DIANN pipeline fails in the diann to msstats conversion

[ypriverol]

Description of the bug

/hps/nobackup/juan/pride/reanalysis/quantms/bin/diann_convert.py:42: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
out_msstats.loc[:,"PeptideSequence"] = out_msstats.apply(lambda x: convert_modification(x["PeptideSequence"], unimod_data), axis=1)
/hps/nobackup/juan/pride/reanalysis/quantms/bin/diann_convert.py:43: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
out_msstats.loc[:,"FragmentIon"] = 'NA'
/hps/nobackup/juan/pride/reanalysis/quantms/bin/diann_convert.py:44: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
out_msstats.loc[:,"ProductCharge"] = '0'
/hps/nobackup/juan/pride/reanalysis/quantms/bin/diann_convert.py:45: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
out_msstats.loc[:,"IsotopeLabelType"] = "L"
/hps/nobackup/juan/pride/reanalysis/quantms/bin/diann_convert.py:46: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
out_msstats["Reference"] = out_msstats.apply(lambda x: os.path.basename(x['Reference']), axis=1)
Traceback (most recent call last):
File "/hps/nobackup/juan/pride/reanalysis/quantms/bin/diann_convert.py", line 89, in
cli()
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1128, in call
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/click/decorators.py", line 26, in new_func
return f(get_current_context(), *args, **kwargs)
File "/hps/nobackup/juan/pride/reanalysis/quantms/bin/diann_convert.py", line 48, in convert
out_msstats[["Fraction", "BioReplicate", "Condition"]] = out_msstats.apply(lambda x: query_expdesign_value(x["Reference"], f_table, s_DataFrame),
File "/usr/local/lib/python3.10/site-packages/pandas/core/frame.py", line 8833, in apply
return op.apply().finalize(self, method="apply")
File "/usr/local/lib/python3.10/site-packages/pandas/core/apply.py", line 727, in apply
return self.apply_standard()
File "/usr/local/lib/python3.10/site-packages/pandas/core/apply.py", line 851, in apply_standard
results, res_index = self.apply_series_generator()
File "/usr/local/lib/python3.10/site-packages/pandas/core/apply.py", line 867, in apply_series_generator
results[i] = self.f(v)
File "/hps/nobackup/juan/pride/reanalysis/quantms/bin/diann_convert.py", line 48, in
out_msstats[["Fraction", "BioReplicate", "Condition"]] = out_msstats.apply(lambda x: query_expdesign_value(x["Reference"], f_table, s_DataFrame),
File "/hps/nobackup/juan/pride/reanalysis/quantms/bin/diann_convert.py", line 67, in query_expdesign_value
Fraction = query_reference["Fraction"].values[0]
IndexError: index 0 is out of bounds for axis 0 with size 0

Command used and terminal output

No response

Relevant files

No response

System information

No response