avoid input the cause RefAligner to fail

RefAligner fails without an error message if a .bnx file in a .bnx list
was never created. Therefore scripts were updated to list .bnx files
only if they were output by Refaligner (e.g. .bnx files split in to
multiple .bnx files (one per scan) from an original flow cell .bnx file
may fail to create output. If RefAligner reads this and attempts to
merge the adjusted .bnxs the ENTIRE merge will fail without warning if
one listed file was not made.