TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'

[JiahuaQu]

Hi, thank you for the new program. When I was trying it in Linux system within a conda env, I got the error first: File "/home/.conda/envs/starCAT_env/lib/python3.9/site-packages/starcat/starcat.py", line 417, in save_results self.usage_norm.to_csv(os.path.join(output_dir, name+'.rf_usage_normalized.txt'), sep='\t') TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'. Then I revised the line of script manually to be name, '.rf_usage_normalized.txt'). Although the program progressed a little, I had another similar error: File "/home/.conda/envs/starCAT_env/lib/python3.9/genericpath.py", line 152, in _check_arg_types raise TypeError(f'{funcname}() argument must be str, bytes, or ' TypeError: join() argument must be str, bytes, or os.PathLike object, not 'NoneType'

I also tried to install another version of python (3.7) which was tested by you, but it didn't work either.

Hope to get your help to figure it out. Thank you.

[michelle-curtis]

Hi, thanks for your post! Could you provide the full set of commands you are running, and the full error traces?

[JiahuaQu]

Thank you for your quick response. My commands: module load mamba/1.4.2 mamba create -n starCAT_env ipython python=3.9 mamba activate starCAT_env
pip install starcatpy mamba install seaborn scikit-learn pip install scanpy mamba install requests mamba deactivate

module load conda3/202210 source activate starCAT_env (or python=3.7) ref="TCAT.V1" counts_fn="01-make_mtx/matrix.mtx.gz" ouput_name="starCAT-CARneg" output_dir="02-run_starCAT" if [ ! -d "${output_dir}" ]; then mkdir "${output_dir}" fi starcat --reference $ref --counts ${counts_fn} --output-dir ${output_dir} --name ${output_name}

The full errors are: run_229421947.error.txt run_229422374.error.txt run_229423857.error.txt run_229435631.error.txt

[michelle-curtis]

Thank you! I think it might be a typo when assigning the variable output_name. Can you try changing ouput_name="starCAT-CARneg" to output_name="starCAT-CARneg", and see if that solves the issue, when running the original code?

[JiahuaQu]

Thank you. I will revise it and have another try. In addition, I tried to run the program with the reference database or tsv file downloaded in a prior try, but the program returned an error, starcat: error: unrecognized arguments: --score_path or starcat: error: unrecognized arguments: --cachedir?

[michelle-curtis]

The arguments score_path and cachedir actually aren't supported when running starcat via command line. You can find a list of possible command line arguments in the README.md. The argument to specify a scores.yml file via command line is --scores, so an example command would look like this: starcat --reference "TCAT.V1" --counts {counts_fn} --output-dir {output_dir} --name {outuput_name} --scores {score_path}

Also, please note that including a scores file is optional. If you are using the default TCAT.V1 reference, you can just specify its name --reference "TCAT.V1", and both the reference and scores paths can be inferred from this. In this case, the reference and scores file will be downloaded to a cache location in your working directory, i.e './cache'.

Hope this helps!

[JiahuaQu]

Thank you very much. I ran the program successfully and will delve into the results.

[michelle-curtis]

Ok great!