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Magdoll / cDNA_Cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data
BSD 3-Clause Clear License
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pkg_resources.ResolutionError when running "collapse_isoforms_by_sam.py" #220

Open ssaif-cellarity opened 2 years ago

ssaif-cellarity commented 2 years ago

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 commented 2 years ago

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 commented 1 year ago

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.