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.

Is it possible that you sequenced your fragments in the reverse direction or that you flipped them earlier in the pipeline? The warning indicates that the sequences were flipped to the correct orientation in align.seqs, so you should be in good shape.