Problems with q2-quality-control using Mockrobiota

[xchromosome]

Hiya,

Thanks for the quick response, especially on a Saturday!

@Nicholas_Bokulich

I think you took a wrong turn pretty early on. It sounds like you were taking the fastq sequence data from mockrobiota, processing it, and then attempting to use that as the “expected composition”

Yup, that's exactly what I was doing I was trying to follow the instructions I'd found from previous threads but I must have got mixed up!

@Nicholas_Bokulich

Instead, you need to find the “expected taxonomy” file for that mock community and import that as a relative frequency table.

See this tutorial; it is using a fungal mock community but gives you a good idea of how the “expected taxonomy” from mockrobiota should be used:

Ok, I have got to the page where there are 2 things I can download: expected-sequences.fasta or taxonomy.tsv. I right-clicked on taxonomy.tsv and chose "save link as...".
According to the fungal ITS analysis tutorial, the next step is as follows:

@Nicholas_Bokulich

That file was annotated with an older version of the UNITE database, so let’s fix some of the annotations (to match the version we are using) before proceeding:

sed 's/s__Tylospora_asterophora/s__unidentified/' expected-taxonomy.tsv | sed 's/p__Zygomycota;c__Mortierellomycotina_cls_Incertae_sedis/p__Mortierellomycota;c__Mortierellomycetes/' | sed 's/c__Chytridiomycetes/c__Spizellomycetes/' | sed 's/g__Coprinopsis/g__Coprinopsis;s__unidentified/' | sed 's/g__Tricholoma/g__Tricholoma;s__Tricholoma_vaccinum/'> expected-taxonomy-mod.tsv

I don't really know what this means - is it relevant to me? I thought it might be something that only applied to older versions of Qiime 2 so I skipped it to see if I could. The next thing I ran was this:

biom convert \
  -i mockrobiota-taxonomy.tsv \
  -o mockrobiota-taxonomy.biom \
  --table-type="OTU table" \
  --to-json

This was the error message I got:

Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/biom/parse.py", line 660, in load_table
table = parse_biom_table(fp)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/biom/parse.py", line 412, in parse_biom_table
t = Table.from_tsv(fp, None, None, lambda x: x)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/biom/table.py", line 4631, in from_tsv
t_md_name) = Table._extract_data_from_tsv(lines, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/biom/table.py", line 4747, in _extract_data_from_tsv
md_name = header[-1]
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2019.1/bin/biom", line 11, in
sys.exit(cli())
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/biom/cli/table_converter.py", line 114, in convert
table = load_table(input_fp)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/biom/parse.py", line 662, in load_table
raise TypeError("%s does not appear to be a BIOM file!" % f)
TypeError: mockrobiota-taxonomy.tsv does not appear to be a BIOM file!

Where have I screwed up now?!

@Nicholas_Bokulich

yeah, q2-quality-control will show you actual accuracy scores (excel will not), but it will not make a bar chart of the compositions (excel will).

It sounds like it would be beneficial to do both! That's my plan!

Massive thanks,
Lindsay