J-PARC E16 is an experiment to examine the origin of hadron mass through a systematic measurement of spectral changes of vector mesons in nuclei. The measurement of $e^{+}e^{-}$ pairs from the decay of vector mesons will provide the information of the partial restoration of the chiral symmetry in a normal nuclear density. To resolve a pulse pile-up and achieve good discrimination of $e^{pm}$ from the background of a reaction rate of an order of 10 MHz, the data acquisition (DAQ) system uses waveform sampling chips of APV25 and DRS4. The trigger rate and data rate are expected to be 1 kHz and 130--330 MiB/s, respectively. The DAQ system for readout of APV25 and DRS4 were developed, where events were synchronized by common trigger and tag data. The first commissioning in beam, called Run-0a, was performed in June 2020 with about 1/4 of the designed setup. The DAQ worked with a trigger rate of 300 Hz in the Run-0a and the main bottleneck was a large data size of APV25. Further optimization of the DAQ system will improve the performance.
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