segmentation fault in hhblits

[gabrieliacc]

Dear all,

First at all, thank you for the code.

I installed MolPC. When I run the test (bash pipeline.sh), I have the the error:
'''''''''''''''''
mkdir: cannot create directory ‘/home/gabriel.jara/Programas/MoLPC/data/test//hhblits’: File exists

• 15:04:25.259 INFO: Search results will be written to /home/gabriel.jara/Programas/MoLPC/data/test//hhblits/1A8R_1-1-1.hhr

• 15:04:28.903 INFO: Searching 15161831 column state sequences.

• 15:04:28.958 INFO: /home/gabriel.jara/Programas/MoLPC/data/test//hhblits/1A8R_1-1-1.fasta is in A2M, A3M or FASTA format

• 15:04:28.958 INFO: Iteration 1

• 15:04:29.256 INFO: Prefiltering database

• 15:05:14.528 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 118870

• 15:05:15.581 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 585

• 15:05:15.581 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 585

• 15:05:15.581 INFO: Scoring 585 HMMs using HMM-HMM Viterbi alignment

• 15:05:15.606 INFO: Alternative alignment: 0

pipeline.sh: line 33: 5238 Segmentation fault (core dumped) $HHBLITS -i $file -d $HHBLITSDB -E 0.001 -all -n 2 -oa3m $MSADIR/$SUBID'.a3m'

• 15:05:15.964 INFO: Search results will be written to /home/gabriel.jara/Programas/MoLPC/data/test//hhblits/1A8R_1.hhr

• 15:05:19.587 INFO: Searching 15161831 column state sequences.

• 15:05:19.641 INFO: /home/gabriel.jara/Programas/MoLPC/data/test//hhblits/1A8R_1.fasta is in A2M, A3M or FASTA format

• 15:05:19.642 INFO: Iteration 1

• 15:05:19.743 INFO: Prefiltering database

• 15:05:37.682 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 312414

• 15:05:38.853 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 730

• 15:05:38.853 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 730

• 15:05:38.853 INFO: Scoring 730 HMMs using HMM-HMM Viterbi alignment

• 15:05:38.879 INFO: Alternative alignment: 0

pipeline.sh: line 33: 5253 Segmentation fault (core dumped) $HHBLITS -i $file -d $HHBLITSDB -E 0.001 -all -n 2 -oa3m $MSADIR/$SUBID'.a3m'
Creating all interactions of size 3 ...
Traceback (most recent call last):
File "/home/gabriel.jara/Programas/MoLPC/src/preprocess/prepare_folddock_run.py", line 173, in
create_folder_structure(msadir, complex_id, outdir, useqs, interactions, intchain2seq, get_all, subsize)
File "/home/gabriel.jara/Programas/MoLPC/src/preprocess/prepare_folddock_run.py", line 148, in create_folder_structure
create_msas(msadir, complex_id, combo, outdir)
File "/home/gabriel.jara/Programas/MoLPC/src/preprocess/prepare_folddock_run.py", line 66, in create_msas
a3m, species = read_a3m(msadir+complex_id+'_'+str(chain)+'.a3m')
File "/home/gabriel.jara/Programas/MoLPC/src/preprocess/pair_and_block.py", line 27, in read_a3m
with open(infile, 'r') as file:
FileNotFoundError: [Errno 2] No such file or directory: '/home/gabriel.jara/Programas/MoLPC/data/test//hhblits/1A8R_1.a3m'
mkdir: cannot create directory ‘/home/gabriel.jara/Programas/MoLPC/data/test//AF’: File exists
1A8R_1-1-1
/home/gabriel.jara/miniconda3/lib/python3.9/site-packages/Bio/Data/SCOPData.py:18: BiopythonDeprecationWarning: The 'Bio.Data.SCOPData' module will be deprecated in a future release of Biopython in favor of 'Bio.Data.PDBData.
warnings.warn(
Jax plugin configuration error: Exception when calling jax_plugins.xla_cuda12.initialize()
Traceback (most recent call last):
File "/home/gabriel.jara/miniconda3/lib/python3.9/site-packages/jax/_src/xla_bridge.py", line 430, in discover_pjrt_plugins
plugin_module.initialize()
File "/home/gabriel.jara/miniconda3/lib/python3.9/site-packages/jax_plugins/xla_cuda12/init.py", line 78, in initialize
options = xla_client.generate_pjrt_gpu_plugin_options()
AttributeError: module 'jaxlib.xla_client' has no attribute 'generate_pjrt_gpu_plugin_options'
/home/gabriel.jara/miniconda3/lib/python3.9/site-packages/flax/struct.py:132: FutureWarning: jax.tree_util.register_keypaths is deprecated, and will be removed in a future release. Please use register_pytree_with_keys() instead.
jax.tree_util.register_keypaths(data_clz, keypaths)
/home/gabriel.jara/miniconda3/lib/python3.9/site-packages/flax/struct.py:132: FutureWarning: jax.tree_util.register_keypaths is deprecated, and will be removed in a future release. Please use register_pytree_with_keys() instead.
jax.tree_util.register_keypaths(data_clz, keypaths)
Traceback (most recent call last):
File "/home/gabriel.jara/Programas/MoLPC/src/AF2/run_alphafold.py", line 36, in
from alphafold.model import config
File "/home/gabriel.jara/Programas/MoLPC/src/AF2/alphafold/model/config.py", line 18, in
import ml_collections
ModuleNotFoundError: No module named 'ml_collections'
Written pairs to /home/gabriel.jara/Programas/MoLPC/data/test//assembly//pairs/
rm: cannot remove '/home/gabriel.jara/Programas/MoLPC/data/test//assembly//1A8R*': No such file or directory
Traceback (most recent call last):
File "/home/gabriel.jara/Programas/MoLPC/src/complex_assembly/mcts.py", line 547, in
best_path = find_paths(edges, sources, pairdir, plddt_dir, chain_lens, outdir)
File "/home/gabriel.jara/Programas/MoLPC/src/complex_assembly/mcts.py", line 444, in find_paths
sps = edges[np.argwhere(edges=='A')[:,0]][0]
IndexError: index 0 is out of bounds for axis 0 with size 0
Traceback (most recent call last):
File "/home/gabriel.jara/Programas/MoLPC/src/complex_assembly/score_entire_complex.py", line 184, in
model_path = pd.read_csv(args.model_path[0])
File "/home/gabriel.jara/miniconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/gabriel.jara/miniconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 577, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/home/gabriel.jara/miniconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1407, in init
self._engine = self._make_engine(f, self.engine)
File "/home/gabriel.jara/miniconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
self.handles = get_handle(
File "/home/gabriel.jara/miniconda3/lib/python3.9/site-packages/pandas/io/common.py", line 859, in get_handle
handle = open(
FileNotFoundError: [Errno 2] No such file or directory: '/home/gabriel.jara/Programas/MoLPC/data/test//assembly/complex//optimal_path.csv'

'''''''''''''''''

Can you help me with that "Segmentation fault" error?

Thank in advance.

Gabriel Jara

[gabrieliacc]

The setup.sh install hhblits 3.3.0. I red some related issues in soedinglab/hh-suite#260. I test using: export OMP_STACKSIZE=32768 and -premerge 0. However, those changes did not resolve the error. I also remove folder hhblits that is in MolPC/src and then I installed hblits 3.1.0, the problem continued...