"Fatal: deletion at last position in cma file" error in run_gaps

[kalaivaniraju]

Attached file contains 2 test scenarios: test and test2

The following gives the desired supases_aln.cma output:
cd test
fammer.py build --clean --mapgaps Superfamily/
run_gaps Superfamily supases

However, in scenario test2, there is an error. The difference between test and test2 is nothing but an addition of a sequence in each of the fasta files inside the Superfamily directory. Ideally, this should not cause any trouble. However the execution of the following commands gives "Fatal: deletion at last position in cma file 3" error in the run_gaps step:
cd test2
fammer.py build --clean --mapgaps Superfamily/
run_gaps Superfamily supases

Note: I removed the --globalgenafpair flag in the mafft command since it is no longer supported
ex_to_etal.zip