Position of '[]' seems to be incorrect.
echo "[<p1> ][{<i2>}]de jour[] Yes [<\/p>]" | lt-proc /home/owner/Apertium/apertium-en-es/en-es.automorf.bin |apertium-tagger -g /home/owner/Apertium/apertium-en-es/en-es.prob | apertium-pretransfer [<p1> ][{<i2>}]^*de$[]^*jour$ ^Yes<adv>$ [<\/p>]