File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/lib/python3.12/site-packages/pandas/compat/_optional.py", line 138, in import_optional_dependency
raise ImportError(msg)
ImportError: Missing optional dependency 'zstandard'. Use pip or conda to install zstandard.
Was able to overcome the issue by manually installing "zstandard" to the conda enviroment
nextflow run pgscatalog/pgsc_calc -latest -profile test,conda
Output:
pgscatalog.calc.cli.aggregate_cli: 2026-07-07 16:34:26 INFO cineca_22_additive_0.sscore.zst was calculated from good variant sets :)
pgscatalog.calc.cli.aggregate_cli: 2026-07-07 16:34:26 INFO Read 1 from cineca_22_additive_1.sscore.vars
pgscatalog.calc.cli.aggregate_cli: 2026-07-07 16:34:26 INFO Read 1 from cineca_22_additive_1.scorefile.gz
pgscatalog.calc.cli.aggregate_cli: 2026-07-07 16:34:26 INFO cineca_22_additive_1.sscore.zst was calculated from good variant sets :)
pgscatalog.calc.cli.aggregate_cli: 2026-07-07 16:34:26 INFO Initialising aggregation with PolygenicScore(sampleset='cineca', path=PosixPath('cineca_22_additive_0.sscore.zst'))
Traceback (most recent call last):
File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/lib/python3.12/site-packages/pandas/compat/_optional.py", line 135, in import_optional_dependency
module = importlib.import_module(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/lib/python3.12/importlib/__init__.py", line 90, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
File "<frozen importlib._bootstrap>", line 1324, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'zstandard'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/bin/pgscatalog-aggregate", line 10, in <module>
sys.exit(run_aggregate())
^^^^^^^^^^^^^^^
File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/lib/python3.12/site-packages/pgscatalog/calc/cli/aggregate_cli.py", line 94, in run_aggregate
observed_columns.update(set(score.df.columns))
^^^^^^^^
File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/lib/python3.12/site-packages/pgscatalog/calc/lib/polygenicscore.py", line 351, in df
self._df = self.read()
^^^^^^^^^^^
File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/lib/python3.12/site-packages/pgscatalog/calc/lib/polygenicscore.py", line 382, in read
df = pd.read_csv(
^^^^^^^^^^^^
File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 620, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1620, in __init__
self._engine = self._make_engine(f, self.engine)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine
self.handles = get_handle(
^^^^^^^^^^^
File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/lib/python3.12/site-packages/pandas/io/common.py", line 849, in get_handle
zstd = import_optional_dependency("zstandard")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jupyter/local_files/work/conda/env-afaa80f79ea46ebdea42bfd472478072/lib/python3.12/site-packages/pandas/compat/_optional.py", line 138, in import_optional_dependency
raise ImportError(msg)
ImportError: Missing optional dependency 'zstandard'. Use pip or conda to install zstandard.
Description of the bug
Trying to run pgsc_calc in conda mode (
nextflow run pgscatalog/pgsc_calc -latest -profile test,conda) fails due to missing "optional" dependency zstandardWas able to overcome the issue by manually installing "zstandard" to the conda enviroment
Command used and terminal output
Relevant files
No response
System information
Netxflow version 25.10.2
Running in an AoUs Jupyter Lab instance