Date: 202007
Local time of day: 1201-1800
Location: ZZZ.Tower, US
Aircraft: Small Aircraft; Low Wing; 1 Eng; Fixed Gear
Flight plan: VFR
Flight phase: Taxi
ATC / advisory: Tower ZZZ
Second aircraft: Any Unknown or Unlisted Aircraft Manufacturer
Reporter organization: Government
Reporter function: Supervisor / CIC
Reporter qualification: Air Traffic Control Fully Certified
Human factors: Situational Awareness; Workload; Distraction
Second reporter function: Single Pilot; Pilot Flying
Anomaly: ATC Issue All Types; Conflict Ground Conflict; Less Severe; Deviation / Discrepancy - Procedural Clearance; Ground Incursion Runway
Detector: Person Air Traffic Control
When detected: Taxi
Result: Air Traffic Control Separated Traffic; Air Traffic Control Issued New Clearance
Contributing factors: Procedure; Human Factors; Environment - Non Weather Related
Primary problem: Human Factors

Narrative: I was working all positions combined. Aircraft X called ready for departure on Runway XX.  I knew that prior to the clearance that a maintenance aircraft had previously been taxiing on it but I assumed that he was long gone as plenty of time had passed.  After clearing the aircraft for departure; I saw that the taxiing aircraft had stopped and was still on the runway and it would seem Aircraft X noticed it also as we stepped on each other.  Departure roll never occurred.   I canceled his takeoff clearance and re-cleared him once the taxiing aircraft was off the runway.  In my opinion; there were several causes for this mistake:1.  First and foremost; I was distracted by other duties and my scan failed.  I also was the victim of my own expectation bias as plenty of time had passed that most of the other maintenance aircraft would have been off the runway at the time.2.  The ramp construction has gone on for an incredible length of time and the only way that maintenance aircraft have to get from one area to the next is on the runway. Taxiing on the runway is a standard operation and is a safety issue in and of itself.3.  I was distracted by updating the binders in the Tower Cab and other FLM duties.4. The FLMs are required to be in the Cab for 5 hours a shift.  Due to the social distancing requirements associated with COVID-19; the only way to accomplish all duties and meet all requirements is for the FLMs to work 5 hours a shift while the staffing only works 3.I don't know if there's anything that can be done on a facility level but I can speak for myself.  No amount of paperwork nor organizational rules will ever pre-empt providing a safe environment for aircraft. I may have lost sight of that and I know now that there's nothing that cannot wait to be done.  Paperwork can always be done later.


Second narrative: I conducted a local flight at ZZZ. I obtained the ATIS info and contacted Clearance Delivery with my request to conduct 3 practice approaches at ZZZ.I obtained a clearance with squawk code and altitude; with correct read back.I contacted Ground for taxi; the Controller initially said taxi to [Runway] XR via delta; then corrected himself and changed it to Runway XX via Hotel. From my FBO position on the airport; taxi to XX via Hotel is the usual procedure. I did notice the Controller was the same voice as Clearance; and I also noticed Controller was simultaneously working the Tower frequency.I taxied to [Runway] XX hotel intersection and called Tower notifying them Aircraft X ready at Hotel for XX. Tower cleared me for takeoff; heading 310; and gave the current wind; which was a light right crosswind. I taxied to position and was about to apply takeoff power; but looked down the runway and I see a commercial jet sitting abeam at the other end of the runway!I was only at taxi speed and stopped. I called the Tower saying 'I was aborting takeoff; there [is] a Jet sitting on the runway.' Tower said 'sorry about that; and hold position.'I held position; and confirmed I was on the runway and holding there. The jet then turned directly down the runway and taxied toward me; and subsequently exited the runway to my left towards the main terminal ramp. When clear; Tower then cleared me for takeoff; the remainder of flight with my 3 approaches was uneventful.Why the commercial jet was sitting there is not apparent to me. If it arrived on XL it would not need to taxi on [Runway] XX to get to the airport terminal. Chain of events; Controller simultaneously operating Clearance Delivery; Ground and Tower operations at a Class C facility. Controller changing my instructions; and perhaps distracted by other operations.


Synopsis: Tower Controller and pilot reported a runway incursion due to expectation bias. Pilot stated the Controller was working multiple positions at the time of the event.