Metaphlan2 v2.9 causes error with Humann2 v2.9

Microbial community profiling HUMAnN
1

In my case, I had created an environment and then installed humann2 v2.9 from source at first. Running command humann2_test returned ok at last.
Then I installed metaphlan2 v2.9.22 by conda with command conda install metaphlan2=2.9. After the installation of metaphlan2 v2.96.22, rerunning command humann2_test returned 5 errors. All the 5 errors concerned about blastx:

test_blastx_coverage (advanced_tests_blastx_coverage.TestBasicHumann2Blastx_CoverageFunctions) … ERROR
test_blastx_coverage_gene_names_chocophlan_annoation (advanced_tests_blastx_coverage.TestBasicHumann2Blastx_CoverageFunctions) … ERROR
test_blastx_coverage_gene_names_custom_annotation (advanced_tests_blastx_coverage.TestBasicHumann2Blastx_CoverageFunctions) … ERROR
test_blastx_coverage_gene_names_default (advanced_tests_blastx_coverage.TestBasicHumann2Blastx_CoverageFunctions) … ERROR
test_blastx_coverage_gene_names_id_mapping (advanced_tests_blastx_coverage.TestBasicHumann2Blastx_CoverageFunctions) …ERROR

Command humann2 --input *.fastq --output DIR still work in this situation, but it seems that the step in the log file “translated alignment post-processing” was strangely shorter compared with the same sample processed by Humann2 v2.8.1 (1.5h vs 6.7h).

2

Hello, I believe the difference in run times you are seeing are likely caused by using different databases (demo vs full). This is okay and expected since the demo database was built to be very small (for testing and tutorial purposes) and as such runs much faster. It sounds like the tests ran okay before you changed your metaphlan version. My suggestion would be to update your metaphlan install to make sure you have the latest version as you might have ended up with one that was a bit out of sync with the humann version installed. The most recent metaphlan2 version is 2.96.1 .

Thanks,
Lauren