rnahybrid "Error in nextSQ. Aborting"

Question

[nathanielsaxe]

I've been running rnahybrid on some custom UTR and mirna sequences and it seems to work fine as I get a long list of possible targets, however, the last entry on all the files is an error message

Error in nextSQ. Aborting

I've googled it and nothing has appeared, I found the source file for it, but I can't understand it at all.

https://github.com/semenko/mirna-scanner/blob/master/rnahybrid/src/fasta.c

Could someone explain to me what the error message means?

Thanks

Answer 1

[David Fredman]

A guess on the error message - your fasta file ends with an empty line or similar, that makes the Fasta parser in RNAhybrid fail on trying to parse it. Alternatively, you have a malformatted fasta entry in a multi-fasta sequence. Do you get results for all your UTR and miRNA sequences, or does it stop mid-way somewhere?

On a side note, the latest version of the source code is here

http://bibiserv.techfak.uni-bielefeld.de/download/tools/rnahybrid.html