pkg_resources.ResolutionError when running "collapse_isoforms_by_sam.py"

[ssaif-cellarity]

collapse_isoforms_by_sam.py --input HL60_fltnc_dedup.fasta -s HL60_fltnc_dedup.fasta.sorted.sam -c 0.99 -i 0.95 --gen_mol_count -o HL60_fltnc_dedup.5merge &
[1] 41376
(SQANTI3.env) [/home/ubuntu/Yale_PacBio_Data/isoseq_single-cell_analysis] Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/SQANTI3.env/bin/collapse_isoforms_by_sam.py", line 4, in
import('pkg_resources').run_script('cupcake==28.0.0', 'collapse_isoforms_by_sam.py')
File "/home/ubuntu/miniconda3/envs/SQANTI3.env/lib/python3.9/site-packages/pkg_resources/init.py", line 672, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/ubuntu/miniconda3/envs/SQANTI3.env/lib/python3.9/site-packages/pkg_resources/init.py", line 1460, in run_script
raise ResolutionError(
pkg_resources.ResolutionError: Script 'scripts/collapse_isoforms_by_sam.py' not found in metadata at '/home/ubuntu/cDNA_Cupcake/cupcake.egg-info'

[ssaif-cellarity]

echo $PYTHONPATH
/home/ubuntu/cDNA_Cupcake/sequence/:/home/ubuntu/cDNA_Cupcake/sequence/:/home/ubuntu/cDNA_Cupcake/sequence/:/home/ubuntu/cDNA_Cupcake/

echo $PATH
/home/ubuntu/miniconda3/envs/SQANTI3.env/bin:/home/ubuntu/bioinfo/STAR-2.7.0a/bin/Linux_x86_64:/home/ubuntu/bioinfo/cellranger-3.1.0:/home/ubuntu/.local/bin:/home/ubuntu/miniconda3/bin:/home/ubuntu/miniconda3/condabin:/home/ubuntu/cDNA_Cupcake/sequence:/home/ubuntu/cDNA_Cupcake/rarefaction

which collapse_isoforms_by_sam.py
/home/ubuntu/miniconda3/envs/SQANTI3.env/bin/collapse_isoforms_by_sam.py

[wx904]

I had the same issue after running the python script sqanti3.py. When I went back to rerun collapse_isoforms_by_sam.py, the same "pkg_resources.ResolutionError..." error occurred, and same to other cupcake programs.