ValueError: No more features left. Check to make sure that the sample names between `sample-metadata` and `table` are consistent

Running the stand-alone version of `gemelli` on the example data used in the tutorial I get the error `ValueError: No more features left. Check to make sure that the sample names between `sample-metadata` and `table` are consistent`

As I'm not a `Python` person, I filter the example data in `R`.

```
mdat <- read.table("IBD-2538/data/metadata.tsv", sep='\t', header=T) # nrow(mdat) 516
ftbl <- biomformat::read_biom("IBD-2538/data/table.biom")
ftbl <- as(biomformat::biom_data(ftbl), "matrix") # ncol(ftbl) 470

mdat <- mdat %>% filter(sample_name %in% colnames(ftbl))
rownames(mdat) <- mdat $sample_name

ps <- phyloseq(otu_table(ftbl, taxa_are_rows=T),
sample_data(mdat))
# here I skip adding the taxonomy

ps <- metagMisc::phyloseq_filter_prevalence(ps, prev.trh=0.2, abund.trh=10, abund.type="total", threshold_condition="AND")

> ps
phyloseq-class experiment-level object
otu_table() OTU Table: [ 236 taxa and 318 samples ]
sample_data() Sample Data: [ 318 samples by 128 sample variables ]

# Do we need to filter to only keep subjects with >=t timepoints?

biomformat::write_biom(biomformat::make_biom(t(otu_table(ps))), "table_filt.biom")
write.table(sample_data(ps), "metadata_filt.txt", sep="\t", quote=F)
```

Having made sure that samples match between the feature table and the metadata (plus filtered the our rare stuff), I run `gemelli` and get the following error

```
gemelli \
--in-biom table_filt.biom \
--sample-metadata-file metadata_filt.txt \
--individual-id-column 'host_subject_id' \
--state-column-1 'timepoint' \
--output-dir results

Traceback (most recent call last):
File "/Users/johannesbjork/python/miniconda3/bin/gemelli", line 8, in
sys.exit(standalone_ctf())
File "/Users/johannesbjork/python/miniconda3/lib/python3.7/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/Users/johannesbjork/python/miniconda3/lib/python3.7/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/Users/johannesbjork/python/miniconda3/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/johannesbjork/python/miniconda3/lib/python3.7/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/Users/johannesbjork/python/miniconda3/lib/python3.7/site-packages/gemelli/scripts/_standalone_ctf.py", line 131, in standalone_ctf
feature_metadata)
File "/Users/johannesbjork/python/miniconda3/lib/python3.7/site-packages/gemelli/ctf.py", line 97, in ctf_helper
raise ValueError(("No more features left. Check to make sure that "
ValueError: No more features left. Check to make sure that the sample names between `sample-metadata` and `table` are consistent
```

Start by reproducing the reported command with the filtered table_filt.biom and metadata_filt.txt, then inspect gemelli/scripts/_standalone_ctf.py and gemelli/ctf.py at the traceback locations. Determine why valid matching samples and retained features lead to the ValueError; done means the example invocation completes or reports the actual invalid input clearly.

Written by the indexing model from the issue text.