Kodoja failed unexpectedly

[sanchari24]

Hello,
I was trying to build a new database, but I am getting this error. I installed the package through bioconda. Please help.

kodoja_build.py -o kodoja_db
Kodoja failed unexpectedly with the following:

Traceback (most recent call last):
File "/home/ssir/miniconda3/envs/kodoja/bin/kodoja_build.py", line 168, in
main()
File "/home/ssir/miniconda3/envs/kodoja/bin/kodoja_build.py", line 125, in main
subset_vir_assembly = list(vir_assembly.assembly_accession[vir_assembly['taxid'].isin(vir_host)])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ssir/miniconda3/envs/kodoja/lib/python3.11/site-packages/pandas/core/generic.py", line 5902, in getattr
return object.getattribute(self, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'DataFrame' object has no attribute 'assembly_accession'

If this happens consistently, please check you are using the
latest version, then check the issue tracker to see if this is
a known issue, and if not please report the problem:

https://github.com/abaizan/kodoja/issues

Kodoja aborted.

[peterjc]

What version of pandas do you have? My guess from there dataframe error is your Pandas is too new, try pandas v0.14 as per the kodoja README.

If that fixes it, we could look into making this work on modern pandas too...

[sanchari24]

Hi Peter, we could modify the code to suit the present pandas settings, however other errors came up such as
ERROR: No entry for file ending in '_genomic.fna.gz'

The kodoja_search.py works fine for me with the pre-built database. So its just that if you can update the prebuilt database in the repository, then I can move ahead with the analysis. I understand that this is a temporary solution for now.

[peterjc]

I don't have enough context to say where that error message comes from. I don't see anything like that error message in the kodoja scripts, so this is most likely kraken or kaiju.

It is quite possible that this and the underlying problem in #43 are both from changes on the NCBI FTP site.