There are several problems.
The CONTROL file that you posted will not work with your EMISS1.txt file.
The number of starting locations in the CONTROL file needs to match the number in EMISS1.txt.
Also in EMISS1, you have 10 starting locations in your top line, but you only provide 5.
Also please check your initd, numpar, maxpar settings in SETUP file.
1. change your EMISS1 file to indicate the correct number of lines.
emissions group header: YYYY MM DD HH QINC NUMBER
each emission's source: YYYY MM DD HH MM DUR_HHMM LAT LON HT RATE AREA HEAT
18 11 08 08 01
0005
18 11 08 08 00 0100 39.7290 -121.6260 10 5545739.48 1133055.52 0.00
18 11 08 08 00 0100 39.7290 -121.6260 2650 26342262.54 1133055.52 0.00
18 11 08 08 00 0100 39.7290 -121.6260 3286 26342262.54 1133055.52 0.00
18 11 08 08 00 0100 39.7290 -121.6260 3922 26342262.54 1133055.52 0.00
18 11 08 08 00 0100 39.7290 -121.6260 4558 26342262.54 1133055.52 0.00
2. Change your CONTROL file to have 5 starting locations as well.
18 11 08 08
5
39.729 -121.626 15.000
39.729 -121.626 15.000
39.729 -121.626 15.000
39.729 -121.626 15.000
39.729 -121.626 15.000
0036
0
3. After you successfully run, check your MESSAGE file to make sure that the EMISS1 file was read properly.
NOTICE metinp: NAM 1 637 39 39 136 205 62510940 18 11 8 9
NOTICE advrng: (kg ,xyr,xy1) - 1 39 39 136 205
NOTICE main: Initial time step (min) 6
NOTICE emsmat: opened emission file - EMISS1.txt
NOTICE emsmat: emissions updated - 18 11 8 8
NOTICE main: 1 62510886 10000 8456700.0
NOTICE main: 1 62510892 20000 16916694.
NOTICE main: 1 62510898 30000 25376688.
NOTICE main: 1 62510904 40000 33836148.
NOTICE main: 1 62510910 50000 42276140.
4. If you are going to use puffs (initd=3), then you need to start out with far fewer of them because they split.
Currently you start with 25,000 puffs and set the upper limit, maxpar at 50,000.
Please see:
https://ready.arl.noaa.gov/hysplitusersguide/S622.htm