aligning sequences to SILVA bacterial reference database


I get the below warning when I try to align my contigs to the SILVA bacterial reference database (silva.bacteria.fasta/silva.v4.fasta).

“[WARNING]: 249594 of your sequences generated alignments that eliminated too many bases, a list is provided in F:\Normal_Mare_Project\Data_2\stability.trim.contigs.good.unique.flip.accnos.
[NOTE]: 121800 of your sequences were reversed to produce a better alignment.”

Would greatly appreciate if someone can help me with this.

Thank you.

it’s a warning, not an error so you may not need to do anything.

the ones that eliminated too many bases are likely bad though that’s a pretty big number so I’d be a little suspicious. flipping the seqs is usually fine unless you know that your seqs are all 5’->3’