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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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assign_taxonomy.py fails with exception (mothur) #1002

Closed xapple closed 11 years ago

xapple commented 11 years ago

I tested the taxonomic assignment script on a very small test sample with the MOTHUR classifier and it produces an error.

The offending command is the following:

 assign_taxonomy.py -i rep_set.fna -o taxonomy/ -m mothur

This produces a KeyError exception:

Traceback (most recent call last):
  File "home/qiime/scripts/assign_taxonomy.py", line 307, in <module>
    main()
  File "home/qiime/scripts/assign_taxonomy.py", line 285, in main
    result_path=temp_result_path,log_path=log_path)
  File "home/qiime/qiime/assign_taxonomy.py", line 367, in __call__
    output_fp=result_path,
  File "home/qiime/qiime/pycogent_backports/mothur.py", line 508, in mothur_classify_file
    assignments = list(parse_mothur_assignments(result['assignments']))
KeyError: 'assignments'

I am running the latest version of qiime at 9918b60016069bdb8c72546d08695e1e25742b8b.

Sample file rep_set.fna is attached rep_set (extension changed from fna to jpg)

As well as output of print_qiime_config.py config (extension changed from txt to jpg).

gregcaporaso commented 11 years ago

@kylebittinger, can you take a look into this?

gregcaporaso commented 11 years ago

Closing in favor of related #995.