Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:
Error executing process > 'calculateGroupings (1)'
Caused by:
Process `calculateGroupings (1)` terminated with an error exit status (1)
Command executed:
python /app/workflows_user/feature_based_molecular_networking_workflow/bin/scripts/group_abundances.py featuretable_reformated.csv merged_metadata.tsv clustersummary_with_groups.tsv
Command exit status:
1
Command output:
filename ... ATTRIBUTE_HALO_DIMENSION_mm_EC
0 58352.mzML ... 5.0
1 84625.mzML ... NaN
2 48226.mzML ... 6.0
3 46585.mzML ... NaN
4 47090.mzML ... 4.0
... ... ... ...
11910 NaN ... NaN
11911 NaN ... NaN
11912 NaN ... NaN
11913 NaN ... NaN
11914 NaN ... NaN
[11915 rows x 18 columns]
Command error:
Traceback (most recent call last):
File "/app/workflows_user/feature_based_molecular_networking_workflow/bin/scripts/group_abundances.py", line 127, in
main()
File "/app/workflows_user/feature_based_molecular_networking_workflow/bin/scripts/group_abundances.py", line 116, in main
clustersummary_df = calculate_groups_metadata(feature_table_df, metadata_df)
File "/app/workflows_user/feature_based_molecular_networking_workflow/bin/scripts/group_abundances.py", line 49, in calculate_groups_metadata
metadata_df["filename"] = metadata_df["filename"].apply(lambda x: os.path.basename(x).rstrip())
File "/app/launchserver/env/conda_envs/conda_env-1481db6234eceaa7db05ba6454e78bde/lib/python3.8/site-packages/pandas/core/series.py", line 4630, in apply
return SeriesApply(self, func, convert_dtype, args, kwargs).apply()
File "/app/launchserver/env/conda_envs/conda_env-1481db6234eceaa7db05ba6454e78bde/lib/python3.8/site-packages/pandas/core/apply.py", line 1025, in apply
return self.apply_standard()
File "/app/launchserver/env/conda_envs/conda_env-1481db6234eceaa7db05ba6454e78bde/lib/python3.8/site-packages/pandas/core/apply.py", line 1076, in apply_standard
mapped = lib.map_infer(
File "pandas/_libs/lib.pyx", line 2834, in pandas._libs.lib.map_infer
File "/app/workflows_user/feature_based_molecular_networking_workflow/bin/scripts/group_abundances.py", line 49, in
metadata_df["filename"] = metadata_df["filename"].apply(lambda x: os.path.basename(x).rstrip())
File "/app/launchserver/env/conda_envs/conda_env-1481db6234eceaa7db05ba6454e78bde/lib/python3.8/posixpath.py", line 142, in basename
p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not float
Work dir:
/data/nf_data/server/nf_work/83537f3f19fe4f9f9b02979e12f4c8eb/b7/ae35822495730e96b052bf6afce4e5
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`