Three months after John Lynch earned plenty of praise for a 10-man draft that began with Stanford defensive tackle Solomon Thomas, the 49ers rookie general manager is giving himself a poor grade.

The reason: Thomas, the No. 3 overall pick, was absent and unsigned Thursday morning as his 89 other teammates reported for training camp. The 49ers will have their first practice Friday.

“I wish this we’re done,” Lynch said. “I think it should be done. I’m disappointed in myself in a certain way that it’s not, but I think I’m also learning that this part of the business part of the game. But … I’m encouraged and hopeful that we can get it done.”

While Lynch has been part of the negotiations with Thomas, executive vice president Paraag Marathe, the chief contract negotiator, has had the lead role in those conversations.

Thomas, Titans wide receiver Corey Davis (No. 5) and Raiders cornerback Gareon Conely (No. 24) are the only unsigned first-round picks.

Thomas is already behind as a rookie because of NFL rules that prevented him from participating in the offseason program after the 49ers’ rookie minicamp. Thomas had to stay away from the facility until Stanford’s semester ended in mid-June.

When asked if there was a point at which Thomas’ absence could affect his readiness for the regular season, Lynch said, “I’m concerned right now.”

“There’s been a lot of productive conversations here in the last couple days,” Lynch said about two hours before the team took part in a conditioning test. “Just left some of those. We’re hopeful that we can get this done in the necessary time. I’m aware from my experience as a player … in the business of football that deadlines typically get these things done. We’re drawing close to that and hopeful that we continue to make progress and tie this thing up so Solomon can be here with his teammates.”

Thomas is represented by CAA, which represents Chargers defensive end Joe Bosa, last year’s No. 3 pick who held out of training camp before finally signing on Aug. 29. CAA also represents 49ers guard Joshua Garnett, a 2016 first-round pick who signed last year on the eve of training camp.

Twitter: @Eric_Branch

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