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JiekaiLab / scTE

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IndexError: list index out of range #79

Open Kiliankleemann opened 6 months ago

Kiliankleemann commented 6 months ago

trying to run scTE_build getting this error: File "/home/kilian/anaconda3/envs/scte/bin/scTE_build", line 4, in import('pkg_resources').run_script('scTE==1.0', 'scTE_build') File "/home/kilian/anaconda3/envs/scte/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/scte/lib/python3.10/site-packages/pkg_resources/init.py", line 1561, in run_script exec(code, namespace, namespace) File "/home/kilian/anaconda3/envs/scte/lib/python3.10/site-packages/scTE-1.0-py3.10.egg/EGG-INFO/scripts/scTE_build", line 468, in main() File "/home/kilian/anaconda3/envs/scte/lib/python3.10/site-packages/scTE-1.0-py3.10.egg/EGG-INFO/scripts/scTE_build", line 461, in main genomeIndex(args.genome,args.mode,tefile,genefile, args.out,'No path','No path') File "/home/kilian/anaconda3/envs/scte/lib/python3.10/site-packages/scTE-1.0-py3.10.egg/EGG-INFO/scripts/scTE_build", line 127, in genomeIndex gls.load_list(clean) File "/home/kilian/anaconda3/envs/scte/lib/python3.10/site-packages/scTE-1.0-py3.10.egg/scTE/miniglbase/genelist.py", line 1472, in load_list list_to_load[0] IndexError: list index out of range

cyyisbest commented 6 months ago

hello, have you overcome the above issue , i have met the same error

Kiliankleemann commented 6 months ago

nope

goubo1st commented 4 months ago

For me, GTF file chrom col should start with chr not Chr or others

jphe commented 3 months ago

can you paste the cmd that you use to build the index, and a few rows of the bed/GTF file for TEs/Genes annotation, thanks