FAILED! Humann2 test run error

Microbial community profiling HUMAnN
1

Hi friends!!! (@franzosa @f.asnicar @fbeghini )
I am very new in HUmann2 and I have installed HUMANN2 2.8.1 and done test run with command:
$humann2_test --run-functional-tests-end-to-end

But I ended up with one failure:

FAIL: test_humann2_fastq_biom_output_pathways (functional_tests_biom_humann2.TestFunctionalHumann2EndtoEndBiom)
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Traceback (most recent call last):
  File "/home/dc7/anaconda3/envs/h2/lib/python2.7/site-packages/humann2/tests/functional_tests_biom_humann2.py", line 56, in test_humann2_fastq_biom_output_pathways
    self.assertEqual(pathways_found,cfg.expected_demo_output_files_biom_pathways)
AssertionError: Items in the first set but not the second:
u'PWY-5423'

Can you tell me what’s wrong?

Thanks and Regards,
DC7

2

Hi DC7, Thanks for the detailed post! That error is from running a test with the output biom format to determine the expected pathways. That one pathway is sometimes present in the output file based on minpath versions in different compute environments. Please feel free to ignore that one test that failed and we will look at making that test a bit more flexible in the next HUMAnN release.

Thanks,
Lauren