Narrative:

I was the local 1 controller. Small aircraft X (VFR) was on final to runway 11L (approximately 2 1/2 mi out) cleared to land. Small transport Y asked remaining ft of runway from taxiway 6 when he called ready for departure. I told small aircraft Y 9810 ft available. I told small aircraft Y runway 11L. Fly heading 120. Cleared for takeoff. I observed small transport Y depart runway 29R (closed portion). I told small aircraft X to turn left immediately. Due to runway 11L threshold being displaced between taxiways 5 and 6. When I saw small transport Y turn right on the runway, I thought he was making the turn so as to have full length for departure. (I have observed many aircraft taxi on the runway in this manner). When I saw small transport Y depart runway 29R. For safety, I felt the safer option was to move the traffic (small aircraft X) off of the final.

Related reports:

Google
 

Original NASA ASRS Text

Title: SMT Y NON ADHERENCE TO ATC CLRNC WRONG DIRECTION TKOF ON CLOSED PORTION OF RWY CAUSED CONFLICT WITH SMA X. PLTDEV.

Narrative: I WAS THE LCL 1 CTLR. SMA X (VFR) WAS ON FINAL TO RWY 11L (APPROX 2 1/2 MI OUT) CLRED TO LAND. SMT Y ASKED REMAINING FT OF RWY FROM TAXIWAY 6 WHEN HE CALLED READY FOR DEP. I TOLD SMA Y 9810 FT AVAILABLE. I TOLD SMA Y RWY 11L. FLY HDG 120. CLRED FOR TKOF. I OBSERVED SMT Y DEPART RWY 29R (CLOSED PORTION). I TOLD SMA X TO TURN L IMMEDIATELY. DUE TO RWY 11L THRESHOLD BEING DISPLACED BTWN TAXIWAYS 5 AND 6. WHEN I SAW SMT Y TURN R ON THE RWY, I THOUGHT HE WAS MAKING THE TURN SO AS TO HAVE FULL LENGTH FOR DEP. (I HAVE OBSERVED MANY ACFT TAXI ON THE RWY IN THIS MANNER). WHEN I SAW SMT Y DEPART RWY 29R. FOR SAFETY, I FELT THE SAFER OPTION WAS TO MOVE THE TFC (SMA X) OFF OF THE FINAL.

Data retrieved from NASA's ASRS site as of July 2007 and automatically converted to unabbreviated mixed upper/lowercase text. This report is for informational purposes with no guarantee of accuracy. See NASA's ASRS site for official report.