local variable ‘feature_db’ referenced before assignment


I want to map annotations from rich gencode human gtf or gff3 to great apes’ genome.

I tried to run liftoff (github.com/agshumate/Liftoff)

but it returns error the below.
Following the github issue’s post,
I confirmed

  1. there’s no _db file before running,
  2. the annotation file is .gff3,
  3. the permission of the annotation file is -rwxrwxrwx,
    and I did umask 0000 as default permission setting.

However, there comes still the similar error like,

Traceback (most recent call last): 
File "/home/usr/anaconda3/envs/liftoff/bin/liftoff", line 10, in sys.exit(main()) 
File "/home/usr/anaconda3/envs/liftoff/lib/python3.6/site-packages/liftoff/run_liftoff.py", line 10, in main run_all_liftoff_steps(args) 
File "/home/usr/anaconda3/envs/liftoff/lib/python3.6/site-packages/liftoff/run_liftoff.py", line 25, in run_all_liftoff_steps parent_features_to_lift) 
File "/home/usr/anaconda3/envs/liftoff/lib/python3.6/site-packages/liftoff/liftover_types.py", line 13, in lift_original_annotation parents_to_lift, args) 
File "/home/usr/anaconda3/envs/liftoff/lib/python3.6/site-packages/liftoff/extract_features.py", line 17, in extract_features_to_lift feature_db = create_feature_db_connections(args) 
File "/home/usr/anaconda3/envs/liftoff/lib/python3.6/site-packages/liftoff/extract_features.py", line 32, in create_feature_db_connections feature_db = build_database(args.db, args.g, disable_transcripts, disable_genes) 
File "/home/usr/anaconda3/envs/liftoff/lib/python3.6/site-packages/liftoff/extract_features.py", line 47, in build_database 
return feature_db 
UnboundLocalError: local variable 'feature_db' referenced before assignment

My command is

liftoff /home/usr/genome/seq/PTRv2_chrxm.fa /home/usr/genome/seq/GRCh38p12_chrxm.fa -g gencode.GRCh38p13_chrxm_wo_header.gff3 -o lifted_off.panTro6_chrxm.gff3 -u NOT_liftedoff.panTro6_chrxm.gff3 -p 32 2>&1 1> chimp_liftoff.log

My liftoff version is v1.6.1

Does anyone successfully solve this problem?

Thank you in advance,

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