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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... | 2022-12-30T17:02:08Z | 2022-12-30T17:08:29Z | 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"
] | 2022-12-29T02:30:48Z | 2022-12-29T02:41:03Z | 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... | 2022-12-28T07:04:19Z | 2022-12-28T07:09:03Z | 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... | 2022-12-26T08:22:37Z | 2023-01-05T10:37:26Z | 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 ... | 2022-12-22T18:15:57Z | 2023-01-06T21:47:36Z | 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... | 2022-12-22T14:17:35Z | 2022-12-22T16:15:23Z | 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 ... | 2022-12-21T10:18:24Z | 2022-12-21T17:28:15Z | 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... | 2022-12-20T22:21:02Z | 2022-12-23T17:45:01Z | 2022-12-23T17:45:00Z | 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... | 2022-12-20T21:35:55Z | 2023-01-04T22:13:29Z | 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... | 2022-12-20T19:46:41Z | 2022-12-23T19:58:21Z | 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... | 2022-12-18T12:02:11Z | 2022-12-20T13:16:10Z | 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... | 2022-12-18T04:02:45Z | 2022-12-19T20:13:33Z | 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.... | 2022-12-15T19:05:05Z | 2022-12-20T18:46:02Z | 2022-12-20T18:46:01Z | 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"
] | 2022-12-13T02:21:05Z | 2022-12-13T10:32:36Z | 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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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."
] | 2022-12-07T15:06:44Z | 2022-12-13T11:55:11Z | 2022-12-13T11:55:11Z | 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."
] | 2022-12-05T08:55:33Z | 2022-12-13T11:55:30Z | 2022-12-13T11:55:30Z | 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"
] | 2022-12-02T11:32:40Z | 2022-12-02T14:56:42Z | 2022-12-02T14:56:42Z | 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"
] | 2022-12-01T08:23:26Z | 2022-12-02T14:30:31Z | 2022-12-02T14:30:30Z | 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... | 2022-11-29T13:22:15Z | 2022-12-26T05:56:10Z | 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\"... | 2022-11-26T14:24:51Z | 2022-12-02T11:25:16Z | 2022-11-30T18:35:18Z | 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... | 2022-11-24T20:54:55Z | 2022-12-05T23:05:20Z | 2022-11-30T18:32:15Z | 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... | 2022-11-23T16:22:49Z | 2022-11-28T20:09:13Z | 2022-11-28T20:09:12Z | 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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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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"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... | 2022-11-22T19:24:16Z | 2022-11-28T20:58:33Z | 2022-11-28T20:13:53Z | 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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"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... | 2022-11-22T17:58:00Z | 2022-11-28T21:02:53Z | 2022-11-28T21:02:53Z | 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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"This is addressed in the \"Inferencing many proteins\" section of the README. The short answer is not exactly, but you can reduce the runtime for similar proteins by keeping the network a fixed size, and a bulk inference script could be built on the RunModel.predict method.",
"This is good to know. Could you ple... | 2022-11-16T10:52:49Z | 2022-11-17T08:37:53Z | null | NONE | null | We have built a mutant library for cucumber and have completed resequencing some of the individual plants, finding a number of proteins with non-synonymous mutations. We have translated these proteins and hope to predict the protein structure using AlphaFold2. These proteins have minimal differences from the original p... | {
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"start from jax - 0.3.15",
"Thanks, fixed in v2.3.0.",
"\r\n`\r\n File \"<stdin>\", line 1, in <module>\r\nAttributeError: module 'jax.tree_util' has no attribute 'tree_multimap'\r\n`\r\n\r\nI dont think it is fixed?\r\n\r\nUsing \r\n`jax==0.3.25\r\njaxlib==0.3.25+cuda11.cudnn82`",
"> `File \"<stdin>\", line... | 2022-11-16T07:28:04Z | 2022-12-20T02:11:39Z | 2022-12-13T11:55:55Z | NONE | null | https://github.com/google/jax/blob/c1192f383750d5d64a69c19914b7481239b9a327/jax/__init__.py#L120
jax remove `jax.tree_xxx` . use `jax.tree_util.tree_xxx` instead | {
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"[result_model_1_multimer_v2_pred_0.zip](https://github.com/deepmind/alphafold/files/10017395/result_model_1_multimer_v2_pred_0.zip)\r\n",
"you can fix this by installing jax[cpu] into your environment. At least that work with my visualizer",
"Yes installing jax and jaxlib can work. But this effects thousands ... | 2022-11-16T01:45:24Z | 2022-11-29T15:47:31Z | null | NONE | null | In AlphaFold 2.2.4 the pickled per-structure output files from a multimer prediction such as
result_model_1_multimer_v2_pred_0.pkl
now contains a JAX dependency (apparently a jax DeviceArray structure was pickled). This prevents the .pkl data from being read by Python interpreters that do not have jax instal... | {
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There are 1 security vulnerabilities found in tensorflow-cpu 2.9.0
- [CVE-2022-36000](https://www.oscs1024.com/hd/CVE-2022-36000)
### What did I do？
Upgrade tensorflow-cpu from 2.9.0 to 2.9.1 for vulnerability fix
### What did you expect to happen？
Ideally, no insecure libs should be used.
### Th... | {
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"Hi! This looks like its in ColabFold so I would suggest raising a question there. It does look like you need to rerun the earlier cells to define cf_af. Thanks!",
"Thank you so much for your help\r\n"
] | 2022-11-10T14:18:29Z | 2022-11-10T14:54:44Z | 2022-11-10T14:26:02Z | NONE | null | Dear alphafold developers,
I faced some errors while trying to predict protein structures. Finally, I obtained a predicted structure so alphafold ran normally. I am just wondering if these errors will have a major effect on the prediction or not?
Thank you so much for your help,
Best regrards,
Here are ... | {
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When `--model_preset=monomer` is used I could find `template_domain_names` as a key name of the dictionary unpickled, but not upon `--model_preset=multimer`.
```python
import pickle
with open("../feature... | {
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"This is by design, the sequences should be in all-uppercase letters, although I agree that AlphaFold should fail earlier and with a nicer error message."
] | 2022-11-09T14:00:18Z | 2022-12-13T11:58:10Z | 2022-12-13T11:58:10Z | NONE | null | In multimer mode, the following test sequence runs without error:
```
>HBA_HUMAN_2a Hemoglobin subunit alpha OS=Homo sapiens OX=9606 GN=HBA2 PE=1 SV=2
MALSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLS
HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFK
LLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
>HBB_HUMAN_2a He... | {
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"I also am getting a similar error during the hmmbuild query step :\r\n\r\n```\r\nI1110 08:13:51.837537 140292054591296 run_docker.py:255] Parse failed (sequence file /mnt/pdb_seqres_database_path/pdb_seqres.txt):\r\nI1110 08:13:51.837775 140292054591296 run_docker.py:255] Line 1366492: illegal character 0\r\n```\r... | 2022-11-03T21:07:43Z | 2022-12-13T11:56:25Z | 2022-12-13T11:56:24Z | NONE | null | Parse failed (sequence file /db/pdb_seqres/pdb_seqres.txt):
Line 1366022: illegal character 0
Errors in file:
>7ooo_B mol:na length:11 DNA (5'-D(*CP*TP*(RWQ)P*TP*CP*TP*TP*TP*G)-3')
CT05ATCTTTG
>7ooo_E mol:na length:11 DNA (5'-D(*CP*TP*(RWQ)P*TP*CP*TP*TP*TP*G)-3')
CT05ATCTTTG
>7ozz_B mol:na length:11 DNA (5'... | {
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"Based on those specs, you can probably run AlphaFold with reduced databases on your local computer, though if you do not have a dedicated graphics card it will probably be very slow.",
"Assuming you have a dedicated graphics card and do not need high speed results, you could also run with full databases on the H... | 2022-11-02T15:44:41Z | 2022-11-02T16:31:25Z | null | NONE | null | Hi,
It is possible to install and run Alpha Fold on my local computer (not on VM or cloud) with the given specification:
I9-12900 CPU
128gb ddr4-3200
Asus Prime Z690P 2tb NVME + 8TB HDD
Regards,
Gal.
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<img width="692" alt="image" src="https://user-images.githubusercontent.com/105665325/199346204-4843da4c-808a-4231-aed9-78cd723b25b3.png">
something similar to this.
Thanks | {
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"Hi thanks for raising this. Can you please provide more details e.g. about your machine, docker version etc?",
"> 嗨，谢谢你提出这个问题。您能否提供更多详细信息，例如关于您的机器、docker 版本等？\r\n\r\n
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"It is not necessary, that is a different database. Database which AlphaFold uses for inference of a new structure hasn't changed, only database that contains already predicted structures is growing but that one is not used by AlphaFold for future predictions. ",
"I thought, that the --max_template_date correspon... | 2022-10-28T07:13:41Z | 2022-11-07T13:09:37Z | null | NONE | null | Considering the more and more protein structures deposited in PDB, do I need to upgrede my AlphaFold database? and how to? | {
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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/617/checks?check_run_id=91... | 2022-10-27T21:01:21Z | 2022-10-30T21:15:38Z | null | NONE | null | Use `-p` option to make download scripts work both on Linux and macOS. | {
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"Hi! This looks like you are using AlphaPullDown, so I would suggest raising this issue on their github. From the stacktrace it looks like you may need to update your CUDA driver. The recommended version for the Alphafold repo is 11.1.1 and we provide a Docker image with a working environment. Thanks!"
] | 2022-10-27T02:51:09Z | 2022-10-27T13:39:50Z | 2022-10-27T13:39:50Z | NONE | null | Hello, I try to use the AlphafoldMultimerV2 to predict interactions between baits and candidates in pulldown mode, but every time it showed the same error, could anybody help me to deal with the error issues?
(AlphaPulldown) [LAZY@spgpu ~]$ run_multimer_jobs.py --mode=pulldown --num_cycle=3 --num_predictions_per_mod... | {
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I was trying to predict predict the structure of an octamer, and got the following error:
alphafold.data.templates.SequenceNotInTemplateError: Could not find the template sequence in 7a0l_A
Traceback (most recent call last):
File "/mnt/nas/tools/alphafold_non_docker_v220/alphafold/data/templates.py", line... | {
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"Hi thanks for the question. I haven't been able to reproduce this error. Are you using the same Dockerfile in the latest version release or have you made some changes?",
"> Hi thanks for the question. I haven't been able to reproduce this error. Are you using the same Dockerfile in the latest version release or ... | 2022-10-21T12:11:29Z | 2022-11-03T12:37:21Z | null | NONE | null | The code always reports the following error, I don't know how to solve it
```
The following packages will be UPDATED:
ca-certificates 2022.3.29-h06a4308_1 --> 2022.07.19-h06a4308_0
certifi 2021.10.8-py39h06a4308_2 --> 2022.9.24-py39h06a4308_0
conda ... | {
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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."
] | 2022-10-19T12:56:30Z | 2022-12-13T11:58:50Z | 2022-12-13T11:58:49Z | NONE | null | I am running a multimer analysis using local AlphaFold 2.2.2 installed on our server and have successfully predicted structures for monomer and multimer analyses. Recently I need to predict a protein complex using 3 protein sequences, one of which is 2482 amino acids long while other two are shorter.
I have provided... | {
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"I am expierencing the same issue with another protein not being found (7nvm) even though max_template_date is set.",
"Hi thanks for raising this. Have you updated the pdb_seqres file more recently than the PDB mmcif files? This error is likely to happen when they are out of sync. In the future we can add a more ... | 2022-10-15T09:47:08Z | 2022-12-01T05:47:14Z | null | NONE | null | Now l'm running AF2 multimer with "run_alphafold.py" . Both MSAs' generation for two chains are success, as well as the template search for the first chain. BUT python report an error during that of the second:
`FileNotFoundError: [Errno 2] No such file or directory: '.../pdb_mmcif/mmcif_files/7xiv.cif'`
The publ... | {
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"Just replacing the /geometry/, r3.py and quat_affine.py math functions with GA equivalents should not have to be a lot of work, come to think of it, as long as the state representations are kept the same..",
"Note that the current JAX backend only implements array-of-struct memory layout multivectors. Adding sup... | 2022-10-14T10:37:34Z | 2022-10-17T15:06:50Z | null | NONE | null | Ive recently authored a [geometric algebra](https://github.com/EelcoHoogendoorn/numga) package for JAX, and it occurred to me that a project like alphafold might benefit quite a bit from adopting it.
If nothing else, one feature of using numga I have found very useful in my own work, is to easily swap out the execut... | {
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"Carriage returns should be handled ok by the MSA search tools, fine to leave as is."
] | 2022-10-07T16:37:09Z | 2022-12-13T11:59:49Z | 2022-12-13T11:59:49Z | NONE | null | Hello,
I see carriage returns in some database input files:
$ ./alphafold/scripts/download_pdb_seqres.sh TEST
$ grep -r $'\r' TEST/pdb_seqres/pdb_seqres.txt | wc -l
1476032
Should I remove them (e.g., sed -i "s/\r$//" TEST/pdb_seqres/pdb_seqres.txt) or is it not expected to represent any problem?
Thank yo... | {
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"I created this thread for those that are having the same issue"
] | 2022-10-06T15:32:55Z | 2022-10-06T15:33:45Z | 2022-10-06T15:33:45Z | NONE | null | I just installed AlphaFold and for the first time that I tried to run it gived to me the next error:
File "alphafold/docker/run_docker.py", line 22, in <module>
from absl import app
ModuleNotFoundError: No module named 'absl'
I used:
pip uninstall absl-py
pip install absl-py
pip3 uninstall absl-py
pip... | {
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I would like to access Alphafold DB from a third party application. As I understand the link format is **https://alphafold.ebi.ac.uk/files/AF-[a UniProt accession]-F[a fragment number]-model_v3.pdb**. Can I use this format in my application to download PDB files? I would like to know whether it is guaranteed ... | {
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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/605/checks?check_run_id=87... | 2022-10-05T12:08:22Z | 2022-10-05T12:08:27Z | null | NONE | null | Fix the following errors which occured when running the singularity transformed docker image of alphafold 2.2.4 Dockerfile:
```
Could not load dynamic library 'libcusolver.so.11'
```
Which generates the error:
```
RuntimeError: jaxlib/cuda/cusolver_kernels.cc:44: operation cusolverDnCreate(&handle) failed: cuS... | {
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I tried to find a solution, but there is no one report the same issu**e ... | {
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"Hi Chris thanks for reaching out. We haven't tested AlphaFold with this version of Cuda. I would recommend running some test structures and checking that the metrics match what is expected. We have recently seen some variability depending on hardware https://github.com/deepmind/alphafold/issues/597 so its worth ch... | 2022-09-29T20:35:38Z | 2022-09-30T12:51:52Z | 2022-09-30T12:51:52Z | NONE | null | Hello,
our cluster has nvidia kernel driver version 510.85.02. I can build the container with cudatoolkit 11.1.1, but when I run I get the errors listed below and the GPUs are not found/used. When I modify the Dockerfile to use cuda 11.7.0, it builds and runs just fine and the output structure is sensible. Is there ... | {
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"Hi yes its possible to get different results as they are different environments and the model is stochastic. Could you please provide full reproducibility details about your run? Also, have you updated to the latest version?",
"Hello Htomlinson14\r\n\r\nSorry about the late response.\r\n\r\nI normally use AlphaF... | 2022-09-26T02:07:14Z | 2022-10-10T23:02:59Z | null | NONE | null | Hello. I am making structural predictions using the colab version and the local version.
I have confirmed that there is a big difference between the two versions.
To solve this difference, I run alphafold locally with -db_preset=reduced_dbs and max_template_date=1000-01-01.
But there is still a big difference.
Is i... | {
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I traced back to the feature of AlphaFold2 used for training and found in the Nature pa... | {
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"Hi thanks for raising this. Can you please provide more details of the test\nrun so this can be reproduced?\n\nOn Thu, 22 Sept 2022 at 17:12, Luca Jovine ***@***.***> wrote:\n\n> Hello, this is ranking_debug.json from a test multimer run that I had\n> performed with version 2.2.3:\n>\n> { \"iptm+ptm\": { \"model_1... | 2022-09-22T16:12:05Z | 2022-10-19T04:34:59Z | null | NONE | null | Hello, this is ranking_debug.json from a test multimer run that I had performed with version 2.2.3:
`{
"iptm+ptm": {
"model_1_multimer_v2_pred_0": 0.8584136076107545,
"model_2_multimer_v2_pred_0": 0.8055674020453231,
"model_3_multimer_v2_pred_0": 0.6845710872128711,
"model_4_... | {
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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/596/checks?check_run_id=84... | 2022-09-22T11:05:41Z | 2022-11-01T14:18:28Z | 2022-11-01T14:18:27Z | NONE | null | null | {
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"Hi thanks for raising this! This duplicates https://github.com/deepmind/alphafold/issues/589 so will close this issue",
"Thank you so much for getting back."
] | 2022-09-19T20:49:26Z | 2022-09-20T14:43:31Z | 2022-09-20T11:17:25Z | NONE | null | This is related to #[456 ](https://github.com/deepmind/alphafold/issues/456).
"5. Run AlphaFold and download prediction" (in Colab notebook [example](https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb)), started throwing an error recently and now expects 'jax.tree_multim... | {
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"`--model_names=monomer` may be `--model_preset=monomer`.",
"Hi, \r\n\r\nI'm running into the same issue and below is my command:\r\n\r\n```\r\nsingularity run --home /scratch/users/sbusi/af2/alphafold/alphafold -B /scratch/users/sbusi/af2/alphafold/alphafold/data:/data -B .:/etc --pwd /scratch/users/sbusi/af2 --... | 2022-09-16T00:12:06Z | 2022-12-04T15:12:00Z | null | NONE | null | Hello, I'm trying to run alphafold using the command indicated below. I'm getting the error "Too many command-line arguments". I made sure to remove all the spaces. I'm not sure why I still get this error. I would appreciate any help to figure out the problem.
```
singularity run --home /Alphafold/alphafold-2.2.0 ... | {
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报错：I0910 11:42:53.106589 139985805367104 hhsearch.py:76] Launching subprocess "hhsearch -i /tmp/tmpd42j2lo8/query.a3m -o /tmp/tmpd42j2lo8/output.hhr -maxseq 1000000 -d /mnt/pdb70/pdb70"
I0910 11:42:53.259523 139985805367104 utils.py:36] Started HHsearch query
I0910 11:42:53.617978 139985805367104 util... | {
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"I've also encountered this issue. I hope `pdb_seqres.txt` itself or the AlphaFold pipeline will be improved.",
"Duplicate of #569 - please follow updates on that issue."
] | 2022-09-14T09:10:51Z | 2022-09-19T15:13:10Z | 2022-09-19T15:13:09Z | NONE | null | Dear all,
I had trouble running a prediction with updated pdb_seqres.txt files since some entries contain unusual DNA residue names, PDB code 7ooo, 7oos and 7ozz. These nucleic acids are modified residues but do not follow DNA alphabet, so the parser fails with an error on the letter "0" (zero)
Traceback here and d... | {
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"Hi Trine! Thanks for the question. Since PDBx/mmCIF is now the default file format, we don't plan to support pdb formats in general and they aren't available in the cloud dataset. They are, however, available on the EMBL FTP site for SwissProt and various proteomes. There are also open source converters between th... | 2022-09-09T08:21:27Z | 2022-09-12T12:44:04Z | 2022-09-12T12:44:04Z | NONE | null | Using the described method for whole-proteome structure file download from the Google Cloud database produces the structure files in mmCIF format. Are the structure files available in pdb format for bulk download, and how do I specify this in the download command? | {
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"I am getting the same error message. Just in case it might be related to this problem, I was able to obtain protein predictions before the relax_use_gpu option was included in the notebook. \r\n\r\nError message:\r\n\r\n/opt/conda/lib/python3.7/site-packages/haiku/_src/data_structures.py:195: FutureWarning: jax.tr... | 2022-09-07T09:36:08Z | 2022-09-22T11:23:15Z | 2022-09-21T16:59:52Z | NONE | null | Was getting deprecation warnings for a while, now appears not to work at all.
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"And I found there is only one result_model_1_multimer_v2_pred_0.pkl, one unrelaxed_model_1_multimer_v2_pred_0.pdb and one features.pkl file in the output file, not 5 pdb files and 5 unrelaxed pdb files as usual. "
] | 2022-09-06T07:54:11Z | 2022-09-07T09:28:11Z | null | NONE | null | Hello,
I had a problem with running alphafold. The first two hours are very smooth, and I think the MSA part is finished in these two hours. However, when it showd:
I0905 13:06:56.466166 140453353674560 model.py:175] Output shape was {'distogram': {'bin_edges': (63,), 'logits': (691, 691, 64)}, 'experimentally_... | {
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"Hi! Is it possible that your colab runtime restarted? When this happens, you will need to rerun steps 1 and 2 to make sure that the relevant packages have been installed, as these do not persist between sessions. Thanks!",
"> Hi! Is it possible that your colab runtime restarted? When this happens, you will need ... | 2022-09-02T03:49:38Z | 2022-10-03T09:25:39Z | 2022-10-03T09:25:39Z | NONE | null | Hi, I'm new to using Alphafold2 and I have been looking for the solution for this problem but haven't found it so sorry in advance if it has already been posted. I am running 3 sequences and around halfway through the second or third sequence I keep getting this error when I do the whole thing just stops working for a ... | {
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since I am working on complexes I was very happy about the multimer modeling.
However, if one has available distance constraints from the lab saying which residues interact with
each other, it would be highly useful if those constraints could be considered somehow.
With a normal docking approach I would just... | {
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I am thinking for a while about alphafold model variability for multimer models. Even if use 20 multimer predictions (100 models) the resulting complex prediction are very very similar, but in reality there should be be some variability in the models as the complex is accommodating its potential energy sur... | {
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just in case, I want to confirm if the up-to-date Alphafold2 only accepts amino acids sequence as input.
Is it possible to add some restrictions before the predictions?
Also, there seem to be no options to specify whether the protein is from prokaryotes and eukaryotes,
will it influence the results?
Tha... | {
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"Lines 105-109 in run_alphafold.py seem very relevant, and the README also has a note on reproducibility that is important. As interpreted by me, the gist of it is that runs are consistently similar, but not identical. You can make the runs even more consistent by setting the random seed used, but GPU inference is ... | 2022-08-30T14:51:39Z | 2022-09-13T19:57:18Z | 2022-09-13T19:57:18Z | NONE | null | Hi,
Thank you for sharing this great tool. I noticed that when I run Alphafold2 on the same sequence, I would get slightly different result each time. Is there any way we can ensure getting identical output from identical sequence, or is that something that's unavoidable?
Thank you
Barbara | {
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"Are `EUXXXX` and `12H` sequence names? If so, the [FASTA format](https://en.wikipedia.org/wiki/FASTA_format) requires the following formatting:\r\n\r\n```\r\n>EUXXXX\r\nMKMASNDATPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQQNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGGFEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIV... | 2022-08-29T14:58:00Z | 2022-08-29T15:28:39Z | null | NONE | null | Hi, I am new to protein folding area and I am having a little issue with running protein protein interaction with Alphafold.
My inputs:
```
>EUXXXX
MKMASNDATPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQQNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGGFEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPDVR... | {
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"It looks like the functionality is there, based on the existence of [truncate_stockholm_msa(stockholm_msa_path: str, max_sequences: int)](https://github.com/deepmind/alphafold/blob/86a0b8ec7a39698a7c2974420c4696ea4cb5743a/alphafold/data/parsers.py#L277) and the places it is called, like in the [Jackhmmer wrapper](... | 2022-08-25T18:59:13Z | 2022-08-26T16:35:43Z | null | NONE | null | We have some users at our site folding large protein complexes using the multimer workflow, and have run into issues with memory exhausted on the GPUs even using the reduced databases. In the log file we notice it reporting what looks like a deep MSA:
`I0822 12:49:34.498847 140441650169664 pipeline.py:238] Final (de... | {
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"Sorry about this! See https://github.com/deepmind/alphafold/issues/573 for a workaround, we are working on a fix.",
"> Sorry about this! See #573 for a workaround, we are working on a fix.\r\n\r\nthank you !!",
"Fixed in https://github.com/deepmind/alphafold/commit/dad1f286aeaa158702a98aeee0f5661f30de6da8"
] | 2022-08-25T06:46:35Z | 2022-08-25T09:26:47Z | 2022-08-25T09:26:47Z | NONE | null | Hello everyone,
I am using alphafold to predict protein structure. while running the first step, i found the following error. Can anyone helps me please.
CalledProcessError Traceback (most recent call last)
[<ipython-input-1-0c215f21152d>](https://localhost:8080/#) in <module>
35 ... | {
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"Sorry about this! See https://github.com/deepmind/alphafold/issues/573 for a workaround, we are working on a fix.",
"Fixed in https://github.com/deepmind/alphafold/commit/dad1f286aeaa158702a98aeee0f5661f30de6da8."
] | 2022-08-25T03:16:57Z | 2022-08-25T09:27:00Z | 2022-08-25T09:27:00Z | NONE | null | Trying to build a recent clone of the repo on our HPC and i am receiving the following error:
cryptography-37.0.2 | 1.5 MB | ########## | 100%
ocl-icd-system-1.0.0 | 4 KB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...wor... | {
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"Thank you! I submitted the fix separately."
] | 2022-08-24T16:26:12Z | 2022-08-25T09:28:14Z | 2022-08-25T09:28:14Z | NONE | null | Solves #573 by not updating to latest conda version | {
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"Did you run the command line. I had the same error but it worked when I assigned a directory.\r\n`/home/usrn/alphafold/scripts/download_pdb70.sh directory_path`\r\n\r\nIf you are in the alphafold directory then it should look like this\r\n`scripts/download_pdb70.sh directory_path`\r\n\r\nOne thing also is that the... | 2022-08-24T15:40:05Z | 2022-08-25T14:58:49Z | null | NONE | null | I got this error when running download_all_data.sh, which runs download_mgnify.sh.
I looked into the latter and these lines were causing the error.
pushd "${ROOT_DIR}"
gunzip "${ROOT_DIR}/${BASENAME}"
popd
It went to the directory to unzip the file, but the path was wrong. The ${ROOT_DIR}/ should be removed. | {
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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."
] | 2022-08-24T06:56:18Z | 2022-12-13T12:02:12Z | 2022-12-13T12:02:12Z | NONE | null | Can you reduce the GPU memory occupation, improve the computing speed and save the running time? | {
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"The latest version (4.14.0) of conda is in some way causing this. This is auto-installed when we run `conda update -qy conda` in the \"Install 3rd part software\" section. There is a workaround:\r\n\r\nIn the section you want to locate this piece of code:\r\n\r\n```python\r\n%shell conda update -qy conda \\\r\n ... | 2022-08-23T19:28:05Z | 2022-10-06T12:56:13Z | 2022-08-25T09:27:36Z | NONE | null | Here is the log:
`17%
17/100 [elapsed: 05:10 remaining: 02:43]
Found existing installation: tensorflow 2.8.2+zzzcolab20220719082949
Uninstalling tensorflow-2.8.2+zzzcolab20220719082949:
Successfully uninstalled tensorflow-2.8.2+zzzcolab20220719082949
Reading package lists...
Building dependency tree...
Re... | {
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https://api.github.com/repos/deepmind/alphafold/issues/572 | https://api.github.com/repos/deepmind/alphafold | https://api.github.com/repos/deepmind/alphafold/issues/572/labels{/name} | https://api.github.com/repos/deepmind/alphafold/issues/572/comments | https://api.github.com/repos/deepmind/alphafold/issues/572/events | https://github.com/deepmind/alphafold/issues/572 | 1,348,150,048 | I_kwDOFoWQLM5QWyMg | 572 | AlphaFold Multimer v2.2.2 Incorrectly Predicts Homo-oligomer Despite PDB Structure | {
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"gists_url": "https://... | [] | open | false | null | [] | null | [] | 2022-08-23T15:35:49Z | 2022-08-23T15:36:12Z | null | NONE | null | An interesting case of ~accurate protomer prediction but poor multimer prediction:
I predicted a homo-oligomer complex (ring) for a well-characterized protein with AlphaFold Multimer v2.2.2 (using the full database). The protein has a nearly complete PDB structure which AlphaFold uses as a template. The predicted st... | {
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"Okay, I'm running the idea that this runtime error could be a lack of vRAM. Going to plug in my dinosaur GPU acc and see if it does the trick. I'm praying it doesn't short or explode while running.\r\n\r\nUpdate:\r\nIt didn't work, I got the same error message.",
"Updated to v2.2.3 and attempted to truncate the ... | 2022-08-22T16:20:36Z | 2022-08-27T00:11:44Z | 2022-08-27T00:11:44Z | NONE | null | Hi all, I ran into this issue running .fasta for a DRA/B pMHC TRA/B complex model.
### Input-
`python3 docker/run_docker.py \
--data_dir=/media/eric/NewCupcake \
--output_dir=/media/eric/OldCupcake/tmp/alphafold \
--fasta_paths=/media/eric/OldCupcake/FastaFiles/TRpep79_HLA–DQB10201DQA10201.fasta\
--m... | {
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