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cov-lineages / pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages.
GNU General Public License v3.0
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new updated pangolin doesn't work #535

Open yl315504 opened 10 months ago

yl315504 commented 10 months ago

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

Capture1 Capture2

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'  Pangolin running in usher mode.   --no-temp: all intermediate files will be written to /scratch/08270/yanliu74/UTSW_covid/Project_JAS_2023_12_06_COV212_13461_0/output

Maximum ambiguity allowed is 0.5.  Query file: /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  Data files found: usher_pb: /work/08270/yanliu74/ls6/MC/envs/CovidBashR.v.0.7/lib/python3.8/site-packages/pangolin_data/data/lineageTree.pb ****

aineniamh commented 10 months ago

Hi @yl315504, googling your error message, it seems that this has been flagged before: https://github.com/cov-lineages/pangolin/issues/504 https://github.com/cov-lineages/pangolin/issues/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 commented 10 months ago

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

aineniamh commented 9 months ago

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 commented 9 months ago

@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