recycle=14 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:32:44,325 alphafold2_multimer_v3_model_1_seed_000 recycle=15 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:33:14,150 alphafold2_multimer_v3_model_1_seed_000 recycle=16 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:33:43,984 alphafold2_multimer_v3_model_1_seed_000 recycle=17 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:34:13,821 alphafold2_multimer_v3_model_1_seed_000 recycle=18 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:34:43,648 alphafold2_multimer_v3_model_1_seed_000 recycle=19 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:35:13,484 alphafold2_multimer_v3_model_1_seed_000 recycle=20 pLDDT=nan pTM=nan ipTM=nan tol=nan 2023-03-09 07:35:13,486 alphafold2_multimer_v3_model_1_seed_000 took 657.2s (20 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/python3.9/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

Context

Providing context helps us come up with a solution and improve our documentation for the future.

See above. Breaks down since this week. Last week's calculations using the same settings worked.

Your Environment

Include as many relevant details about the environment you experienced the bug in.

milot-mirdita commented 1 year ago

Does this error occur on on Google Colab or in a local installation?

TobiasMadl commented 1 year ago

Thank you for your quick reply. It happens on Google Colab. Best wishes, Tobias

Am 09.03.2023 um 10:01 schrieb Milot Mirdita:

Does this error occur on on Google Colab or in a local installation?

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milot-mirdita commented 1 year ago

Did you change any of the default options? E.g. enable amber, enable templates, etc.

TobiasMadl commented 1 year ago

No

Am 09.03.2023 um 10:14 schrieb Milot Mirdita:

Did you change any of the default options? E.g. enable amber, enable templates, etc.

— Reply to this email directly, view it on GitHubhttps://github.com/sokrypton/ColabFold/issues/408#issuecomment-1461625892, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A6L4PQN7KE5F6FO5P23KQMLW3GNQJANCNFSM6AAAAAAVUYVP6E. You are receiving this because you authored the thread.Message ID: @.***>

milot-mirdita commented 1 year ago

It seems to work correctly for me. I can't reproduce the error. Can you try starting a completely new session? You are using the main notebook right (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb)?

TobiasMadl commented 1 year ago

Thank you for your suggestions

I restarted Firefox, the website and the calculation using the standard settings and a homodimer.

It seems to work now.

Thanks a lot, Tobias

Am 09.03.2023 um 10:21 schrieb Milot Mirdita:

It seems to work correctly for me. I can't reproduce the error. Can you try starting a completely new session? You are using the main notebook right (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb)?

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