Hi,
Before you program the flash, you need to configure the FPGA.
In order to program the FPGA, you need to performed "quartus_jli.exe -aconfigure -c1 Beta2_00wEcodST.jam" then only you performed "quartus_jli.exe -aprogram -c1 Beta2_00wEcodST.jam"
You may refer to the AN425 (https://www.intel.com/content/www/us/en/programmable/documentation/sam1403762199737.html). Below is the Note that I copy from the document
Note: To program serial configuration devices with the Jam STAPL Player, you must first configure the FPGA with the Serial FlashLoader image. The following commands are required:
jam -aconfigure <filename>.jam
jam -aprogram <filename>.jam