So can Qiime be customized for any data? Are Qiime Feature IDs absolutely necessary for analysis? I tried to create my own here and I am thinking this might be the problem, but please confirm. Thanks!
I think so, too! Can you share metadataFINAL.txt? I tried exporting and converting your FINALfeaturetable.qza, but met some issues:
$ qiime tools export --input-path FINALfeaturetable.qza --output-path ft
$ biom convert -i ft/feature-table.biom -o table.from_biom.txt --to-tsv
Traceback (most recent call last):
File "/Users/matthew/.conda/envs/qiime2-2020.8/bin/biom", line 11, in <module>
sys.exit(cli())
File "/Users/matthew/.conda/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/Users/matthew/.conda/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/Users/matthew/.conda/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/matthew/.conda/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/matthew/.conda/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/Users/matthew/.conda/envs/qiime2-2020.8/lib/python3.6/site-packages/biom/cli/table_converter.py", line 114, in convert
table = load_table(input_fp)
File "/Users/matthew/.conda/envs/qiime2-2020.8/lib/python3.6/site-packages/biom/parse.py", line 672, in load_table
table = parse_biom_table(fp)
File "/Users/matthew/.conda/envs/qiime2-2020.8/lib/python3.6/site-packages/biom/parse.py", line 397, in parse_biom_table
return Table.from_hdf5(file_obj, ids=ids, axis=axis)
File "/Users/matthew/.conda/envs/qiime2-2020.8/lib/python3.6/site-packages/biom/table.py", line 3931, in from_hdf5
obs_ids, obs_md, obs_grp_md = axis_load(h5grp['observation'])
File "/Users/matthew/.conda/envs/qiime2-2020.8/lib/python3.6/site-packages/biom/table.py", line 3919, in axis_load
data = dset[:]
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/Users/matthew/.conda/envs/qiime2-2020.8/lib/python3.6/site-packages/h5py/_hl/group.py", line 264, in __getitem__
oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
File "/Users/matthew/.conda/envs/qiime2-2020.8/lib/python3.6/site-packages/h5py/_hl/base.py", line 137, in _e
name = name.encode('ascii')
AttributeError: 'slice' object has no attribute 'encode'
Actually this biom file is the source of the dysfunction, not the QZA. I can't get biom to parse this file.
I think the issue is that you have slashes in the feature IDs, which is breaking the biom parser.
sed 's/\//-/g' FINALmetadata.txt > no-slashes.txt
Another note, this isn't related to the issue you ran into here, but might be a problem later - your table appears to be transposed - biom expects there to be features as rows and samples as columns. You can use the feature-table transpose command to fix that, after importing, if you wish.