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micom-dev / databases

Workflows and input data for the construction of the standard MICOM model databases.
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TypeError in convert_to_gtdb Process #3

Closed Amit-H closed 4 weeks ago

Amit-H commented 4 weeks ago

The Nextflow pipeline agora2.nf fails during the execution of the convert_to_gtdb process due to a TypeError in the Python script. The error occurs when attempting to concatenate DataFrames using pd.concat.

Traceback (most recent call last):
  File ".command.sh", line 16, in <module>
    meta = pd.concat([meta, tax], 1).drop(["gtdb_taxonomy"], axis=1).drop_duplicates()
TypeError: concat() takes 1 positional argument but 2 were given

I modified the script slightly to pass the axis parameter directly to pd.concat and this seems to have worked:

meta = pd.concat([meta, tax], axis=1).drop(["gtdb_taxonomy"], axis=1).drop_duplicates()

cdiener commented 4 weeks ago

Makes sense. Newer pandas versions don't support unnamed args.