sidle tutorial missing aligned sequence file

[elsamdea]

Hi again!
I think my question is also useful in this post, because it is related to another database. So that is the reason why I am posting this here and do not in a new post.

I would love to reproduce the last step of sidle documentation's Phylogenetic Tree Reconstruction. However I could not find the rep_set_aligned folder in NCBI 16S database or neither the SEPP references file. That’s the crux of the matter.

I have found some post as:

rescript get-ncbi-data

Dear qiime team, I am trying using the code below to download functional gene sequence by accession number, but it can only do 1000 number, if more than that, the timeout error will appear, how can i solve this problem; Thank you very much. qiime rescript get-ncbi-data \ --m-accession-ids-file "/home/rodrigues-lab/Laibin_Project/data/urec_accnum.txt" \ --o-sequences /home/rodrigues-lab/Laibin_Project/data/urec-refseqs.qza \ --o-taxonomy /home/rodrigues-lab/Laibin_Project/data/urec-ta…

Reference Alignments: Best Way to Download Many Sequences from NCBI GenBank

Welcome to the forum @alexkrohn ! Sounds like you are on the right track with RESCRIPt! I’d go for the latter. Would be slow to loop 400 times, also slow to merge. Also your provenenance graph would look really ugly! Probably not faster. merge-seqs is correct, but merge will merge feature tables, not FeatureData[Taxonomy] artifacts. There is a separate merge-taxa action (one in RESCRIPt with more complex functionality, one in q2-taxa that has simpler functio…

But didn't find a solution.

Maybe I need to merge-seqs? What approximation could I use?

Any help would be appreciated!!

Thank you so much!

Elsa