RWY TRANSGRESSION BY COMMUTER. LTSS AND NMAC AS ACR Y OVERFLEW COMMUTER X.

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TWR ISSUED CLRNC 'BACK TAXI INTO POS AND HOLD RWY 29 AT R.' I BACK TAXIED THROUGH 29R TO NEXT TAXIWAY 29P. THIS CREATED A CONFLICT WITH DEP PATH OF ANOTHER RWY. CREW FATIGUE DEFINITELY WAS A FACTOR IN THIS INCIDENT DUE TO REDUCED REST PERIOD SCHEDULES. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: MADE CALLBACK AS PART OF RWY INCURSION STUDY. RPTR GAVE TYPE ACFT. SAYS NORMAL TAXI RTE FOR RWY 29 INTXN TAXIWAY R TKOF IS VIA RAMP; TAXIWAY U; TAXIWAY X; TAXIWAY S; THEN BACK TAXI ON 29 TO TAXIWAY R. ON THIS DAY THE CLRNC WAS DIFFERENT AND THEY WENT VIA TAXIWAY U; TAXIWAY X TO TAXIWAY R; SO THERE WAS NO NEED TO BACK TAXI; BUT FROM FORCE OF HABIT WHEN CLRED INTO POS AND HOLD THEY TAXIED ONTO RWY AND MADE R TURN TO NEXT TAXIWAY WHICH WAS ACTUALLY TAXIWAY P IN THIS CASE. WDB ACR TAKING OFF ON RWY 4L PASSED OVER RPTR ACFT AT ALT OF ABOUT 400 FT. FLC THOUGHT THEY WERE AT TAXIWAY S WHEN CLRED INTO POS. SAYS FATIGUE WAS BIG FACTOR IN BAD SITUATIONAL AWARENESS FOR FLC. THEY HAD 6 HRS SLEEP THE PREVIOUS NIGHT; BUT ON FIRST NIGHT OF 3 DAY TRIP THEY HAD VERY LITTLE REST. RPTR THINKS COMMUTER FLC SCHEDULING CONTRIBUTES TO FATIGUE AND MENTAL LAPSES SUCH AS OCCURRED IN THIS INCIDENT.