Puppy Barking Nonstop in Crate

We just got a border collie puppy who’s currently 13 weeks. We’ve had him for a little over a week now. I knew that we wanted to crate train as I believe it’s the best method for nighttime and naps and them having a safe spot. We crated first night and he did get up a few times we took him out to potty and he went back to bed. Now he sleeps from 9:30pm and wakes up around 6am. Which is good for our sanity and sleep. He has a cover over his crate and a loud sound machine and he’s been doing naps in his crate. For naps I usually make sure that he’s had some mind stimulation beforehand to wear him out and has been out to potty. Sometimes he naps fine but will only sleep for about 45 mins to an hour. Most often though he will be up barking and barking (what he’s currently doing now and has been the past hour) and really doesn’t stop until I relent and let him out and it’s just a cycle. He also DOES NOT just lay down somewhere and sleep and can never settle I know he must be exhausted through the day because of how much sleep a puppy needs. I guess my question would be how do I get him to settle easier I feel like we’ve done everything. We’ve done training in the crate too and I whatever I try I can’t command him to go into the crate on his own. He also recently had giardia found in his stool sample and he’s getting treatment for that currently. He seems to be asymptomatic for it but I don’t know if it’s affecting his daytime naps at all. I’m losing some patience for sure as I feel like I can’t ever get anything done anything helps!