funannotate: NameError: name 'log' is not defined

I am trying to use the gff2prot utility to create a proteome file. However I am running into an error.

My command line input is: funannotate util gff2prot -g species.gff -f species.fa

And I am getting the error:

Traceback (most recent call last): File “/home/sm4974/.conda/envs/funannotate/bin/funannotate”, line 8, in <module> sys.exit(main()) File “/home/sm4974/.conda/envs/funannotate/lib/python3.9/site-packages/funannotate/funannotate.py”, line 717, in main mod.main(arguments) File “/home/sm4974/.conda/envs/funannotate/lib/python3.9/site-packages/funannotate/utilities/gff2prot.py”, line 30, in main Genes = lib.gff2dict(args.gff3, args.fasta, Genes) File “/home/sm4974/.conda/envs/funannotate/lib/python3.9/site-packages/funannotate/library.py”, line 5362, in gff2dict log.debug( NameError: name ‘log’ is not defined

About this issue

Original URL
State: closed
Created 8 months ago
Comments: 16 (6 by maintainers)

Commits related to this issue

unclear if this fixes bug #977 but attempts to make sure logger is available — committed to nextgenusfs/funannotate by hyphaltip 8 months ago

Most upvoted comments

gfftk convert works great - thank you!

I am also trying to create proteomes for genomes where the gff file was created by liftoff, this seems to be causing some problems and I am wondering if it is due to the format of the liftoff gff, as gfftk convert works perfectly for species where the gff file is not from liftoff.

This is the error I am getting for liftoff species: Traceback (most recent call last): File “/home/sm4974/.conda/envs/funannotate/bin/gfftk”, line 8, in <module>
sys.exit(main()) File “/home/sm4974/.conda/envs/funannotate/lib/python3.9/site-packages/gfftk/main.py”, line 22, in main
convert(args) File “/home/sm4974/.conda/envs/funannotate/lib/python3.9/site-packages/gfftk/convert.py”, line 89, in convert
gff2proteins( File “/home/sm4974/.conda/envs/funannotate/lib/python3.9/site-packages/gfftk/convert.py”, line 366, in gff2proteins
Genes = gff2dict(gff, fasta, table=table, debug=debug) File “/home/sm4974/.conda/envs/funannotate/lib/python3.9/site-packages/gfftk/gff.py”, line 2349, in gff2dict
annotation = validate_models( File “/home/sm4974/.conda/envs/funannotate/lib/python3.9/site-packages/gfftk/gff.py”, line 1258, in validate_models
gene, update = r.result() File “/home/sm4974/.conda/envs/funannotate/lib/python3.9/concurrent/futures/_base.py”, line 439, in result
return self.__get_result() File “/home/sm4974/.conda/envs/funannotate/lib/python3.9/concurrent/futures/_base.py”, line 391, in __get_result
raise self._exception File “/home/sm4974/.conda/envs/funannotate/lib/python3.9/concurrent/futures/thread.py”, line 58, in run
result = self.fn(self.args, **self.kwargs) File “/home/sm4974/.conda/envs/funannotate/lib/python3.9/site-packages/gfftk/gff.py”, line 1359, in validate_and_translate_models
if protSeq[-1] == "": IndexError: string index out of range

Here is an example liftoff gff file: Addax_nasomaculatus_gff.zip

sophie-03 on Oct 31, 2023