subprocess.CalledProcessError:

[ShaktiprasadM]

The code runs and shows markers included and excluded and then the error comes as :
"Traceback (most recent call last):
File "/userdata/shakti/test2/../conda_envs/Cytophenograph/cytophenograph.v6.py", line 84, in
DictInfo["flowsom_adata"] = run.runflowsom()
File "/userdata/shakti/conda_envs/Cytophenograph/PhenoFunctions_v6.py", line 845, in runflowsom
subprocess.check_call(['Rscript', '--vanilla',
File "/userdata/shakti/tools/mambaforge/envs/Cytophenograph6/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['Rscript', '--vanilla', '/userdata/shakti/conda_envs/Cytophenograph/flowsom.Rscript', '/userdata/shakti/test2/day17_output//tmp.csv', '/userdata/shakti/test2/day17_output/', '/userdata/shakti/test2/day17_output//FiguresFlowSOM/UMAP', '31']' returned non-zero exit status 1.

@@@execution Error!"

[luglilab]

Hi,

could you update the conda environment with this yml file

environment_Cytophenograph6.yml.zip

[ShaktiprasadM]

Thanks a lot. It was an error with the package FlowSOM, flowAI. I reinstalled them. Read your entire script and found the error is happening at calling the Rscript part. I had one more question. If I don't want to downsample, what should I do? With Regards Shaktiprasad Mishra

…

On Mon, 13 May 2024, 17:58 LugliLab, ***@***.***> wrote: Hi, could you update the conda environment with this yml file environment_Cytophenograph6.yml.zip <https://github.com/luglilab/Cytophenograph/files/15294442/environment_Cytophenograph6.yml.zip> — Reply to this email directly, view it on GitHub <#16 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A4MU44HIF4OHQXCA26MM5WTZCCWVXAVCNFSM6AAAAABHQDWX6GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBXGQ2DINZSGA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[luglilab]

Just run the analysis without setting the downsampling flag.