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It appears that hhfilter has an undocumented limit on the number of sequences it outputs (65535). This should be documented and a clear warning given to the user. I just lost 100,000s of compute hours…
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### Description of the bug
Hi,
We are trying to run the nfcore proteinfold pipeline in ec2. While running the alphafold, we are getting an error message saying HHblits failed. It comes from the pyth…
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Hi, as mentioned in #135 , even when I am trying to run sequences of length 300-350 residues, an HHBlits error continuously causes AlphaFold to exit without results and print warnings:
```
I0803 0…
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Hello,
I think I've found an annoying bug that makes HHsearch v.3.x barely usable.
The description below relates to the latest HH-Suite version (and possibly to all the v.3.x releases).
## Expe…
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When I run speedppi with Uniref_30 database, I get the following warning
```
- 23:11:17.538 WARNING: Warning in /big/martin/hh-suite/src/hhalignment.cpp:3518: MergeMasterSlave:
- 23:11:17.538 WAR…
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For the pilot studies (HLA-A*02:01 and HLA-DBR1*01:01) the following sequence features were used:
FullPSSM for the MHC
one-hot encoding for the peptide
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Who could do me a favor?
when I run AF2, came up with HHblits error.
script:
**python ./run_alphafold.py --fasta_paths=XXX.fas**
results:
/home/linlab/.local/lib/python3.8/site-packages/absl…
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Dear developers,
I was trying to run the individual features script for two proteins. One of them consistently fails to produce a .pkl file.
The process keeps being interrupted after starting th…
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* PIGT version:
* Python version : 3.10.12
* Operating System : linux
### Description
I am installing the package using commands in the tutorial but got stuck while using make environment.
I …
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**Bug description**
Unable to install openfold
**Reproduction steps**
I have run `pip install "fair-esm[esmfold]"` and `pip install 'dllogger @ git+https://github.com/NVIDIA/dllogger.git'` as t…