I got an error using QIIME 1.9.1 group_significance.py for rarefied BIOM data, whether original BIOM data went without any problem or error.
group_significance.py -i unzip_table_even5000_from_core_diversity_analysis.biom -m map.txt -c Group -s mann_whitney_u -o out.txt
Traceback (most recent call last):
File "/usr/local/bin/group_significance.py", line 344, in <module>
main()
File "/usr/local/bin/group_significance.py", line 326, in main
GROUP_TEST_CHOICES, int(opts.permutations))
File "/usr/local/lib/python2.7/dist-packages/qiime/otu_significance.py", line 147, in run_group_significance_test
test_stat, pval = test_choices[test](row[0], row[1])
File "/usr/local/lib/python2.7/dist-packages/qiime/stats.py", line 1882, in mw_t
u, pval = mannwhitneyu(x, y, continuity)
File "/usr/local/lib/python2.7/dist-packages/scipy/stats/stats.py", line 4092, in mannwhitneyu
raise ValueError('All numbers are identical in amannwhitneyu')
ValueError: All numbers are identical in amannwhitneyu