INPUT_FILE=$(ls -1 input/*.fasta)

When assigning multiple strings (files) separated with space in shell, only the first value is assigned.

You would use for or while loop , find --exec, parallel, or xargs to process every file separately.

If this is bash script, this is unnecessarily complex. Let us say you have all the fasta files in test directory, want to use ls for listing files and store the file information along with directory (test here). You can create an array and use the array elements as you like.

$ a=($(ls test/*.fasta))

$ echo ${a[@]}  

test/seq1_1.fasta test/seq1_2.fasta test/seq2_1.fasta test/seq2_2.fasta

$ printf "%s\n" ${a[@]}  

test/seq1_1.fasta
test/seq1_2.fasta
test/seq2_1.fasta
test/seq2_2.fasta

you can also loop through array:

$ for i in ${a[@]}; do echo $i ;done

test/seq1_1.fasta
test/seq1_2.fasta
test/seq2_1.fasta
test/seq2_2.fasta

All string manipulations work on arrays and list items. works with bash on ubuntu.