MLG CROSSED ACTIVE RWY 30R AND THEN TOOK OFF ON RWY 30L FROM THE INTERSECTION AT SJC.

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THIS INCIDENT WAS THE CULMINATION OF SEVERAL FACTORS THAT COULD HAVE LED TO A POTENTIALLY DISASTROUS RESULT. I WAS JUST TAXIING OUT FOR DEP ON RWY 30L AT SJC. IT WAS MY FIRST OPERATION IN AND OUT OF THAT PARTICULAR ARPT (HAD FLOWN IN THE PREVIOUS NIGHT) AND I WAS UNFAMILIAR WITH IT EXCEPT FOR REF TO CHARTS. THE GND CTLR INSTRUCTED ME TO FOLLOW ACR B TO RWY 30L. AS WE WERE TAXIING (SHORT DISTANCE TO DEP RWY); WE WERE ACCOMPLISHING HIGH COCKPIT LOAD CHKLISTS; RADIOING FOR GROSS WT FIGURES; ETC. ALONG THE WAY; WE WERE TOLD TO CALL TWR AS WE MADE THE RIGHT TURN. I LOOKED UP AND SAW ACR B TAXIING ACROSS THE THRESHOLD OF RWY 30R (GA RWY). SO; I THEN ALSO MADE THE RIGHT TURN; CROSSED OVER RWY 30R AND THE F/O CALLED THE TWR. AT THAT POINT; THE TWR INFORMED US 'BE ADVISED YOU JUST CROSSED AN ACTIVE RWY.' I WAS SHOCKED AND SO WAS THE F/O. AFTER A MOMENT; I CALLED THE TWR AND SAID THAT MY UNDERSTANDING WAS THAT WE WERE CLRED TO TAXI TO RWY 30L BEHIND ACR B. THE TWR THEN SAID; 'NO; YOU WERE CLRED TO RWY 20L TO HOLD SHORT OF TXWY ALPHA. WE STILL DIDN'T QUITE GET THE PICTURE AS TO WHAT HAD HAPPENED AND THE TWR CLRED US FOR TKOF. THIS IS WHERE MISTAKE #2 OCCURRED. WE PROCEEDED TO TKOF FROM THAT THRESHOLD POINT THAT WAS ABEAM THE END OF RWY 20R WHERE WE HAD ENTERED THE RWY FROM. WE DISCOVERED LATER AS WE WERE DISCUSSING IT ENRTE THAT WE HAD NOT UTILIZED THE FULL LENGTH OF AN ALREADY VERY SHORT RWY. HAD WE BEEN HEAVIER OR HAD THERE BEEN AN ABORT OR AN ENG FAILURE AFTER V1; WE MAY NOT HAVE MADE IT. WE NOW REALIZE THAT THE ACTUAL AVAILABLE RWY WAS REDUCED AT THAT DISPLACED THRESHOLD POINT BY ABOUT 1400'. HUMAN FACTORS: WE WERE UNFAMILIAR WITH THE ARPT. THE CTLR DID NOT ADVISE US THAT WE WERE NOT UTILIZING THE FULL LENGTH. WE EITHER DID NOT RECEIVE OR WE DID NOT UNDERSTAND THAT WE WERE TO CONTINUE ALONG THE PARALLEL RATHER THAN FOLLOW THE COMMUTER. MAYBE THE COM REQUESTED A REDUCED LENGTH TKOF AFTER HE SWITCHED TO TWR?! I CAN SAY THAT I WILL CERTAINLY LEARN FROM THIS ONE; BUT WHAT ABOUT THE 'WHAT IF'S?' MAYBE THE SITUATION COULD HAPPEN AGAIN AND THE NEXT ONE WON'T BE SO LUCKY. PERHAPS THE 2-M CREW CONCEPT NEEDS TO BE WATCHED A LITTLE MORE CLOSELY. PERHAPS THE CTLRS SHOULD BE REQUIRED TO CONFIRM WITH A PLT THAT HE IS REQUESTING A REDUCED LENGTH TKOF IF HE APPEARS TO BE IN A SIMILAR SITUATION.