I’m having trouble running qiime feature-table rarefy from a count table I have imported into qiime.
The table was a .tsv file converted into .biom format by:
biom convert -i otu-dada2-min5in5-combat.tsv -o otu-dada2-min5in5-combat. biom --table-type=“OTU table” --to-hdf5
I added “#OTU ID” to the first column name as per: https://github.com/biocore/biom-format/issues/763
The commands I am running in qiime to then load the .biom file and rarefy the counts:
module load miniconda/3
source activate /project/crml-bio/.conda/envs/qiime2-2019.7
qiime tools import --input-path ./otu-dada2-min5in5-combat.biom
qiime feature-table rarefy
The error that is generated:
Traceback (most recent call last):
File “/project/crml-bio/.conda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</project/crml-bio/.conda/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-305>”, line 2, in rarefy
File “/project/crml-bio/.conda/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
File “/project/crml-bio/.conda/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/project/crml-bio/.conda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_feature_table/_normalize.py”, line 15, in rarefy
File “/project/crml-bio/.conda/envs/qiime2-2019.7/lib/python3.6/site-packages/biom/table.py”, line 2809, in subsample
_subsample(data, n, with_replacement)
File “biom/_subsample.pyx”, line 60, in biom._subsample._subsample
File “<array_function internals>”, line 6, in repeat
File “/project/crml-bio/.conda/envs/qiime2-2019.7/lib/python3.6/site-packages/numpy/core/fromnumeric.py”, line 481, in repeat
return _wrapfunc(a, ‘repeat’, repeats, axis=axis)
File “/project/crml-bio/.conda/envs/qiime2-2019.7/lib/python3.6/site-packages/numpy/core/fromnumeric.py”, line 61, in _wrapfunc
return bound(*args, **kwds)
ValueError: repeats may not contain negative values.
Plugin error from feature-table:
repeats may not contain negative values.
Thinking this error might be indicating I have negative counts in my table, I checked, and I do not.
My OTU table looks correct after creating the .biom file -> loading into qiime -> extracting table as .tsv, so I’m not sure it’s that. I’m a little stuck on what to try next.
I’d appreciate any help! Thank you!