Error when running the ABFE #44
Description
bash output/job.sh
['/home/disk6/homes/cveranso/ABFE_workflow/examples/DNMT3A_ABFE/ligand/dnmt3a_mr046978a_105_Lig.sdf']
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads
abfe_recptor_result 1 1 1
build_ligand_system 1 1 1
calculate_ABFE 3 1 1
fep_complex 3 1 1
fep_ligand 3 1 1
gather_files 1 1 1
gather_receptor_results 1 1 1
total 13 1 1
Select jobs to execute...
/homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/stopit/init.py:10: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
[Wed Jul 30 16:06:14 2025]
rule gather_files:
input: /home/disk6/homes/cveranso/ABFE_workflow/examples/DNMT3A_ABFE/ligand/dnmt3a_mr046978a_105_Lig.sdf
output: /home/disk6/homes/cveranso/ABFE_workflow/examples/output/orig_input/dnmt3a_mr046978a_105_Lig.sdf
jobid: 5
reason: Missing output files: /home/disk6/homes/cveranso/ABFE_workflow/examples/output/orig_input/dnmt3a_mr046978a_105_Lig.sdf
resources: tmpdir=/tmp
/home/disk6/homes/cveranso/ABFE_workflow/examples/DNMT3A_ABFE/ligand/dnmt3a_mr046978a_105_Lig.sdf
[Wed Jul 30 16:06:14 2025]
Finished job 5.
1 of 13 steps (8%) done
Select jobs to execute...
[Wed Jul 30 16:06:14 2025]
rule build_ligand_system:
input: /homes/cveranso/ABFE_workflow/examples/DNMT3A_ABFE/dnmt3a_mr046978a_105_Pro_noH.pdb, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/orig_input/dnmt3a_mr046978a_105_Lig.sdf, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input
output: /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/ligand/ligand.gro, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/ligand/ligand.top, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/complex/complex.gro, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/complex/complex.top
jobid: 4
reason: Missing output files: /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/complex/complex.gro, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/complex/complex.top, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/ligand/ligand.top, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/ligand/ligand.gro; Input files updated by another job: /home/disk6/homes/cveranso/ABFE_workflow/examples/output/orig_input/dnmt3a_mr046978a_105_Lig.sdf
wildcards: ligand_name=dnmt3a_mr046978a_105_Lig
resources: tmpdir=/tmp
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/abfe/scripts/preparation/gener │
│ ate_ABFE_systems.py:9 in │
│ │
│ 6 import subprocess │
│ 7 import sys │
│ 8 │
│ ❱ 9 import BioSimSpace as bss │
│ 10 │
│ 11 from abfe.scripts.preparation.parametrize import gen_ffparams │
│ 12 from abfe.scripts.preparation.topology_fixer import fix_topology │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/BioSimSpace/init.py:237 in │
│ │
│ │
│ 234 │ del _shlex │
│ 235 │ del _subprocess │
│ 236 │
│ ❱ 237 from . import Align │
│ 238 from . import Box │
│ 239 from . import Convert │
│ 240 from . import FreeEnergy │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/BioSimSpace/Align/init.py: │
│ 43 in │
│ │
│ 40 │ viewMapping │
│ 41 """ │
│ 42 │
│ ❱ 43 from ._align import * │
│ 44 │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/BioSimSpace/Align/_align.py:86 │
│ in │
│ │
│ 83 _networkx = _try_import("networkx") │
│ 84 │
│ 85 if _have_imported(_rdkit) and _have_imported(_networkx): │
│ ❱ 86 │ import lomap as _lomap │
│ 87 elif _have_imported(_rdkit): │
│ 88 │ _lomap = _networkx │
│ 89 elif _have_imported(_networkx): │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/lomap/init.py:68 in │
│ │
│ │
│ 65 from .dbmol import SMatrix │
│ 66 from .dbmol import Molecule │
│ 67 from .mcs import MCS │
│ ❱ 68 from .gufe_bindings import ( │
│ 69 │ generate_lomap_network, │
│ 70 │ LomapAtomMapper, │
│ 71 │ default_lomap_score, │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/lomap/gufe_bindings/init.p │
│ y:1 in │
│ │
│ ❱ 1 from . import mapper │
│ 2 from .mapper import LomapAtomMapper │
│ 3 from . import scorers │
│ 4 from .scorers import default_lomap_score │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/lomap/gufe_bindings/mapper.py: │
│ 5 in │
│ │
│ 2 The MCS class wrapped to provide a gufe interface │
│ 3 │
│ 4 """ │
│ ❱ 5 import gufe │
│ 6 from gufe import AtomMapper, LigandAtomMapping │
│ 7 from typing import Iterable │
│ 8 │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/gufe/init.py:6 in │
│ │
│ 3 │
│ 4 from importlib.metadata import version │
│ 5 │
│ ❱ 6 from . import tokenization, visualization │
│ 7 from .chemicalsystem import ChemicalSystem │
│ 8 from .components import Component, ProteinComponent, SmallMoleculeComponent, SolventComp │
│ 9 from .ligandnetwork import LigandNetwork │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/gufe/tokenization.py:23 in │
│ │
│ │
│ 20 import networkx as nx │
│ 21 from typing_extensions import Self │
│ 22 │
│ ❱ 23 from gufe.custom_codecs import ( │
│ 24 │ BYTES_CODEC, │
│ 25 │ DATETIME_CODEC, │
│ 26 │ NPY_DTYPE_CODEC, │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/gufe/custom_codecs.py:11 in │
│ │
│ │
│ 8 from uuid import UUID │
│ 9 │
│ 10 import numpy as np │
│ ❱ 11 from openff.units import DEFAULT_UNIT_REGISTRY │
│ 12 │
│ 13 import gufe │
│ 14 from gufe.compression import zst_compress, zst_decompress │
│ in _handle_fromlist:1075 │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/openff/units/init.py:57 in │
│ getattr │
│ │
│ 54 │ module = _objects.get(name) │
│ 55 │ if module is not None: │
│ 56 │ │ try: │
│ ❱ 57 │ │ │ return importlib.import_module(module).dict[name] │
│ 58 │ │ except ImportError as error: │
│ 59 │ │ │ raise ImportError from error │
│ 60 │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/importlib/init.py:126 in import_module │
│ │
│ 123 │ │ │ if character != '.': │
│ 124 │ │ │ │ break │
│ 125 │ │ │ level += 1 │
│ ❱ 126 │ return _bootstrap._gcd_import(name[level:], package, level) │
│ 127 │
│ 128 │
│ 129 _RELOADING = {} │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/openff/units/units.py:9 in │
│ │
│ │
│ 6 import warnings │
│ 7 from typing import TYPE_CHECKING │
│ 8 │
│ ❱ 9 import pint │
│ 10 from openff.utilities import requires_package │
│ 11 from pint import Measurement as _Measurement │
│ 12 from pint import Quantity as Quantity │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/pint/init.py:18 in │
│ │
│ │
│ 15 │
│ 16 from importlib.metadata import version │
│ 17 │
│ ❱ 18 from .delegates.formatter.format_helpers import formatter │
│ 19 from .errors import ( # noqa: F401 │
│ 20 │ DefinitionSyntaxError, │
│ 21 │ DimensionalityError, │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/pint/delegates/init.py:12 │
│ in │
│ │
│ 9 """ │
│ 10 from future import annotations │
│ 11 │
│ ❱ 12 from . import txt_defparser │
│ 13 from .base_defparser import ParserConfig, build_disk_cache_class │
│ 14 from .formatter import Formatter │
│ 15 │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/pint/delegates/txt_defparser/ │
│ init.py:12 in │
│ │
│ 9 """ │
│ 10 from future import annotations │
│ 11 │
│ ❱ 12 from .defparser import DefParser │
│ 13 │
│ 14 all = [ │
│ 15 │ "DefParser", │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/pint/delegates/txt_defparser/d │
│ efparser.py:10 in │
│ │
│ 7 import flexparser as fp │
│ 8 │
│ 9 from ..base_defparser import ParserConfig │
│ ❱ 10 from . import block, common, context, defaults, group, plain, system │
│ 11 │
│ 12 │
│ 13 class PintRootBlock( │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/pint/delegates/txt_defparser/c │
│ ommon.py:24 in │
│ │
│ 21 │
│ 22 │
│ 23 @DataClass(frozen=True) │
│ ❱ 24 class DefinitionSyntaxError(errors.DefinitionSyntaxError, fp.ParsingError): │
│ 25 │ """A syntax error was found in a definition. Combines: │
│ 26 │ │
│ 27 │ DefinitionSyntaxError: which provides a message placeholder. │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/dataclasses.py:1175 in wrap │
│ │
│ 1172 │ """ │
│ 1173 │ │
│ 1174 │ def wrap(cls): │
│ ❱ 1175 │ │ return _process_class(cls, init, repr, eq, order, unsafe_hash, │
│ 1176 │ │ │ │ │ │ │ frozen, match_args, kw_only, slots) │
│ 1177 │ │
│ 1178 │ # See if we're being called as @DataClass or @DataClass(). │
│ │
│ /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/dataclasses.py:990 in _process_class │
│ │
│ 987 │ │ │
│ 988 │ │ # Raise an exception if we're frozen, but none of our bases are. │
│ 989 │ │ if not any_frozen_base and frozen: │
│ ❱ 990 │ │ │ raise TypeError('cannot inherit frozen dataclass from a ' │
│ 991 │ │ │ │ │ │ │ 'non-frozen one') │
│ 992 │ │
│ 993 │ # Remember all of the fields on our class (including bases). This │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
TypeError: cannot inherit frozen dataclass from a non-frozen one
[Wed Jul 30 16:06:17 2025]
Error in rule build_ligand_system:
jobid: 4
output: /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/ligand/ligand.gro, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/ligand/ligand.top, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/complex/complex.gro, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/complex/complex.top
shell:
python /homes/cveranso/miniconda3/envs/abfe/lib/python3.10/site-packages/abfe/scripts/preparation/generate_ABFE_systems.py --ligand_sdf_dir /home/disk6/homes/cveranso/ABFE_workflow/examples/output/orig_input/dnmt3a_mr046978a_105_Lig.sdf --protein_pdb_path /homes/cveranso/ABFE_workflow/examples/DNMT3A_ABFE/dnmt3a_mr046978a_105_Pro_noH.pdb --cofactor_sdf_path None --output_dir_path /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input -ff gaff
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-07-30T160613.189125.snakemake.log