UnboundLocalError: local variable 'i' referenced before assignment

[ghm17]

Hi, I was trying to predict the chromatin profiles by running sh 1_sequence_prediction.sh $input_filepath $genome_version $outdir --cuda but got the following errors. Can anyone helps for this? Thanks in advance.

Input argments: test.vcf test hg19 --cuda
use_cuda: True
Setting random seed = 999
Traceback (most recent call last):
File "1_sequence_prediction.py", line 73, in
parse_configs_and_run(configs)
File "/home/users/hmguo/.local/lib/python3.6/site-packages/selene_sdk/utils/config_utils.py", line 351, in parse_configs_and_run
execute(operations, configs, current_run_output_dir)
File "/home/users/hmguo/.local/lib/python3.6/site-packages/selene_sdk/utils/config_utils.py", line 251, in execute
analyze_seqs.get_predictions(**predict_info)
File "/home/users/hmguo/.local/lib/python3.6/site-packages/selene_sdk/predict/model_predict.py", line 595, in get_predictions
strand_index=strand_index)
File "/home/users/hmguo/.local/lib/python3.6/site-packages/selene_sdk/predict/model_predict.py", line 438, in get_predictions_for_bed_file
sequences = sequences[:i % self.batch_size + 1, :, :]
UnboundLocalError: local variable 'i' referenced before assignment

[kathyxchen]

Hi @ghm17 , what version of selene are you using? This might be a bug that we fixed in the latest version.

[ghm17]

The selene version is 0.5.1.

[lihaicheng7003]

Change the file suffix to .fa or .fasta.

[kathyxchen]

Thanks @lihaicheng7003 good catch -- @ghm17 did you ever figure this out?
From your error it looks like you are passing in a VCF to sequence prediction, when VCF should be used with the variant effect prediction scripts?