A disposable reaction vessel for performing nucleic acid amplification assay. The disposable reaction vessel has a penetrable cap that can be penetrated by an automated pipettor to aspirate a portion of an amplified reaction product. The disposable reaction vessel contains the reagents necessary to perform a nucleic acid amplification assay. A patient specimen is added to the unit dose reagents in the disposable reaction vessel and the penetrable cap is closed. The disposable reaction vessel containing the reaction mixture and the specimen undergoes amplification, typically by placing it in a thermal cycler. After amplification the intact disposable reaction vessel is transferred to an automated analyzer where an automated pipettor penetrates the closure membrane and aspirates a portion of the amplified sample for further processing, without removal of the reaction vessel cap. This avoids the generation of potentially contaminating aerosols or droplets.