fglaser
commented
6 months ago Hi, it seems I solved most problems,
My test run starts to run correctly, but it dies after hhblit and hhfilter end, I installed everything as suggested and added all missing packages, but some where missing and I installed manually, like hydra and dgl.
Maybe dgl package it's not the correct version?
How should I try to install it exactly?
Thanks A lot, Fabian
python -m rf2aa.run_inference --config-name protein.yaml
/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/hydra/_internal/defaults_list.py:251: UserWarning: In 'protein.yaml': Defaults list is missing _self_. See https://hydra.cc/docs/1.2/upgrades/1.0_to_1.1/default_composition_order for more information
warnings.warn(msg, UserWarning)
Using the cif atom ordering for TRP.
/home/fabian/RoseTTAFold-All-Atom/rf2aa/chemical.py:20: UserWarning: Using torch.cross without specifying the dim arg is deprecated.
Please either pass the dim explicitly or simply use torch.linalg.cross.
The default value of dim will change to agree with that of linalg.cross in a future release. (Triggered internally at ../aten/src/ATen/native/Cross.cpp:62.)
Z = torch.cross(Xn,Yn)
./make_msa.sh examples/protein/7u7w_A.fasta 7u7w_protein/A 4 64 pdb100_2021Mar03/pdb100_2021Mar03
signalp6 6.0g has not been installed yet.
Due to license restrictions, this recipe cannot distribute signalp6 directly. Please download signalp-6.0g.fast.tar.gz from: https://services.healthtech.dtu.dk/services/SignalP-6.0g/9-Downloads.php#
and run the following command to complete the installation: $ signalp6-register signalp-6.0g.fast.tar.gz
This will copy signalp6 into your conda environment. Running HHblits against UniRef30 with E-value cutoff 1e-10
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21:34:15.672 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-10.a3m
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21:34:15.672 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-10.id90cov75.a3m
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21:34:15.900 WARNING: Maximum number 100000 of sequences exceeded in file 7u7wprotein/A/hhblits/t000.1e-10.a3m
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21:34:42.416 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-10.a3m
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21:34:42.416 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-10.id90cov50.a3m
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21:34:42.609 WARNING: Maximum number 100000 of sequences exceeded in file 7u7wprotein/A/hhblits/t000.1e-10.a3m
Running PSIPRED Running hhsearch cat: 7u7wprotein/A/t000.ss2: No such file or directory Error executing job with overrides: [] Traceback (most recent call last): File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 206, in main runner.infer() File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 155, in infer outputs = self.run_model_forward(input_feats) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 121, in run_model_forward outputs = recycle_step_legacy(self.model, File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/training/recycling.py", line 30, in recycle_step_legacy output_i = ddp_model(input_i) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(*args, *kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(args, kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/RoseTTAFoldModel.py", line 368, in forward msa, pair, xyz, alpha_s, xyz_allatom, state, symmsub, quat = self.simulator( File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(*args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(*args, *kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/Track_module.py", line 1109, in forward msa_full, pair, xyz, state, alpha, symmsub, quat = self.extra_block[i_m](msa_full, pair, File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(*args, kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/Track_module.py", line 963, in forward xyz, state, alpha, quat = self.str2str( File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(*args, *kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 16, in decorate_autocast return func(*args, kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/Track_module.py", line 545, in forward shift = self.se3(G, node.reshape(BL, -1, 1), l1_feats, edge_feats) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(*args, kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/layers/SE3_network.py", line 99, in forward return self.se3(G, node_features, edge_features) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(*args, *kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(args, kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/SE3Transformer/se3_transformer/model/transformer.py", line 185, in forward node_feats = self.graph_modules(node_feats, edge_feats, graph=graph, basis=basis) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(*args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(*args, *kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/SE3Transformer/se3_transformer/model/transformer.py", line 47, in forward input = module(input, args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(*args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(*args, *kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/SE3Transformer/se3_transformer/model/layers/attention.py", line 162, in forward fused_key_value = self.to_key_value(node_features, edge_features, graph, basis) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(*args, *kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/SE3Transformer/se3_transformer/model/layers/convolution.py", line 319, in forward src, dst = graph.edges() File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/view.py", line 166, in call return self._graph.all_edges(args, **kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/heterograph.py", line 3417, in all_edges src, dst, eid = self._graph.edges(self.get_etype_id(etype), order) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/heterograph_index.py", line 609, in edges edge_array = _CAPI_DGLHeteroEdges(self, int(etype), order) File "dgl/_ffi/_cython/./function.pxi", line 293, in dgl._ffi._cy3.core.FunctionBase.call File "dgl/_ffi/_cython/./function.pxi", line 225, in dgl._ffi._cy3.core.FuncCall File "dgl/_ffi/_cython/./function.pxi", line 215, in dgl._ffi._cy3.core.FuncCall3 dgl._ffi.base.DGLError: [21:39:54] /opt/dgl/src/array/array.cc:34: Operator Range does not support cuda device. Stack trace: [bt] (0) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(dmlc::LogMessageFatal::~LogMessageFatal()+0x4f) [0x7f58be7686ef] [bt] (1) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(dgl::aten::Range(long, long, unsigned char, DLContext)+0xc1) [0x7f58be740b61] [bt] (2) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(dgl::UnitGraph::COO::Edges(unsigned long, std::string const&) const+0x9b) [0x7f58bebaa22b] [bt] (3) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(dgl::UnitGraph::Edges(unsigned long, std::string const&) const+0xa1) [0x7f58beba4f31] [bt] (4) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(dgl::HeteroGraph::Edges(unsigned long, std::string const&) const+0x2a) [0x7f58beaa44ba] [bt] (5) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(+0x4e6e2c) [0x7f58beaade2c] [bt] (6) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(DGLFuncCall+0x48) [0x7f58bea30118] [bt] (7) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/_ffi/_cy3/core.cpython-310-x86_64-linux-gnu.so(+0x1525c) [0x7f58be1bf25c] [bt] (8) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/_ffi/_cy3/core.cpython-310-x86_64-linux-gnu.so(+0x1578b) [0x7f58be1bf78b]
Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.
Sue-Fwl
Dear RoseTTAFold-All-Atom community,
First thanks a lot for this Wonderfull tool. I am having some trouble running RFAA, although the installation seems done correctly. I paste the output below, maybe somebody can give a hand to find the problem.
Thanks! Fabian
python rf2aa/run_inference.py --config-name protein | grep protein Traceback (most recent call last): File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 15, in
from rf2aa.model.RoseTTAFoldModel import RoseTTAFoldModule
File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/RoseTTAFoldModel.py", line 6, in
from rf2aa.model.layers.Embeddings import MSA_emb, Extra_emb, Bond_emb, Templ_emb, recycling_factory
File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/layers/Embeddings.py", line 7, in
from rf2aa.util_module import Dropout, get_clones, create_custom_forward, rbf, init_lecun_normal, get_res_atom_dist
File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/util_module.py", line 7, in
import dgl
File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/init.py", line 16, in
from . import (
File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/dataloading/init.py", line 13, in
from .dataloader import
File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/dataloading/dataloader.py", line 27, in
from ..distributed import DistGraph
File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/distributed/init.py", line 5, in
from .dist_graph import DistGraph, DistGraphServer, edge_split, node_split
File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/distributed/dist_graph.py", line 11, in
from .. import backend as F, graphbolt as gb, heterograph_index
File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/graphbolt/init.py", line 8, in
from .base import
File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/graphbolt/base.py", line 8, in
from torchdata.datapipes.iter import IterDataPipe
File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torchdata/init.py", line 9, in
from . import datapipes
File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torchdata/datapipes/init.py", line 9, in
from . import iter, map, utils
File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torchdata/datapipes/iter/init.py", line 79, in
from torchdata.datapipes.iter.util.cacheholder import (
File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torchdata/datapipes/iter/util/cacheholder.py", line 24, in
from torch.utils.data.datapipes.utils.common import _check_unpickable_fn, DILL_AVAILABLE
ImportError: cannot import name 'DILL_AVAILABLE' from 'torch.utils.data.datapipes.utils.common' (/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/utils/data/datapipes/utils/common.py)