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I have standalone ATMega328p and I'm using external 16MHz oscillator, I hooked up and I triple checked my connections for Pololu AVR programmer and I make sure that I select a proper programmer \ board \ com port in Arduino Studio (I have these: Board - Arduino Uno, Programmer POLOLU USB Avr Programmer, and it's on my COM9 port).

And when I hit "burn bootloader" I get this:

        C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CC:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf -v -patmega328p -cstk500v2 -PCOM9 -e -Ulock:w:0x3F:m -Uefuse:w:0x05:m -Uhfuse:w:0xDE:m -Ulfuse:w:0xFF:m 

    avrdude: Version 6.0.1, compiled on Apr 15 2015 at 19:59:58
             Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
             Copyright (c) 2007-2009 Joerg Wunsch

             System wide configuration file is "C:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf"

             Using Port                    : COM9
             Using Programmer              : stk500v2
             AVR Part                      : ATmega328P
             Chip Erase delay              : 9000 us
             PAGEL                         : PD7
             BS2                           : PC2
             RESET disposition             : dedicated
             RETRY pulse                   : SCK
             serial program mode           : yes
             parallel program mode         : yes
             Timeout                       : 200
             StabDelay                     : 100
             CmdexeDelay                   : 25
             SyncLoops                     : 32
             ByteDelay                     : 0
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                      Block Poll               Page                       Polled
               Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom        65    20     4    0 no       1024    4      0  3600  3600 0xff 0xff
               flash         65     6   128    0 yes     32768  128    256  4500  4500 0xff 0xff
               lfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
               hfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
               efuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
               lock           0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
               calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
               signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

             Programmer Type : STK500V2
             Description     : Atmel STK500 Version 2.x firmware
             Programmer Model: STK500
             Hardware Version: 15
             Firmware Version Master : 2.10
             Topcard         : Unknown
             Vtarget         : 4.8 V
             SCK period      : 17.4 us
             Varef           : 0.0 V
             Oscillator      : 3.686 MHz

    avrdude: stk500v2_command(): command failed
    avrdude: initialization failed, rc=-1
             Double check connections and try again, or use -F to override
             this check.


    avrdude done.  Thank you.

    Error while burning bootloader.
    avrdude: stk500v2_ReceiveMessage(): timeout
    avrdude: stk500v2_ReceiveMessage(): timeout
    avrdude: stk500v2_ReceiveMessage(): timeout
    avrdude: stk500v2_ReceiveMessage(): timeout
    avrdude: stk500v2_ReceiveMessage(): timeout
    avrdude: stk500v2_getsync(): timeout communicating with programmer
             AVR Part                      : ATmega328P
             Chip Erase delay              : 9000 us
             PAGEL                         : PD7
             BS2                           : PC2
             RESET disposition             : dedicated
             RETRY pulse                   : SCK
             serial program mode           : yes
             parallel program mode         : yes
             Timeout                       : 200
             StabDelay                     : 100
             CmdexeDelay                   : 25
             SyncLoops                     : 32
             ByteDelay                     : 0
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                      Block Poll               Page                       Polled
               Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom        65    20     4    0 no       1024    4      0  3600  3600 0xff 0xff
               flash         65     6   128    0 yes     32768  128    256  4500  4500 0xff 0xff
               lfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
               hfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
               efuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
               lock           0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
               calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
               signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

             Programmer Type : STK500V2
             Description     : Atmel STK500 Version 2.x firmware
             Programmer Model: Unknown
    avrdude: stk500v2_ReceiveMessage(): timeout
    avrdude: stk500v2_ReceiveMessage(): timeout
    avrdude: stk500v2_ReceiveMessage(): timeout
    avrdude: stk500v2_ReceiveMessage(): timeout
    avrdude: stk500v2_ReceiveMessage(): timeout
    Error while burning bootloader.

UPDATE Everything was OK with boards and with wiring. The issue was with poor connections. Even when I tested these connections with my multimeter and everything seems ok, they were not good enough for programming. So when I make sure that the jumper wires are not loose everything start working properly.

It looks like this process is very sensitive and that's why need extra attention on a breadboard.

  • That may be a problem with the setup of the programmer and computer, rather than the target chip. See if you get these same messages when the programmer is not even connected to the target chip. – Chris Stratton Aug 12 '16 at 23:06
  • How can I see that? And how can I fix it if that is the problem? – ShP Aug 12 '16 at 23:08
  • As I said, try the same operation but without the programmer connected to the ATmega you are trying to program, and see if the error messages are different. – Chris Stratton Aug 12 '16 at 23:11
  • I'm getting the same error when I unplug the cable from programmer to atmega. But I checked with buzzer to make sure that there's a connection to each of these pins on the breadboard... – ShP Aug 12 '16 at 23:14
  • The fact that you are getting the same error suggests that the problem is not with your breadboard or the connections to it, but rather that your computer, drivers, port selection, avrdude configuration, programmer, or its firmware are not cooperating. – Chris Stratton Aug 12 '16 at 23:45
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The OP itself answer this question:

Everything was OK with boards and with wiring. The issue was with poor connections. Even when I tested these connections with my multimeter and everything seems ok, they were not good enough for programming. So when I make sure that the jumper wires are not loose everything start working properly.

It looks like this process is very sensitive and that's why need extra attention on a breadboard.

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