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python3 docker/run_docker.py \
--fasta_paths=complex1.fasta \
--max_template_date=2022-12-30 \
--model_preset=multimer \
--data_dir=/data --gpu_devices=0,1,2,3 > complex1.log &
1) The program was always calculating the model until now.
I0107 01:49:08.176561 140086208259904 run_docker.py:255... | {
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"Thanks for your pull request! It looks like this may be your first contribution to a Google open source project. Before we can look at your pull request, you'll need to sign a Contributor License Agreement (CLA).\n\nView this [failed invocation](https://github.com/deepmind/alphafold/pull/672/checks?check_run_id=10... | 2022-12-30T17:02:08 | 2022-12-30T17:08:29 | null | NONE | null | When running the Google Colab notebook implementation cell `5. Run AlphaFold and download prediction` is throwing the following error:
```
NotImplementedError Traceback (most recent call last)
[<ipython-input-1-bc0091fa34e2>](https://localhost:8080/#) in <module>()
577 sequence = 'AKIGLF... | {
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"Replace ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz with https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90. fasta.gz solves the problem of not being able to download\r\n\r\n"
] | 2022-12-29T02:30:48 | 2022-12-29T02:41:03 | null | NONE | null | 
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"Thanks for your pull request! It looks like this may be your first contribution to a Google open source project. Before we can look at your pull request, you'll need to sign a Contributor License Agreement (CLA).\n\nView this [failed invocation](https://github.com/deepmind/alphafold/pull/670/checks?check_run_id=10... | 2022-12-28T07:04:19 | 2022-12-28T07:09:03 | null | NONE | null | [Alphafold database](https://github.com/deepmind/alphafold/tree/main/afdb) cif-s are annotated with capitalized PEPTIDE. Parsing these files with the existing case-sensitive function results in empty `mmcif_object`. Suggest switching to case-insensitive parsing. | {
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"Hi @sz-1002 \r\nI am having the same issue on the relaxation step.\r\nhttps://github.com/deepmind/alphafold/issues/660\r\n\r\nI tried with newer version of CUDA (11.6) and had the same issue.",
"Hi @leiterenato \r\nThanks for letting me know! Hopefully there will be a solution for this.",
"a different non-rela... | 2022-12-26T08:22:37 | 2023-01-05T10:37:26 | null | NONE | null | Hi!
I am trying to run AlphaFold 2.3.0 multimer and encountered this error: `Execution of replica 0 failed: INTERNAL: Failed to load in-memory CUBIN: CUDA_ERROR_ILLEGAL_ADDRESS: an illegal memory access was encountered` (see details below). I was wondering if you could help me resolve it? Thank you very much!!
... | {
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Here is what I am getting:
<img width="1234" alt="Alpha fold " sr... | {
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"Could you try running with `--db_preset=reduced_dbs`?",
"My preference is to use full_dbs, but I will try.",
"I enabled --db_preset=reduced_dbs and ran into the same issue after about 40 minutes. It really seems like swap is not being used... or do I just need to scale up RAM.",
"What stage is it working on ... | 2022-12-22T18:15:57 | 2023-01-06T21:47:36 | null | NONE | null | I am running predictions for 2500 residue protein on a system with 80GB RAM, 8TB diskspace, and 1TB swap running Alphafold v2.2 via docker. The process fails with the message "RuntimeError: Resource exhausted: Out of memory while trying to allocate 51935261664 bytes." The ram was upgraded to 128GB, but the job dies wit... | {
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"While you certainly can do this with AlphaFold, you will probably only explore \"near-native\" conformations with it, because of what it is trained to produce (crystal structures). If you want to explore conformational space more thoroughly, I would recommend using molecular dynamics.\r\nIf you would like to use A... | 2022-12-22T14:17:35 | 2022-12-22T16:15:23 | null | NONE | null | Hi all
I'm new to the field. I would like to generate between 100 and 50 models for my target sequence to explore conformal flexibility of a specific region. This region is often (comparing prediction on my target and various orthologs) predicted with lower confidence, and sometimes with different conformation. We ... | {
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"Is this affecting only one or two of your structures, or is there a widespread degradation in quality?\r\n\r\nMonomer models should be unchanged by v.2.3.0, but the msa databases used to generate the inputs to the monomer model have been updated. it is possible that for some targets this can reduce the quality of ... | 2022-12-21T10:18:24 | 2022-12-21T17:28:15 | null | NONE | null | I run AlphaFold Colab with a lot of similar peptides which are characterized by alpha helices and beta sheets. I always get nice structures with the right assumed conformation, but since the new version of AlphaFold Colab is released structure prediction went wrong. I attach two predictions of the same sequence, one is... | {
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"If the pdb files come from a non-Alphafold model, any confidence metrics will be output by that other model.\r\n\r\nOne has to run the alphafold model to get alphafold confidence metrics, since those metrics are the models own measure of its certainty.",
"If you have the .npz files from the AlphaFold variant, yo... | 2022-12-20T22:21:02 | 2022-12-23T17:45:01 | 2022-12-23T17:45:00 | NONE | null | Hello,
I've found the lddt script here but am unsure how to implement it outside of the AlphaFold. Recently I've obtained many predictions using a variant of AlphaFold, however it did not include pLDDT scores in the PDB outputs. Is there a way to calculate the scores retroactively using the PDB outputs?
Thank you... | {
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"The uniref30 db has been updated in v2.3.0 which can cause different behaviour for this hhblits search. HHBlits is sensitive and the new db can cause errors for some targets which did not error before.\r\n\r\nA suggested workaround is to try with the db_preset flag set to 'reduced_dbs'.",
"There seems to be anot... | 2022-12-20T21:35:55 | 2023-01-04T22:13:29 | null | NONE | null | AlphaFold is crashing due to an HHblits error in v2.3.0 but not in v2.2.4. This happens, for example, with the input sequence:
>chain_A
LEVQVPEDPVVALVGTDATLCCSFSPEPGFSLAQLNLIWQLTDTKQLVHSFAEGQDQGSAYANRTALFPDLLAQGNASLRLQRVRVADEGSFTCFVSIRDFGSAAVSLQVAAPYSKPSMTLEPNKDLRPGDTVTITCSSYQGYPEAEVFWQDGQGVPLTGNVTTSQMANEQGLFDVHSILRV... | {
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"we are looking into this, but might not come back with something until after the holiday period.\r\n\r\ncan i check: if you run inference+relax all in v2.2.4, rather than inference and then separately relax, it does work?",
"Hi @joshabramson \r\n\r\nI tried to run v2.3.0 using the `run_docker.py` from `https://g... | 2022-12-20T19:46:41 | 2022-12-23T19:58:21 | null | NONE | null | Relaxation step is failing for multimers using AlphaFold v2.3.0.
Monomers are working fine.
Error:
```
jaxlib.xla_extension.XlaRuntimeError: INTERNAL: Failed to load in-memory CUBIN: CUDA_ERROR_ILLEGAL_ADDRESS: an illegal memory access was encountered
E external/org_tensorflow/tensorflow/compiler/xla/stream_exec... | {
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"Hi @lamyankin \r\nI had the same issue with a different file from `pdb_mmcif`. \r\nI solved this problem by downloading a newer version of the database.",
"Hi, glad to hear your reply!\r\nDid you download the newer pdb_mmcif database or all databases ?",
"I downloaded the full database again (but I don't thi... | 2022-12-18T12:02:11 | 2022-12-20T13:16:10 | null | NONE | null | I am running the alphafold multimer to predict a complex composed of A and B and the problem occurs , here are the error message:
1218 18:46:51.980194 139874231673472 run_docker.py:255] Traceback (most recent call last):
I1218 18:46:51.980485 139874231673472 run_docker.py:255] File "/app/alphafold/run_alphafold.py"... | {
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"@lamyankin \r\nWhen you run the multimer system you use 5 different models and, possibly, 5 different runs for each model (each one with a different seed).\r\nTo make sure you are comparing the same results you need to check the model name and seed used to run the inference.\r\n\r\nThere are v3 (from v2.3.0) and v... | 2022-12-18T04:02:45 | 2022-12-19T20:13:33 | null | NONE | null |
I run the alphafold in different version（one is v2.2.4, another is earlier ）and get different results using the model_preset of multimer. As shown in the picture:
This is a complex composed of Cas9 a... | {
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"You need to rebuild after pulling the newest version \r\n\r\n```docker build -f docker/Dockerfile -t alphafold .```",
"Hi @AChatzigoulas\r\nThank you for your help.\r\nI still have a problem in building the docker image.\r\n\r\n`Step 11/18 : RUN wget -q -P /app/alphafold/alphafold/common/ https://git.scicore.... | 2022-12-15T19:05:05 | 2022-12-20T18:46:02 | 2022-12-20T18:46:01 | NONE | null | Hi,
I am trying to run the new ver. 2.3.0 for multimer predictions.
I had no issue with previous versions, including 2.2.4.
I tried to use direct download from the releases, and I also tried to use from git clone repository.
In both cases, I get an error message and the job terminates.
`I1215 18:59:41.374994... | {
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"I think this was caused by the changes in v2.3.0 which happened recently - your Colab notebook likely got out of sync with the code. Could you try running in a fresh notebook?\r\n https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb"
] | 2022-12-13T02:21:05 | 2022-12-13T10:32:36 | null | NONE | null | When I entered the amino acid sequence, the program reported an error：
AttributeError Traceback (most recent call last)
[<ipython-input-4-6962bd6ebd6c>](https://localhost:8080/#) in <module>
23
24 # Validate the input.
---> 25 sequences, model_type_to_use = notebook_utils.va... | {
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https://github.com/deepmind/alphafold/blob/569eb4fea3733b979cb0442750b875759dd5ecc0/README.md?plain=1#L190-L191
I may have misunderstood, but wouldn't it be helpful to explicitly add the instruction to `git pull` if fetching returns no errors/displays merge conf... | {
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"descr... | open | false | null | [] | null | [] | 2022-12-10T14:33:09 | 2022-12-11T14:25:32 | null | NONE | null | When I run the run_docker.py with the following command,
python3 docker/run_docker.py \
--fasta_paths=/data/xiaoai/alphafold2_software/alphafold-main/T1082.fasta \
--max_template_date=2020-05-14 \
--model_preset=monomer \
--db_preset=full_dbs \
--data_dir=/data/xiaoai/alphafold2_software/download_file
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"We improved the GPU usage for AlphaFold-Multimer in [v2.3.0](https://github.com/deepmind/alphafold/releases/tag/v2.3.0) - hopefully this addresses your issue. Closing this issue now, feel free to reopen if you still encounter this in v2.3.0."
] | 2022-12-07T15:06:44 | 2022-12-13T11:55:11 | 2022-12-13T11:55:11 | NONE | null | `Allocator (GPU_0_bfc) ran out of memory trying to allocate 163.17GiB (rounded to 175203296000) requested by op`
I've been using the Alphafold for more than a year, and the GPU problem is annoying many users to run complex/ long sequences.
Alphafold is not supporting multi GPUs, and it's only using one GPU core ... | {
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"solved in pr #630 \r\n\r\njust replace all tree_utils\r\n",
"Thanks, fixed in v2.3.0."
] | 2022-12-05T08:55:33 | 2022-12-13T11:55:30 | 2022-12-13T11:55:30 | NONE | null | any one knows of a solution please
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"Hi thanks for raising this. Its a duplicate of https://github.com/deepmind/alphafold/issues/648 so closing"
] | 2022-12-02T11:32:40 | 2022-12-02T14:56:42 | 2022-12-02T14:56:42 | NONE | null | Hi,
I tried to predict structures of complexes with AlphaFold Multimer using the link: https://colab.research.google.com/drive/1J1G8OC6LZwT6Tqdz4uLRmnVzj7WWgUg1?usp=sharinga
It worked well before, but a problem appeared yesterday. In step 5, "Search against genetic database", there's an import error (See below... | {
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"I have the same issue :/",
"Same issue ",
"+1",
"Hi thanks for raising this. We've updated to 3.8 in the latest [commit](https://github.com/deepmind/alphafold/commit/4494af848e41f3acd51a190d4c78d38cb1a7f85d) to match colab"
] | 2022-12-01T08:23:26 | 2022-12-02T14:30:31 | 2022-12-02T14:30:30 | NONE | null | a) ImportError: Python version mismatch: module was compiled for Python 3.7, but the interpreter version is incompatible: 3.8.15 (default, Oct 12 2022, 19:14:39)
[GCC 7.5.0].
b) ImportError: Traceback... | {
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"I got this same error since CUDA moved to v.12. I think there will need to be an update on the side of the developer team here or a downgrade in system drivers. ",
"does this error persist when using AlphaFold v2.3.0?",
"@joshabramson I think so. I did a fresh build with the newest dockerfile. Here's the outpu... | 2022-11-29T13:22:15 | 2022-12-26T05:56:10 | null | NONE | null | Hi.
A problem occurred while I was running the Alphafold.
Could I ask for help on how to solve it?
Please check the command below and if you need any information about that plase let me know.
```
jhyeon@jhyeon-Ubuntu:~/Desktop/data/SW/alphafold$ sudo python3 docker/run_docker.py --fasta_paths=T.fa --max_templat... | {
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I am trying to run Alphafold using a custom template. The template I am using as input is not published yet but I have both realspace-refined Pdb and cif files. When I am trying to run Alphafold with the unpublished Pdb, I get an error saying "no templates found”. I am wondering if is it possible to run Alphafold ... | {
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I have added GitHub repository Fork count badge that tells the visitors how many times the repository has been forked.
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I am wondering if anyone knows a website with Alphafold multimer predicted structures. The reason why I am asking this is that I am interested in exploring the PAE confusion matrix of different oligomeric structures. Also, is anyone aware of any code/rule by which we could say that a particular protein forms a ... | {
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"Did you run all the cells properly, especially the second one \"2. Download AlphaFold\"?",
"> Did you run all the cells properly, especially the second one \"2. Download AlphaFold\"?\r\n\r\nYes, the other steps are all successful. Only the last step failed. \r\n<img width=\"719\" alt=\"AlphaFold Multimer_Step2\"... | 2022-11-26T14:24:51 | 2022-12-02T11:25:16 | 2022-11-30T18:35:18 | NONE | null | Hi,
I have tried to use AlphaFold-Multimer to predict the structures of complexes, I did the prediction from the following link:
https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb
However, problem appeared in the last step, "Run AlphaFold and download prediction". The... | {
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"Colab is also broken here\r\n\r\n\r\n",
"Hi Dan, thanks for raising this. The python dependencies in colab change over time, which means that the environment that the code... | 2022-11-24T20:54:55 | 2022-12-05T23:05:20 | 2022-11-30T18:32:15 | NONE | null | This issue is reported by others earlier, but I rase this separately as a more permanent solution is needed. I've come to rely on Colab version of Alphafold but a couple of times recently it's been down for over a week without us having any idea when it would be fixed
Would it be possible to make a second version a... | {
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"Same error here but unsure how to solve it",
"This is an upgrade from google, the newest version of colab by default takes up jax 0.3.25 (https://colab.research.google.com/notebooks/relnotes.ipynb#scrollTo=iOWrh41ocOca) which has no support for 'jax_experimental_name_stack', I have solved this issue by downgradi... | 2022-11-23T16:22:49 | 2022-11-28T20:09:13 | 2022-11-28T20:09:12 | NONE | null | After running AF Colab multimer for weeks, it started to get unstable this week. Recently it has crashed multiple times. Each when starting task 5 (Run AlphaFold and download prediction) the system crashes within no time although I am Prolab+ user.
The following or similar error message occurs, which is similar to wh... | {
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https://api.github.com/repos/deepmind/alphafold/issues/636 | https://api.github.com/repos/deepmind/alphafold | https://api.github.com/repos/deepmind/alphafold/issues/636/labels{/name} | https://api.github.com/repos/deepmind/alphafold/issues/636/comments | https://api.github.com/repos/deepmind/alphafold/issues/636/events | https://github.com/deepmind/alphafold/issues/636 | 1,462,018,485 | I_kwDOFoWQLM5XJKG1 | 636 | Running without MSA features | {
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I modified alphafold so that it takes my own custom template features. I would like to modify it again so that it runs without MSAs features. Is there any convenient way to do this ?
Does setting all the MSAs features to 0 is equivalent to no MSAs features ?
Thank you,
Gabriel. | {
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https://api.github.com/repos/deepmind/alphafold/issues/635 | https://api.github.com/repos/deepmind/alphafold | https://api.github.com/repos/deepmind/alphafold/issues/635/labels{/name} | https://api.github.com/repos/deepmind/alphafold/issues/635/comments | https://api.github.com/repos/deepmind/alphafold/issues/635/events | https://github.com/deepmind/alphafold/issues/635 | 1,460,435,030 | I_kwDOFoWQLM5XDHhW | 635 | AttributeError: 'Config' object has no attribute 'jax_experimental_name_stack' | {
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"Hi! I'm getting the same error. It seems like Colab version of AlphaFold uses JAX v0.3.25. `jax.config.jax_experimental_name_stack` was removed in this version. If you manage to use older version of JAX with this Colab notebook, I guess it would work.",
"Hi! I'm also receiving this error. The AlphaFold `requirem... | 2022-11-22T19:24:16 | 2022-11-28T20:58:33 | 2022-11-28T20:13:53 | NONE | null | Hello,
I am predicting protein multimers using AlphaFold2 however it always failed and showed something like the following:
UnfilteredStackTrace Traceback (most recent call last)
[<ipython-input-5-ca4ee2dc266d>](https://localhost:8080/#) in <module>
44 processed_feature_dict = mode... | {
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https://api.github.com/repos/deepmind/alphafold/issues/634 | https://api.github.com/repos/deepmind/alphafold | https://api.github.com/repos/deepmind/alphafold/issues/634/labels{/name} | https://api.github.com/repos/deepmind/alphafold/issues/634/comments | https://api.github.com/repos/deepmind/alphafold/issues/634/events | https://github.com/deepmind/alphafold/issues/634 | 1,460,318,554 | I_kwDOFoWQLM5XCrFa | 634 | AlphaFold Colab crashing at cell 5 | {
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"This is the full Stack Trace:\r\n```\r\n/opt/conda/lib/python3.7/site-packages/haiku/_src/data_structures.py:144: FutureWarning: jax.tree_flatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_flatten instead.\r\n leaves, treedef = jax.tree_flatten(tree)\r\n/opt/conda/lib/python3.7... | 2022-11-22T17:58:00 | 2022-11-28T21:02:53 | 2022-11-28T21:02:53 | NONE | null | Today I've tried to run Colab version of AlphaFold v2.2.4, but it crashed every time while executing cell number 5. I'm getting these errors:
**AttributeError: 'Config' object has no attribute 'jax_experimental_name_stack'**
**'Config' object has no attribute 'jax_experimental_name_stack'** | {
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