TypeError: unsupported operand type(s) for |: 'type' and 'type' #103
Description
We installed scTE with python3.9 and I have successfully run scTE_build for mm10.
However I am having issues running scTE. The issue appears to be
TypeError: unsupported operand type(s) for |: 'type' and 'type'
(see at bottom for entire printout).
This issue appears both when I attempt to run my own 10X genomics file using
scTE -i ${BAM_FILE} -o ${prefixFilename} -x ${mm10_sc_index} -CB CB -UMI UB
and it also appears when I run the test.bam provided with the code:
scTE -i test.bam -o secondTest -x test.exclusive.idx -CB CR -UMI UR
I have examined the numerous github issues listed for scTE and is seems as though others have indicated that python 3.9 should be OK for this software. Can you provide some help or suggestion?
Thanks,
Rob
Output from the failed run is:
/public/apps/conda3/bin/scTE:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import('pkg_resources').run_script('scTE==1.0', 'scTE')
DEBUG : Creating converter from 7 to 5
DEBUG : Creating converter from 5 to 7
DEBUG : Creating converter from 7 to 5
DEBUG : Creating converter from 5 to 7
Traceback (most recent call last):
File "/public/apps/conda3/bin/scTE", line 4, in
import('pkg_resources').run_script('scTE==1.0', 'scTE')
File "/public/apps/conda3/lib/python3.9/site-packages/pkg_resources/init.py", line 722, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/public/apps/conda3/lib/python3.9/site-packages/pkg_resources/init.py", line 1561, in run_script
exec(code, namespace, namespace)
File "/gs/gsfs0/hpc01/rhel8/apps/conda3/lib/python3.9/site-packages/scTE-1.0-py3.9.egg/EGG-INFO/scripts/scTE", line 13, in
from scTE.base import *
File "/public/apps/conda3/lib/python3.9/site-packages/scTE-1.0-py3.9.egg/scTE/base.py", line 16, in
import anndata as ad
File "/public/apps/conda3/lib/python3.9/site-packages/anndata-0.11.0rc3-py3.9.egg/anndata/init.py", line 29, in
from ._core.anndata import AnnData
File "/public/apps/conda3/lib/python3.9/site-packages/anndata-0.11.0rc3-py3.9.egg/anndata/_core/anndata.py", line 25, in
from .. import utils
File "/public/apps/conda3/lib/python3.9/site-packages/anndata-0.11.0rc3-py3.9.egg/anndata/utils.py", line 15, in
from ._core.sparse_dataset import BaseCompressedSparseDataset
File "/public/apps/conda3/lib/python3.9/site-packages/anndata-0.11.0rc3-py3.9.egg/anndata/_core/sparse_dataset.py", line 30, in
from .._settings import settings
File "/public/apps/conda3/lib/python3.9/site-packages/anndata-0.11.0rc3-py3.9.egg/anndata/_settings.py", line 17, in
from anndata.compat import CAN_USE_SPARSE_ARRAY
File "/public/apps/conda3/lib/python3.9/site-packages/anndata-0.11.0rc3-py3.9.egg/anndata/compat/init.py", line 49, in
Index1D = slice | int | str | np.int64 | np.ndarray
TypeError: unsupported operand type(s) for |: 'type' and 'type'