error with running mikado
Closed this issue · 3 comments
ChemaMD commented
Hi,
I tried to install the latest version of mikado via different approaches (conda/mamba, pip3, and as Luca proposed here: #256) without success. When I try to run e.g. mikado configure --help
I get:
Traceback (most recent call last):
File "/data/home/btx333/mambaforge/envs/mikado2/bin/mikado", line 8, in <module>
sys.exit(main())
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/Mikado/__main__.py", line 18, in main
from Mikado.subprograms import configure, prepare, serialise, pick, compare, util
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/Mikado/subprograms/__init__.py", line 6, in <module>
from . import configure
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/Mikado/subprograms/configure.py", line 28, in <module>
from .prepare import parse_prepare_options
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/Mikado/subprograms/prepare.py", line 22, in <module>
from ..preparation.prepare import prepare
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/Mikado/preparation/prepare.py", line 4, in <module>
from .checking import create_transcript, CheckingProcess
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/Mikado/preparation/checking.py", line 9, in <module>
from ..transcripts.transcriptchecker import TranscriptChecker
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/Mikado/transcripts/__init__.py", line 8, in <module>
from .transcript import Transcript, Metric
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/Mikado/transcripts/transcript.py", line 4, in <module>
from .transcript_methods import splitting, retrieval
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/Mikado/transcripts/transcript_methods/retrieval.py", line 12, in <module>
from ...serializers.junction import Junction
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/Mikado/serializers/__init__.py", line 6, in <module>
from . import orf
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/Mikado/serializers/orf.py", line 34, in <module>
class Orf(DBBASE):
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/Mikado/serializers/orf.py", line 62, in Orf
query = column_property(select([Query.query_name]).where(
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/sqlalchemy/sql/_selectable_constructors.py", line 493, in select
return Select(*entities)
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/sqlalchemy/sql/selectable.py", line 5160, in __init__
self._raw_columns = [
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/sqlalchemy/sql/selectable.py", line 5161, in <listcomp>
coercions.expect(
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/sqlalchemy/sql/coercions.py", line 413, in expect
resolved = impl._literal_coercion(
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/sqlalchemy/sql/coercions.py", line 652, in _literal_coercion
self._raise_for_expected(element, argname)
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/sqlalchemy/sql/coercions.py", line 1143, in _raise_for_expected
return super()._raise_for_expected(
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/sqlalchemy/sql/coercions.py", line 711, in _raise_for_expected
super()._raise_for_expected(
File "/data/home/btx333/mambaforge/envs/mikado2/lib/python3.10/site-packages/sqlalchemy/sql/coercions.py", line 536, in _raise_for_expected
raise exc.ArgumentError(msg, code=code) from err
sqlalchemy.exc.ArgumentError: Column expression, FROM clause, or other columns clause element expected, got [<sqlalchemy.orm.attributes.InstrumentedAttribute object at 0x7f324070fb00>]. Did you mean to say select(<sqlalchemy.orm.attributes.InstrumentedAttribute object at 0x7f324070fb00>)?
If I try to run the test:
(mikado2) [btx333@frontend11 mikado]$ python -c "import Mikado; Mikado.test(); Mikado.test(label='slow')"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/data/SBCS-MartinDuranLab/02-Chema/src/mikado/Mikado/__init__.py", line 29, in <module>
from .utilities.log_utils import create_default_logger
File "/data/SBCS-MartinDuranLab/02-Chema/src/mikado/Mikado/utilities/__init__.py", line 19, in <module>
from .overlap import overlap
ModuleNotFoundError: No module named 'Mikado.utilities.overlap'
Any idea of what is causing this?
Thanks for your help.
Best wishes,
Chema
ChemaMD commented
And this is the log if I try to install it via pip3
(I'm running all this in my session in an HPC cluster)
(base) [btx333@frontend11 ~]$ pip3 install mikado --user
Collecting mikado
Using cached Mikado-2.3.4.tar.gz (24.7 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [15 lines of output]
Traceback (most recent call last):
File "/data/home/btx333/.local/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/data/home/btx333/.local/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/data/home/btx333/.local/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
File "/tmp/pip-build-env-pxiftnrw/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 338, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
File "/tmp/pip-build-env-pxiftnrw/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 320, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-pxiftnrw/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 335, in run_setup
exec(code, locals())
File "<string>", line 15, in <module>
ModuleNotFoundError: No module named 'scipy._build_utils'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
(base) [btx333@frontend11 ~]$ pip3 install scipy --upgrade
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: scipy in ./.local/lib/python3.8/site-packages (1.10.1)
Requirement already satisfied: numpy<1.27.0,>=1.19.5 in ./.local/lib/python3.8/site-packages (from scipy) (1.24.2)
(base) [btx333@frontend11 ~]$ pip3 install numpy --upgrade
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: numpy in ./.local/lib/python3.8/site-packages (1.24.2)
I get a similar error when I run the same command on my laptop.
EinarBaldvin commented
Hi @ChemaMD,
you need to pin the sqlalchemy to version 1.4.46 during installation: sqlalchemy==1.4.46 .
There is a newer version of sqlalchemy 2.0 in in conda that is being installed and it seems to be incompatible.
Cheers,
Einar
ChemaMD commented
Thanks! Sorted :-)