Error in AnnotationBustR Tutorial

[haruosuz]

I followed the steps in the vignette.

Enclosed are my R code and log files. my_AnnotationBustR-vignette.txt

The following R code printed Error messages:

> #run AnnotationBust function for two duplicate tRNA genes occuring twice and translate CDS
> my.seqs<-AnnotationBust(Accessions=my.longest.seqs$Accession, Terms=mtDNAterms,Duplicates=c("tRNA_Leu","tRNA_Ser"), DuplicateInstances=c(2,2), TranslateSeqs=TRUE, TranslateCode=2, DuplicateSpecies=TRUE, Prefix="Demo", TidyAccessions=TRUE)
[1] "Working On Accession AP011317 Barbonymus_schwanefeldii"

log.2021-12-02-1854.txt Running the R code generated the 12S.txt file, and printed the following Error:

Error in 1:start.loci : argument of length 0
Calls: AnnotationBust
Execution halted

log.2021-12-02-1829.txt Running the R code generated the 12S.txt file, 22 DemotRNA*.fasta files, and printed the following Error and Warning messages:

Error in seqinr::query(paste("SUB", paste0("AC=", new.access), "AND T=rRNA",  : 
  invalid request:NA
Calls: AnnotationBust -> <Anonymous>

[sborstein]

Hi @haruosuz . I will look into this, however, I can not currently give you a timeline on the fix. Based on the error, you are getting that error because it is struggling to retreive the annotation from seqinr and therefore is passing an empty object, so it is failing to process it. I've noticed recently that seqinr connections have been very ubnstable and this has been reported by other AnnotationBustR users as well. I am currently looking for general improvements to seqinr connectivity. I have been able to run the vignette code successfully at times, but occasionally, it fails to retrieve a few of the subsequences or I lose connection to seqinr ACNUC database.

[sgoodman1]

Has this issue been solved? I'm continually getting this error for every accession number I submit over multiple days...