You will need to use at least two secondary structure predictions for fragment generation to make sense, but that’s not the problem here. It seems that blast is failing. Try running the blast command directly to get a better idea of what’s going on. That is, type
/blast/bin/blastpgp -t T -i trhl2.fasta -F F -j2 -o trhl2.blast -d /blast/db/nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C trhl2.check -Q trhl2.pssm
If this fails, check the paths for the blastpgp executable and the nr database and update make_fragments.pl as necessary.