I'm trying to run macse.jar file in my sequence to replace internal stop codons from multifasta sequence using below command

for i in *.fna
do
echo "${i}"
 java -jar macse.jar -prog exportAlignment -align "${i}" -ambi_OFF true -canonize_ON true -codonForFinalStop --- -codonForInternalFS NNN -codonForInternalStop NNN -out_AA "${i}"aaR.faa -out_AA_consensus  "${i}"aaCR.faa -out_NT "${i}"nuR.fasta -out_NT_consensus "${i}"nuCR.fasta -out_stat_per_seq "${i}"statseq.csv -out_stat_per_site "${i}"statsite.csv
done;

But after running it is showing

String index out of range: 2823

KIndly help to get rid of this problem.

Thanks