unique_accession_genome_name

[bheimbu]

Hi there,

I'm encountering following error when I ran

unique_accession_genome_name <- suppressMessages( taxize::genbank2uid(unique_accession_all, batch_size = length(unique_accession_all))) %>% vapply(function(x) attr(x, "name"), character(1))

Error: Request-URI Too Long (HTTP 414)

I'm trying to profile termite microbiomes. I've used Zootermopsis nevadensis as reference genome and Spirochaetia as target reference. So far I've used only one library, which consists of roughly 7x10⁶ reads.

Any help is highly appreciated,

Bastian

[aubreyodom]

Hi Bastian,

Apologies for the late response as I was away on travel.

So, the code that you are using here is taken from a section of the vignette at the very end that takes accession numbers and transforms them to UIDs from a BAM file. However, that is only an applicable step in the vignette as we are evaluating the results of our benchmark. We are taking accessions out of a bam file and turning them into UIDs and then creating a table for the sake of showing what is going on "under the hood."

That step is not applicable to "real life" cases where you don't actually know what is in your sample. In your case, I would skip that code block entirely (and the next one) and go to the metascope_id() step :) The CSV that is output there is the output you're looking for.

I will add a note to the vignette that the step in question is only relevant to the vignette example and can be skipped.

Please let me know if that answers your question! Brie

[bheimbu]

Hi @aubreyodom,

sorry for the late response, I've just realized that the code block is really not applicable to my example as you mentioned in your post. Anyway, thanks for letting me know.

Cheers @bheimbu

[aubreyodom]

Not a problem!