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hsigeman / findZX

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TypeError when running example data #12

Closed faye-romero closed 9 months ago

faye-romero commented 10 months ago

Hello,

I have installed findZX using conda according to the instructions. However, when I try to run findZX on the test data, I get the following errors:

#command: snakemake -s workflow/findZX --configfile .test/config.yml --cores 1 -R all --use-conda -k

TypeError in line 15 of /gpfs/fs2/scratch/nchen11_lab/findZX/workflow/rules/common.smk:
field() got an unexpected keyword argument 'alias'
  File "/gpfs/fs2/scratch/nchen11_lab/findZX/workflow/findZX", line 1, in <module>
  File "/gpfs/fs2/scratch/nchen11_lab/findZX/workflow/rules/common.smk", line 15, in <module>
  File "/home/fromero3/.conda/envs/findZX/lib/python3.9/site-packages/jsonschema/__init__.py", line 13, in <module>
  File "/home/fromero3/.conda/envs/findZX/lib/python3.9/site-packages/jsonschema/_format.py", line 11, in <module>
  File "/home/fromero3/.conda/envs/findZX/lib/python3.9/site-packages/jsonschema/exceptions.py", line 15, in <module>
  File "/home/fromero3/.conda/envs/findZX/lib/python3.9/site-packages/referencing/__init__.py", line 4, in <module>
  File "/home/fromero3/.conda/envs/findZX/lib/python3.9/site-packages/referencing/_core.py", line 29, in <module>
  File "/home/fromero3/.conda/envs/findZX/lib/python3.9/site-packages/referencing/_core.py", line 55, in Specification

Any help diagnosing this error would be much appreciated!

hsigeman commented 10 months ago

Hi Faye,

Sorry you're having problems getting the program to run!

I haven't seen this error message before, but my guess is that it might have something to do with conflicting python packages.

Are you running this on a server or locally, and do you have the possibility to try on a different platform?

It would be great if you could also confirm that you are using python3 (python -V).

Hanna

faye-romero commented 10 months ago

Hi @hsigeman , thanks for the quick reply!

I'm running this on a server; I have a lot of large data files, so I don't think I'll be able to run this locally. I can also confirm that I'm running python3:

python -V
#Python 3.9.4

I'm working with the computing center at my institution to see if they have any insights. I will keep you updated.

faye-romero commented 9 months ago

Hi @hsigeman , it turns out it was a conflicting installation of python3 itself. Marking as resolved.