import sys
from qgis.core import *

QgsApplication.setPrefixPath("/usr", True)
qgs = QgsApplication([], True)
qgs.initQgis()
print(QgsApplication.showSettings())

##Processing initialization
sys.path.extend(['/usr/share/qgis/python/plugins', '/usr/share/qgis/python/plugins/processing',
                 '/usr/share/qgis/python', '/usr/lib/qgis/plugins'])  # Folder for Processing
import processing
from processing.core.Processing import Processing
Processing.initialize()  # needed to be able to use the functions afterwards

##Get and load the project instance
project = QgsProject.instance()
project.setCrs(QgsCoordinateReferenceSystem(2154))

## Chargement d'une couche
vlayer = QgsVectorLayer('/my/place/to/save/zone_etude.shp','zone_etude','ogr')
project.addMapLayer(vlayer)

param = {'INPUT':'/my/place/to/save/zone_etude.shp',
         'TARGET_CRS':QgsCoordinateReferenceSystem('EPSG:4326'),
         'OUTPUT':'TEMPORARY_OUTPUT'}
processing.run("native:reprojectlayer", param)

project.write('/my/place/to/save/tutoproject.qgs')
qgs.exitQgis()

Application state:
QGIS_PREFIX_PATH env var:
Prefix:     /usr
Plugin Path:        /usr/lib/qgis/plugins
Package Data Path:  /usr/share/qgis
Active Theme Name:
Active Theme Path:  /usr/share/qgis/resources/themes//icons/
Default Theme Path: :/images/themes/default/
SVG Search Paths:   /usr/share/qgis/svg/
        /home/edelb/.local/share/profiles/default/svg/
User DB Path:   /usr/share/qgis/resources/qgis.db
Auth DB Path:   /home/edelb/.local/share/profiles/default/qgis-auth.db

Backend TkAgg is interactive backend. Turning interactive mode on.
/usr/lib/python3/dist-packages/osgeo/gdal.py:112: DeprecationWarning:
gdal.py was placed in a namespace, it is now available as osgeo.gdal

Traceback (most recent call last):
  File "/my/place/to/save/repro_bug.py", line 26, in <module>
    processing.run("native:reprojectlayer", param)
  File "/usr/share/qgis/python/plugins/processing/tools/general.py", line 106, in run
    return Processing.runAlgorithm(algOrName, parameters, onFinish, feedback, context)
  File "/usr/share/qgis/python/plugins/processing/core/Processing.py", line 125, in runAlgorithm
    raise QgsProcessingException(msg)
_core.QgsProcessingException: Error: Algorithm native:reprojectlayer not found

>>>for alg in QgsApplication.processingRegistry().algorithms():
       print("{}:{} --> {}".format(alg.provider().name(), alg.name(), alg.displayName()))


GDAL:aspect --> Aspect
GDAL:assignprojection --> Assign projection
...
GRASS:r.spreadpath --> r.spreadpath
...
QGIS:vectorlayerscatterplot --> Vector layer scatterplot
QGIS:voronoipolygons --> Voronoi polygons
QGIS:zonalstatistics --> Zonal statistics