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nextflow run on a single sample with latest version 1.0.1 failed -"multi-dimensional indexing on a pandas Series" #2

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am8265 opened this issue Jul 13, 2023 · 1 comment

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@am8265
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am8265 commented Jul 13, 2023

Hello Authors,
I tried running the nextflow pipleine on a single sample (WGS PCR free and another exome) after building the docker image
from the latest version 1.0.1. I ran into the following errors, which seems to be an issue with "multi-dimensional indexing on a pandas Series" not being supported in python3.10. Thus, docker image would need to be modified.

Elapsed time: 0:00:11 Calculating z scores
  Traceback (most recent call last):
    File "/opt/conda/envs/main/bin/strling-outliers.py", line 451, in <module>
      main()
    File "/opt/conda/envs/main/bin/strling-outliers.py", line 332, in main
      z = z_score(sum_str_log_wide, mu_sd_estimates)
    File "/opt/conda/envs/main/bin/strling-outliers.py", line 140, in z_score
      return (x - df['mu'][:,np.newaxis])/df['sd'][:,np.newaxis]
    File "/opt/conda/envs/main/lib/python3.10/site-packages/pandas/core/series.py", line 1033, in __getitem__
      return self._get_with(key)
    File "/opt/conda/envs/main/lib/python3.10/site-packages/pandas/core/series.py", line 1048, in _get_with
      return self._get_values_tuple(key)
    File "/opt/conda/envs/main/lib/python3.10/site-packages/pandas/core/series.py", line 1082, in _get_values_tuple
      disallow_ndim_indexing(result)
    File "/opt/conda/envs/main/lib/python3.10/site-packages/pandas/core/indexers/utils.py", line 343, in disallow_ndim_indexing
      raise ValueError(
  ValueError: Multi-dimensional indexing (e.g. `obj[:, None]`) is no longer supported. Convert to a numpy array before indexing instead.

Work dir:
  /nfs/tx/in/STRling-nf-1.0.1/work/fb/44a007fe504136862345d22bf2e71b

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

Please let me know if you guys plan on modifying the docker image.
Thanks!

@hdashnow
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Thanks for the bug report. I'll see what I can do.

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