search

benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
459 stars 142 forks source link

Unable to add Species with Silva 138 #1119

Closed awe421 closed 4 years ago

awe421 commented 4 years ago

Hi,

I have been working for the first time with the dada2 pipeline and have no experience with working in Rstudio. As my reads were not merging properly I played around a bit with the trim&filter and tried out working with only forward reads and the JustConcatenate function. I assigned taxonomy to the forward reads with the zipped database from Silva, as I was unable to unpack the zipfile on my macbook. When I arrived at the addSpecies part, it gave me the following error: "Error in assignSpecies(seqs, refFasta = refFasta, allowMultiple = allowMultiple, : Incorrect reference file format for assignSpecies (this looks like a file formatted for assignTaxonomy).

I tried unzipping but this does not work. Is there another way to use the species database?

Thank you in advance!

nr0cinu commented 4 years ago

Hi @awe421!

I have used the SILVA database gzipped and unzipped before, so both should work.

from the error message, it looks like you used the reference file for assignTaxonomy and not the reference file for addSpecies/assignSpecies. Those are two different files, which are differently formatted. For addSpecies you should use silva_species_assignment_v138.fa.gz.

See also https://benjjneb.github.io/dada2/training.html

Best, Bela

awe421 commented 4 years ago

Dear @and3k

Thank you for your quick response. Indeed I downloaded the taxonomy-with-species file instead of the species-assignment. Thank you very much for your help!