Hi I'm getting a deprication waring:
DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.htmlimport('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
The command then appears to run ok but then I'm getting the following:
Traceback (most recent call last):
File "/home/kilian/anaconda3/envs/ONT_pipeline/bin/scTE", line 4, in import('pkg_resources').run_script('scTE==1.0', 'scTE')
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/site-packages/pkg_resources/init.py", line 722, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/site-packages/pkg_resources/init.py", line 1561, in run_script
exec(code, namespace, namespace)
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/site-packages/scTE-1.0-py3.10.egg/EGG-INFO/scripts/scTE", line 173, in
main()
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/site-packages/scTE-1.0-py3.10.egg/EGG-INFO/scripts/scTE", line 155, in main
len_res, genenumber, filename = Countexpression(filename=args.out, allelement=allelement, genenumber=args.genenumber, cellnumber=args.cellnumber, hdf5=args.hdf5)
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/site-packages/scTE-1.0-py3.10.egg/scTE/base.py", line 427, in Countexpression
o = gzip.open('%s_scTEtmp/o4/%s.bed.gz'%(filename, filename), 'rt')
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/gzip.py", line 174, in init
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: 'scTE_out/SRR18609960_scTEtmp/o4/scTE_out/SRR18609960.bed.gz'
Im running command on ubuntu 22.04 machine with python 3.11
command: mkdir scTE_out
cat sample_list.txt | while read sample; do
scTE -i alignments_STAR/${sample}Aligned.out.bam -o scTE_out/${sample} -x reference/hg38.exclusive.idx --hdf5 True -CB CR -UMI UR
done
Hi I'm getting a deprication waring: 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
The command then appears to run ok but then I'm getting the following: Traceback (most recent call last): File "/home/kilian/anaconda3/envs/ONT_pipeline/bin/scTE", line 4, in
import('pkg_resources').run_script('scTE==1.0', 'scTE')
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/site-packages/pkg_resources/init.py", line 722, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/site-packages/pkg_resources/init.py", line 1561, in run_script
exec(code, namespace, namespace)
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/site-packages/scTE-1.0-py3.10.egg/EGG-INFO/scripts/scTE", line 173, in
main()
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/site-packages/scTE-1.0-py3.10.egg/EGG-INFO/scripts/scTE", line 155, in main
len_res, genenumber, filename = Countexpression(filename=args.out, allelement=allelement, genenumber=args.genenumber, cellnumber=args.cellnumber, hdf5=args.hdf5)
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/site-packages/scTE-1.0-py3.10.egg/scTE/base.py", line 427, in Countexpression
o = gzip.open('%s_scTEtmp/o4/%s.bed.gz'%(filename, filename), 'rt')
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/home/kilian/anaconda3/envs/ONT_pipeline/lib/python3.10/gzip.py", line 174, in init
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: 'scTE_out/SRR18609960_scTEtmp/o4/scTE_out/SRR18609960.bed.gz'