luglilab / cytophenograph Goto Github PK

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.

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

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

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!"