def build_index_sortmerna(ref_fp, working_dir):
    logger = logging.getLogger(__name__)
    logger.info('build_index_sortmerna files %s to'
                ' dir %s' % (ref_fp, working_dir))
    all_db = []
    for db in ref_fp:
        fasta_dir, fasta_filename = split(db)
        index_basename = splitext(fasta_filename)[0]
        db_output = join(working_dir, index_basename)
        logger.debug('processing file %s into location %s' % (db, db_output))
        params = ['indexdb_rna', '--ref', '%s,%s' %
                  (db, db_output), '--tmpdir', working_dir]
        sout, serr, res = _system_call(params)
        if not res == 0:
            logger.error('Problem running indexdb_rna on file %s to dir %s. '
                         'database not indexed' % (db, db_output))
            logger.debug('stdout: %s' % sout)
            logger.debug('stderr: %s' % serr)
            logger.critical('execution halted')
            raise RuntimeError('Cannot index database file %s' % db)
        logger.debug('file %s indexed' % db)
        all_db.append(db_output)
    return all_db