trRosetta2

trRosetta2 copied to clipboard

json.decoder issue

5

Generating TAPE features 243B [00:00, 284458.80B/s] Traceback (most recent call last): File "/home/ngayatri/trRosetta2/trRosetta2/tape/get_embeddings.py", line 25, in model = ProteinBertModel.from_pretrained('bert-base') File "/home/ngayatri/miniconda3/envs/casp14-baker/lib/python3.6/site-packages/tape/models/modeling_utils.py", line 470, in from_pretrained **kwargs File "/home/ngayatri/miniconda3/envs/casp14-baker/lib/python3.6/site-packages/tape/models/modeling_utils.py", line 172,...

GayatriNavle

HHSearch: 7701 Segmentation fault (core dumped)

12

I'm getting an error on the hhsearch step: `Running hhsearch ./run_pipeline.sh: line 49: 7701 Segmentation fault (core dumped) $HH -i $WDIR/t000_.msa0.ss2.a3m -o $WDIR/t000_.hhr -v 0 > $WDIR/log/hhsearch.stdout 2> $WDIR/log/hhsearch.stderr` There's...

cclough

Error while running trRosetta2

5

Hi, I get this error while running the pipeline script. No PDB model is generated. Could you please help me out with this ? Traceback (most recent call last): File...

anu-bioinfo

Current install steps will fail when installing latest `pyrosetta` via conda , it would be usefull to state `pyrosetta` version thats supported.

obonyojimmy

I tried TrRosetta2 on 1crn fasta. I had to recompile hhsuite to avoid segmentation fault issue. All the pipeline look works fine but at the end final_pick.py fail because it...

luigidibiasi

If the input has no templates in pdb100_2020Mar11, there will be a no t000_.hhr error.

EstherBear

Hi, Thanks for sharing this tool. And the run_pipeline.sh is just for monomer structure prediction, right? Could you also share the whole pipeline scripts for the homo- and hetero-structure prediction....

ZhiYeG

Error message running Tape about undefined symbol omp_get_num_procs Resolved using conda install --channel conda-forge llvm-openmp https://github.com/ContinuumIO/anaconda-issues/issues/10195

FrBonnardel

The installation is really bloated, and I guess only a tiny fraction of pyrosetta is needed for trRosetta to run -- i suggest unbundling these components. The current install needs...

phiweger

pick_final_models.div.py references Robetta

22

Hello, Fantastic work and thank you so much for releasing this to the public! I have encountered several issues with running trRosetta2 on Ubuntu: 1) some dependencies, like scikit learn...

martinpacesa