assigntaxonomy

[UniAlberta]

Hi, I used https://doi.plutof.ut.ee/doi/10.15156/BIO/2959334 for ITS taxonomic assignment. I run taxa <- assignTaxonomy(seqtab.nochim, unite.ref, multithread = FALSE, tryRC = TRUE) and get an error of Error in .Call2("fasta_index", filexp_list, nrec, skip, seek.first.rec, :
reading FASTA file E:/RDAR_raw_seq_amplicon_2023/Breton_ITS_2023/sh_general_release_all_04.04.2024.tgz: ">" expected at beginning of line 1.
Do you know how I can fix it?

[HitMonk]

Ah! Your file is still zipped. You need to unzip it. the extension reads .tgz. Unzip the file, and check the first 10 lines to confirm it is a fasta file.

[UniAlberta]

Thanks for your reply! I did so. It`s a fast file. I attached the 2 files in the zipped folder downloaded from UNITE here.

[HitMonk]

Yea looks like its good. The command should work when you replaced the zipped file with the unzipped file?

[UniAlberta]

unite.ref <- "~/sh_general_release_all_04.04.2024.tgz"
taxa <- assignTaxonomy(seqtab.nochim, unite.ref, multithread = FALSE, tryRC = TRUE)
Error in .Call2("fasta_index", filexp_list, nrec, skip, seek.first.rec, :
reading FASTA file ~/sh_general_release_all_04.04.2024.tgz: ">" expected at beginning of line 1

[HitMonk]

unite.ref <- "~/sh_general_release_all_04.04.2024.tgz"

This command should be the unzipped fasta file. Not the zipped file. It should read like this:

unite.ref <- "~/sh_general_release_04.04.2024/sh_general_release_dynamic_04.04.2024.fasta

[UniAlberta]

Thanks for your help. I combined the 2 fasta files that were in the zipped folder and worked!