funannotate: RNA free annotation UnicodeDecodeError

I am trying to do an annottion without RNA-seq evidence and am running into some issues.

Version funannotate v1.8.3

*Inputfunannotate predict -i $input -o $outdir --species $species --busco_seed_species $buscoSpecies -d $database --cpus 5

The error


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[03:00 PM]: OS: CentOS Linux 7, 40 cores, ~ 198 GB RAM. Python: 3.6.10
[03:00 PM]: Running funannotate v1.8.3
[03:00 PM]: Skipping CodingQuarry as no --rna_bam passed
[03:00 PM]: Parsed training data, run ab-initio gene predictors as follows:
Traceback (most recent call last):
  File "/services/tools/funannotate/1.8.3/bin/funannotate", line 713, in <module>
    main()
  File "/services/tools/funannotate/1.8.3/bin/funannotate", line 703, in main
    mod.main(arguments)
  File "/services/tools/funannotate/1.8.3/lib/python3.6/site-packages/funannotate/predict.py", line 572, in main
    augustus_version, augustus_functional = lib.checkAugustusFunc()
  File "/services/tools/funannotate/1.8.3/lib/python3.6/site-packages/funannotate/library.py", line 1039, in checkAugustusFunc
    stdout=subprocess.PIPE, universal_newlines=True).communicate()
  File "/services/tools/funannotate/1.8.3/lib/python3.6/subprocess.py", line 850, in communicate
    stdout = self.stdout.read()
  File "/services/tools/funannotate/1.8.3/lib/python3.6/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 80: ordinal not in range(128)

About this issue

  • Original URL
  • State: closed
  • Created 3 years ago
  • Comments: 22 (10 by maintainers)

Most upvoted comments

The unicode error is seriously this one line S. König, – the umlaut in the name was a problem with py2.7. But I can’t reproduce the unicode error locally with any version of python 3. I’m installing on centOS at the moment, let me see if I can get similar behavior.