Custom NCBI: 'ValueError: Length mismatch...'

[onurdogan]

Hello Till,

I encountered an error while attempting to perform the 'Custom NCBI > 4. Filter BLAST results (.csv) - Taxonomy source: Custom NCBI' task under the 'Local Blast' module. Notably, the '3. assigning taxonmy using BLASTn' step produces a '.csv' file that lacks of some information (even column headers (such as ID, Phylum,...Status, Ambigous, Flag) in taxonomic hierarchy.

I got a '[rbcl_SAR] gb' file from NCBI in 'Complete Record' and 'GenBank (full) format' organized by Default order (following your instructions).

Thanks,
Onur

`File "/usr/local/bin/apscale_gui", line 8, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/apscale_gui/main.py", line 802, in main
filter_blast_results(values2['blast_csv'], values2['local_blast_read_table'], project_folder, values2['blast_database'], filter_tresholds, values2['database_taxonomy_source'], float(values2['threshold_e_value']))
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/apscale_gui/blast_utilities.py", line 1125, in filter_blast_results
blast_df_out.columns = ['ID', 'Phylum', 'Class', 'Order', 'Family', 'Genus', 'Species', 'Similarity', 'Status', 'Ambigous', 'Flag']
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pandas/core/generic.py", line 6218, in setattr
return object.setattr(self, name, value)
File "properties.pyx", line 69, in pandas._libs.properties.AxisProperty.set
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pandas/core/generic.py", line 767, in _set_axis
self._mgr.set_axis(axis, labels)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 227, in set_axis
self._validate_set_axis(axis, new_labels)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pandas/core/internals/base.py", line 85, in _validate_set_axis

raise ValueError(
ValueError: Length mismatch: Expected axis has 20 elements, new values have 11 elements`

[TillMacher]

Hi Onur,
sorry I will not have time to look into this issue within the next 3 weeks. I hope you can find a workaround or wait until then.
cheers
Till