import logging


def get_all_gaps(aln):
    """Gets columns with at least one gap."""

    logging.info("Identifying positions with gaps.")

    listcol = []
    for j in range(aln.get_alignment_length()):
        for i in range(len(aln)):
            if aln[i].seq[j] == '-':
                listcol.append(j)
                break
    return listcol