DIAMOND Verification: local variable 'idxDict' referenced before assignment

[mwittep]

After running FeGenie with a reference database (nr.dmnd) I get the error shown below. As an output I get the complete FeGenie-summary.csv and an empty file FeGenie-summary-altered.csv.

I think I can work with the complete summary file, but still wanted to report the bug.

Command FeGenie.py -bin_dir . -bin_ext fsa -out ../output_fegenie_seqs/ --meta -ref /share/references/library/nr -t 10

Error:

Performing Diamond BLASTx search of putative iron genes against reference database
Counting heme-binding motifs
Final processing of output

Traceback (most recent call last):
  File "/XXX/XXX/miniconda3/envs/fegenie/bin/FeGenie.py", line 3020, in <module>
    main()
  File "/XXX/XXX/miniconda3/envs/fegenie/bin/FeGenie.py", line 2355, in main
    ls[0] + "," + ls[1] + "," + str(idxDict[ls[2]]) + "," + ls[3] + "," + ls[4] + "," + ls[
UnboundLocalError: local variable 'idxDict' referenced before assignment

[metalichen]

wanted to bump this issue up. Got the same problem.

Thanks for the tool! Gulya

[Arkadiy-Garber]

Thanks Gulya,

Could you please share the command that you used?

Thanks! Arkadiy

[metalichen]

Sure! It was

FeGenie.py -bin_dir . -bin_ext faa -t 16 --orfs --meta  --heme  --makeplots -out fegenie_out -ref path/to/nr  --all_results

[Arkadiy-Garber]

Thanks, Gulya! I see that you are, like me, having a wild Friday evening! haha

I found and fixed the bug that was causing this issue, and pushed the latest changes to the FeGenie github repo. So if you download the latest version, it should work. Let me know if you have any other questions, or continue having issues.

Cheers, Arkadiy

[metalichen]

Yep, that worked! Thanks a bunch!

oh yes, I'm all about friday fun. have a nice weekend, I hope it'll get nicer :)