Exporting with Taxonomy Error

[Jrand]

Hello,

I have run into a slight issue with exporting my data after running the pipeline. Normally the .tsv file with taxonomy that I have been getting in previous runs doesn't seem to want to generate now. The error that is generate is seen below:

And the code that I ran to generate this error is:

qiime tools export --input-path DADA2/Fungi-Table-dada2-208-187-NS.qza --output-path DADA2/ExportedRaw
cd DADA2/ExportedRaw
mv feature-table.biom Fungi-Table-Filtered.biom
biom convert -i Fungi-Table-Filtered.biom -o Fungi-Table-Filtered.tsv --to-tsv
biom head -i Fungi-Table-Filtered.tsv

cd ..
cd ..

cd Taxonomy

qiime tools export --input-path Fungal-Taxonomy.qza --output-path ./
cp taxonomy.tsv biom-taxonomy.tsv

cd ..

biom add-metadata -i DADA2/ExportedRaw/Fungi-Table-Filtered.biom -o DADA2/ExportedRaw/Fungi-Table-With-Taxonomy.biom --observation-metadata-fp Taxonomy/biom-taxonomy.tsv --sc-separated taxonomy --observation-header OTUID,taxonomy,confidence
biom convert -i DADA2/ExportedRaw/Fungi-Table-With-Taxonomy.biom -o DADA2/ExportedRaw/Fungi-Table-With-Taxonomy.tsv -m Fungal-Metadata-BLM.tsv --to-tsv --header-key taxonomy

I have searched the forums to try to find this exact error and though enlightening nothing tended to work. With Biom add metadata problem, being the closest to the issue and sadly not fixing it.

Any help would be appreciated.

Thank you all in advance!

[SoilRotifer (Mike Robeson)]

Hi @Jrand, welcome to

Try following the procedure outlined here. It appears there are some minor differences with your biom add-metadata command:

Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)

Creating a TSV BIOM table The following is based on a post by @gregcaporaso. $ qiime tools export table.qza --output-dir ./ $ biom convert -i feature-table.biom -o feature-table.tsv --to-tsv $ biom head -i feature-table.tsv # Constructed from biom file #OTU ID L1S105 L1S140 L1S208 L1S257 L1S281 4b5eeb300368260019c1fbc7a3c718fc 2222.0 0.0 0.0 0.0 0.0 fe30ff0f71a38a39cf1717ec2be3a2fc 5.0 0.0 0.0 0.0 0.0 d29fe3c70564fc0f69f2c03e0d1e5561 0.0 0.0 0.0 0.0 0.0 868528ca947bc57b69ffdf83e6b73bae 0.0 227…

and here:

Change header names from Feature ID to OTUID in exported TSVTaxonomyDirectoryFormat file

Hello What is the command line to change header names Feature ID to OTU ID? Best regards, Jasmine

You can also checkout more details about biom convert.

[Jrand]

Thank you Mike for your response!

I looked through the links, and from the first link I have found that the only difference in my problem code segment:

biom convert -i DADA2/ExportedRaw/Fungi-Table-With-Taxonomy.biom -o DADA2/ExportedRaw/Fungi-Table-With-Taxonomy.tsv -m Fungal-Metadata-BLM.tsv --to-tsv --header-key taxonomy

is the addition of my metadata with -m Fungal-Metadata-BLM.tsv. The rest of the code generates the needed files except for this last chunk of code. So I checked the second link. Sadly this is the same attempted fix I did before posting from that other post, Biom add metadata problem, and it didn’t fix the issue either.

Again thank you so much for your help, I am still relatively new to all this so I am likely overlooking something obvious.

[SoilRotifer (Mike Robeson)]

Hi @Jrand,

I am not sure if this is the issue, but the command I referred to was:

@Jrand

biom add-metadata -i DADA2/ExportedRaw/Fungi-Table-Filtered.biom -o DADA2/ExportedRaw/Fungi-Table-With-Taxonomy.biom --observation-metadata-fp Taxonomy/biom-taxonomy.tsv --sc-separated taxonomy --observation-header OTUID,taxonomy,confidence

Is there a reason why you are adding --observation-header OTUID,taxonomy,confidence? You should not need this addition if you are editing the headers, as described in both links. I am wondering if this causes things to fail later on?

@Jrand

biom convert -i DADA2/ExportedRaw/Fungi-Table-With-Taxonomy.biom -o DADA2/ExportedRaw/Fungi-Table-With-Taxonomy.tsv -m Fungal-Metadata-BLM.tsv --to-tsv --header-key taxonomy

Not sure why -m Fungal-Metadata-BLM.tsv is being added to this command.

Also, then editing the taxonomy headers I usually replace:
Feature ID Taxon Confidence
with this:
#OTUID taxonomy confidence

Perhaps you can share your qza files? Hopefully, someone smarter than I will spot the issue.

-Mike

[Jrand]

Well simply removing -m Fungal-Metadata-BLM.tsv from the script allowed for the Fungi-Table-With-Taxonomy.tsv file to generate properly, and from the looks of it seems okay.

Thank you very much @SoilRotifer!