Bowtie: cannot read fasta file?
Since I apparently don't have enough reputation to comment, I'll post this as an answer and let someone move it.

Firstly, try to ensure that the order of the arguments are correct. You should be typing bowtie2 -f -x $TARGET -U $TARGET -S $TARGET.sam, since bowtie2 (as with many other programs) can be a bit picky about the argument order.

Secondly, it's usually advisable for the example input to include lines that are causing the problem (since it's apparently not complaining about the lines you posted, we can only assume that it's aligning them).

Thirdly, you'll typically only get those warnings if they're true. For example, if you were to grep -A 1 -w GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT $target then my guess is that you'd find it to have no remaining sequence. Presumably these are the result of you trimming adapters or something like that, so just have your trimmer discard really short results (they won't align meaningfully anyway).