Error: Error processing taxonomic ID 59201: 17:51:07.885 [ERRO] open C:\Users\krist\AppData\Local\Temp\tmprg7jjz1s-lineage.txt: The process cannot access the file because it is being used by another process.

[kristinebraun]

Hello. I am trying to use pytaxonkit.lineage to extract taxanomic ids from a pandas dataframe I have read by using: df = pd.read_csv(taxanomic_dataframe, sep='\t', header=None) to get associated domains into a new column. The column with taxids is column five. I use this code after reading the table.

staxids = xml_table.iloc[:,5] lineages = pytaxonkit.lineage(list(staxids))

extract domain info from the lineage -> domain is the first element in the lineage

domains = lineages['Lineage'].str.split(';').str[0]
xml_table['domains'] = domains

return xml_table

After running this code, I get the error: TaxonKitCLIError: 16:55:06.202 [ERRO] open C:\Users\krist\AppData\Local\Temp\tmpzthchgl8-lineage.txt: The process cannot access the file because it is being used by another process. I am using windows 11. Why is this happening and how can I fix it?

[standage]

Greetings @kristinebraun!

This is an error message I'm not familiar with. I've tested pytaxonkit mostly on Linux and MacOS.

How large is staxids? Can you confirm its contents are what you expect?

[standage]

Feel free to re-open this thread if the issue persists.