Cool, I found a way and leaving this in the thread for others seeking an similar answer:
linear-to-nbest ark:exp/mono0a/ali.1 "ark:utils/
sym2int.pl -f 2- data/lang/words.txt data/train_yesno/split1/1/text|" '' '' 'ark:1.nbest'
# Step 2
lattice-align-words-lexicon "data/lang/phones/
align_lexicon.int" "exp/mono0a/final.mdl" "ark:1.nbest" "ark:aligned.1"
# Use
lattice-align-words if pos dep training (
word_boundary.int) is not present
# Step 3 Word level
# Convert nbest lattice to ctm and then map the integers to 2 symbols (words are the symbols here)
nbest-to-ctm "ark:aligned.1" - |
utils/int2sym.pl -f 5- data/lang/words.txt > words.1.ctm