Error when preparing background data following guideline

[genomesurveillance]

Hello, civet developers, It might be something small, but I could not figure out the reason. When preparing the background data set following the guideline, with the following command: "civet -bd align_curate -bd-seqs hcov_europe.fasta -bd-metadata hcov_europe.tsv --sequence-id-column strain", I always got this error: AttributeError: 'str' object has no attribute 'name'".

Both the fasta and tsv files were downloaded from GISAID following the guideline of civet. The version of civet installed is 3.0.1. When testing with the command "civet --version" and "civet --art", all appear normal. I tried it with both linux system and macintosh system, and got the same error. I would really appreciate a quick solution for it.

[aineniamh]

Hi @genomesurveillance, if it's possible could you supply the whole error message and I'll look into what the source of the error is?

[aineniamh]

Having a look around it looks like it could be a snakemake version issue (https://github.com/spacegraphcats/spacegraphcats/issues/471).

What version of snakemake have you in the environment?

snakemake --version

[genomesurveillance]

The whole error message is: Traceback (most recent call last): File "/home/yibuq/anaconda3/envs/civet/lib/python3.9/site-packages/snakemake/init.py", line 699, in snakemake success = workflow.execute( File "/home/yibuq/anaconda3/envs/civet/lib/python3.9/site-packages/snakemake/workflow.py", line 1043, in execute logger.run_info("\n".join(dag.stats())) File "/home/yibuq/anaconda3/envs/civet/lib/python3.9/site-packages/snakemake/dag.py", line 2176, in stats yield tabulate(rows, headers="keys") File "/home/yibuq/anaconda3/envs/civet/lib/python3.9/site-packages/tabulate/init.py", line 2048, in tabulate list_of_lists, headers = _normalize_tabular_data( File "/home/yibuq/anaconda3/envs/civet/lib/python3.9/site-packages/tabulate/init.py", line 1471, in _normalize_tabular_data rows = list(map(lambda r: r if _is_separating_line(r) else list(r), rows)) File "/home/yibuq/anaconda3/envs/civet/lib/python3.9/site-packages/tabulate/init.py", line 1471, in rows = list(map(lambda r: r if _is_separating_line(r) else list(r), rows)) File "/home/yibuq/anaconda3/envs/civet/lib/python3.9/site-packages/tabulate/init.py", line 107, in _is_separating_line (len(row) >= 1 and row[0] == SEPARATING_LINE) File "/home/yibuq/anaconda3/envs/civet/lib/python3.9/site-packages/snakemake/rules.py", line 1127, in eq return self.name == other.name and self.output == other.output AttributeError: 'str' object has no attribute 'name'

[genomesurveillance]

The snakemake version in linux system is: 6.8.0.

[genomesurveillance]

Both the error report and snakemake version are the information in Linux system.

[aineniamh]

Ah, that error suggests it's a tabulate error. If you type in the civet environment pip uninstall tabulate and then type pip install tabulate==0.8.9 that should solve. I'll update the civet setup.py to specify a particular tabulate version.

[genomesurveillance]

Thanks a lot for the help! Now it works! Indeed it is caused by the version of tabulate.

[genomesurveillance]

Thank you for helping me solve this issue so quickly!

[aineniamh]

No worries, glad to hear it's working now! 🎉

[ctb]

thanks for linking to the spacegraphcats issue 😆 - suggested a structural fix to snakemake over here and you might go thumbs up that if it resonates!