luglilab / cytophenograph Goto Github PK

During Installation:
Traceback (most recent call last):
File "", line 1, in
File "/Users/simone/opt/anaconda3/envs/cytophenograph2/lib/python3.6/site-packages/anndata/init.py", line 7, in
from ._core.anndata import AnnData, ImplicitModificationWarning
File "/Users/simone/opt/anaconda3/envs/cytophenograph2/lib/python3.6/site-packages/anndata/_core/anndata.py", line 18, in
from natsort import natsorted
File "/Users/simone/opt/anaconda3/envs/cytophenograph2/lib/python3.6/site-packages/natsort/init.py", line 3, in
from natsort.natsort import (
File "/Users/simone/opt/anaconda3/envs/cytophenograph2/lib/python3.6/site-packages/natsort/natsort.py", line 686, in
os_sort_key = os_sort_keygen()
File "/Users/simone/opt/anaconda3/envs/cytophenograph2/lib/python3.6/site-packages/natsort/natsort.py", line 649, in os_sort_keygen
return natsort_keygen(key=key, alg=ns.LOCALE | ns.PATH | ns.IGNORECASE)
File "/Users/simone/opt/anaconda3/envs/cytophenograph2/lib/python3.6/site-packages/natsort/natsort.py", line 177, in natsort_keygen
input_transform = utils.input_string_transform_factory(alg)
File "/Users/simone/opt/anaconda3/envs/cytophenograph2/lib/python3.6/site-packages/natsort/utils.py", line 503, in input_string_transform_factory
thou=re.escape(get_thousands_sep()), nodecimal=nodecimal
File "/Users/simone/opt/anaconda3/envs/cytophenograph2/lib/python3.6/site-packages/natsort/compat/locale.py", line 73, in get_thousands_sep
loc = ".".join(locale.getlocale())
File "/Users/simone/opt/anaconda3/envs/cytophenograph2/lib/python3.6/locale.py", line 581, in getlocale
return _parse_localename(localename)
File "/Users/simone/opt/anaconda3/envs/cytophenograph2/lib/python3.6/locale.py", line 490, in _parse_localename
raise ValueError('unknown locale: %s' % localename)
ValueError: unknown locale: UTF-8

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!"

If after execution of python ./Cytophenograph/cytophenograph.v2_0.py --help shows this message "Illegal instruction" it means that the installation of PARC was incorrect, please change strategy.

Il link di installazione di miniconda3 è errato … manca una l finale nella URL riportata.

Cool project. I thought I'd share that the two links under the "File preparation" section of Test Execution return 404s.