Getting the correct Silva 128 file for Sidle following the rescript download

Hi @jwdebelius, @elsamdea and @nandreani,

I am having problems in the reconstruction of the phylogenetic tree just in this step.

I used the SILVA 128 database to complete the Sidle tutorial with my data. The database was initially downloaded following next command and processed following the tutorial.

qiime rescript get-silva-data \
    --p-version '128' \
    --p-target 'SSURef_NR99' \
    --p-include-species-labels \
    --o-silva-sequences ./silva_128_ssu_nr99_rna_seqs.qza \
    --o-silva-taxonomy ./silva_128_ssu_nr99_tax.qza

When I wanted to reconstruct the Phylogenetic Tree using qiime sidle reconstruct-fragment-rep-seqs, I dowloaded the file Silva_128_release.tgz and I used the fasta file 99_otus_aligned.fasta inside rep_set_aligned folder in the --i-aligned-sequences parameter. I obtained the error attached in the document. It looks like I was using information from different SILVA versions but, I think that this is not the case.

Maybe I'm not using the correct aligned-sequences file?



qiime2-q2cli-err-iyyulykt.txt (104.5 KB)

Hi again,

To complete my previous question, I would like to add the summary visualization for the reconstruction map. Maybe, it could be useful.


database_recons_summ.qzv (6.8 MB)

Hi @andresarroyo,

I apologize for my late reply. I'm struggling a little bit, because the error message is saying that the sequences aren't in your files. That means one of a few things. The first is that you somehow have a database mismatch. (As full disclosure a lot of my Silva 128 tests were pre RESCRIPt). It could be that there's a prefixing step that got skipped, although those look like normal Silva IDs. So, I'm not sure why there is such a discontinuity between the two sets.