You may see the following error if you are trying to program a Jam™ Standard Test and Programming Language (STAPL) Format File (.jam) that was converted from a JTAG Indirect Configuration File (.jic). This occurs when using the quartus_jli executable command and you tried to execute the -aprogram command without executing the -aconfigure command.
Error in reading SFL VERSION
Unrecognized device
Exit code = 6... Unrecognized device
You will need to run the commands in the following order for .jam files containing the serial flash loader (SFL):
1) quartus_jli -c1 -aconfigure <filename>.jam
2) quartus_jli -c1 -aprogram <filename>.jam
*Where -c1=cable index