Open UnixJunkie opened 14 hours ago
UnixJunkie
commented
13 hours ago *** Open Babel Error in LoadAllPlugins
Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
Traceback (most recent call last):
File "/src/plip/plipcmd.py", line 23, in
mestia
commented
13 hours ago Hi,
first, the warning about /etc/localtime I believe can be ignored.
The real problem is most likely your local environment.
Try to run singularity with --no-home or --containeall (-C) flags
for example:
cd /tmp/
singularity exec --no-home ~/plip_v2.3.0.simg python3 /src/plip/plipcmd.py -i 1vsn -yvSee this link for more details: https://docs.sylabs.io/guides/latest/user-guide/bind_paths_and_mounts.html
The singularity container is not working for me:
./plip.simg -i 1vsn -yv
WARNING: underlay of /etc/localtime required more than 50 (110) bind mounts
*** Open Babel Error in LoadAllPlugins Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable. Traceback (most recent call last): File "/src/plip/plipcmd.py", line 23, in
from plip.exchange.report import StructureReport
File "/src/plip/exchange/report.py", line 8, in
from plip.structure.preparation import PDBComplex
File "/src/plip/structure/preparation.py", line 9, in
from openbabel import pybel
File "/usr/local/lib/python3.6/dist-packages/openbabel/pybel.py", line 87, in
informats = _formatstodict(_obconv.GetSupportedInputFormat())
File "/usr/local/lib/python3.6/dist-packages/openbabel/pybel.py", line 66, in _formatstodict
broken = [(x, y.strip()) for x, y in broken]
File "/usr/local/lib/python3.6/dist-packages/openbabel/pybel.py", line 66, in
broken = [(x, y.strip()) for x, y in broken]
ValueError: not enough values to unpack (expected 2, got 1)