chop.seqs command gives empty file


I retrieve an empty .chop file and a list of all sequences in an .accnos file when using the chop.seqs command. I tried all kinds of numbases parameters and different .fasta files. Always the same result. The file from the example (abrecovery.fasta) works fine and is being chopped but no .accnos is produced with this file. Any suggestions?


I think I figured out the problem: chop.seqs does not interpret “.” and “-” as characters when counting characters. This is problematic for me chopping alignments since “-” is important as place holder. I would have liked to use it to extract a certain region of columns from an alignment (the V3 part from a whole 16S alignment) which does not work if “.” and “-” are not considered characters.
The numbases parameter was therefore offscale in my tries before.


Thanks for the suggestion! We will add a countgaps parameter to 1.13.0.

Thank you!