new updated pangolin doesn't work

[yl315504]

I just updated pangolin and it doesn't work. A new directory ".snakemake" was generated.

Below is message in the output.txt file.
Traceback (most recent call last):
File "/work/08270/yanliu74/ls6/MC/envs/CovidBashR.v.0.7/lib/python3.8/site-packages/snakemake/init.py", line 699, in snakemake
success = workflow.execute(
File "/work/08270/yanliu74/ls6/MC/envs/CovidBashR.v.0.7/lib/python3.8/site-packages/snakemake/workflow.py", line 1043, in execute
logger.run_info("\n".join(dag.stats()))
File "/work/08270/yanliu74/ls6/MC/envs/CovidBashR.v.0.7/lib/python3.8/site-packages/snakemake/dag.py", line 2176, in stats
yield tabulate(rows, headers="keys")
File "/work/08270/yanliu74/ls6/MC/envs/CovidBashR.v.0.7/lib/python3.8/site-packages/tabulate/init.py", line 2048, in tabulate
list_of_lists, headers = _normalize_tabular_data(
File "/work/08270/yanliu74/ls6/MC/envs/CovidBashR.v.0.7/lib/python3.8/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 "/work/08270/yanliu74/ls6/MC/envs/CovidBashR.v.0.7/lib/python3.8/site-packages/tabulate/init.py", line 1471, in
rows = list(map(lambda r: r if _is_separating_line(r) else list(r), rows))
File "/work/08270/yanliu74/ls6/MC/envs/CovidBashR.v.0.7/lib/python3.8/site-packages/tabulate/init.py", line 107, in _is_separating_line
(len(row) >= 1 and row[0] == SEPARATING_LINE)
File "/work/08270/yanliu74/ls6/MC/envs/CovidBashR.v.0.7/lib/python3.8/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'
�[32m****
Pangolin running in usher mode.
****�[0m
�[32m
--no-temp: �[0mall intermediate files will be written to /scratch/08270/yanliu74/UTSW_covid/Project_JAS_2023_12_06_COV212_13461_0/output

�[32mMaximum ambiguity allowed is 0.5.
�[0m
�[32mQuery file: �[0m/scratch/08270/yanliu74/UTSW_covid/Project_JAS_2023_12_06_COV212_13461_0/Project_JAS_2023_12_06_COV212_13461_0.trim.t0.5.ivar.fasta
�[32m
Data files found:�[0m
usher_pb: /work/08270/yanliu74/ls6/MC/envs/CovidBashR.v.0.7/lib/python3.8/site-packages/pangolin_data/data/lineageTree.pb
�[32m****�[0m

[aineniamh]

Hi @yl315504, googling your error message, it seems that this has been flagged before:
#504
#489

And is down to a snakemake/tabulate version incompatibility.

How did you install/ update pangolin? Through bioconda or via git clone and an environment update?

[yl315504]

We update pangolin every week. We got this error after update this week.
conda update pangolin --yes

[aineniamh]

Hi @yl315504, I've just re-triggered all tests in pangolin github actions and the current version is passing tests with all the latest installs.

I suspect some part of the install you have is out of date- I notice you're running quite an old python version.
My recommendation would be to create a new environment for pangolin with a newer python version or remove/ uninstall pangolin from your CovidBashR.v.0.7 environment and re-install again from scratch.

I would also recommend using mamba as it is faster than conda.

[corneliusroemer]

@aineniamh Since October, conda comes with the mamba solver so should no longer have the speed issues yay!
See: https://docs.conda.io/projects/conda/en/latest/release-notes.html#with-this-23-10-0-release-we-are-changing-the-default-solver-of-conda-to-conda-libmamba-solver