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 48212.mzML ... NaN
1 48213.mzML ... NaN
2 48214.mzML ... 4.0
3 48215.mzML ... 4.0
4 48231.mzML ... 12.0
... ... ... ...
12219 NaN ... NaN
12220 NaN ... NaN
12221 NaN ... NaN
12222 NaN ... NaN
12223 NaN ... NaN
[12224 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-4e7614d066e4c2282297a9aa547f4051/lib/python3.8/site-packages/pandas/core/series.py", line 4626, in apply
return SeriesApply(self, func, convert_dtype, args, kwargs).apply()
File "/app/launchserver/env/conda_envs/conda_env-4e7614d066e4c2282297a9aa547f4051/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-4e7614d066e4c2282297a9aa547f4051/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-4e7614d066e4c2282297a9aa547f4051/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/154a89144c4643f18329aacd3a93cffc/f2/1a85936c4405ba82ea0b3bb739bd43
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
nextflow run /app/workflows_user/feature_based_molecular_networking_workflow/nf_workflow.nf -params-file /data/nf_data/server/nf_tasks/154a89144c4643f18329aacd3a93cffc/job_parameters.yaml -w /data/nf_data/server/nf_work/154a89144c4643f18329aacd3a93cffc -with-report /data/nf_data/server/nf_tasks/154a89144c4643f18329aacd3a93cffc/job_report.html -with-timeline /data/nf_data/server/nf_tasks/154a89144c4643f18329aacd3a93cffc/job_timeline.html -with-dag /data/nf_data/server/nf_tasks/154a89144c4643f18329aacd3a93cffc/job_dag.html -with-weblog 'http://localhost:4000/nf_weblog/154a89144c4643f18329aacd3a93cffc' -c /app/launchserver/nextflow.configafa4029ddf255d85cb81f38bc52e962aa2a8087a-4522-40f0-a250-dedd58dc8fd7These plots give an overview of the distribution of resource usage for each process.
This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.
Launch time:
Elapsed time:
Legend: job wall time / memory usage (RAM)