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I have a macbook pro (2009) which was dual booted to windows. Windows bluescreened, I restarted, and the mac woulnt boot (blinking folder question mark). I pulled the hard drive out, copied the data that wasnt backed up, made a bootable osx installer and booted from that.

The laptop went to a prohibition screen (stop sign) https://support.apple.com/en-me/HT204156 enter image description here

I then booted gparted, but it doesn't see the hard disk, which is healthy according to SMART and I formatted it to NTFS. I am worried now. I was hoping it was the hard drive.

sudo fdisk -l

Does not show the disk either.

Is this a hardware issue 100% certainty?

This person here claims that it could be the HDD cable: https://www.youtube.com/watch?v=k1IiEe7TSKg (ps I love his accent).

Any way to know if it is the cable or is it likely the motherboard? Gparted ran fine. How can I know for certain it is not the motherboard or the harddrive?

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For me, the problem was the cable connecting the harddrive to the motherboard. Thankfully it was not the motherboard.

After buying the cable (part number 821-0812-A), I installed it into the computer, booted gparted (linux) off a flashdrive and checked to see if my harddrive came online. It did, and I was relieved.

Here is where I bought the part: http://www.aliexpress.com/item/For-Macbook-Pro-15-A1286-HDD-Cable-Connector-Test-OK/504281003.html This might not fit your computer, you need to verify the model number of your cable. My MacBook's identifiers are as follows:

Model number: A1286
EMC:2324
Model ID: MacBookPro5,4

Since I had erased my harddrive, I needed to reinstall mac on it. If you did not format your harddrive, the following information isn't necessary for you.

I then attempted to create a bootable USB flashdrive to install mac OSX Mavericks using TransMac (a windows utility). This failed, even after using a GUID partition table (gpt) on the flashdrive through diskpart.

What worked was using Carbon Copy Cloner to make the bootable USB from an El Capitan .dmg file using a friend's Mac. I first formatted the USB drive using diskutility to Mac OS Extended, Journaled. Carbon Copy Cloner warned that my flashdrive would not be bootable, but it was wrong; the flashdrive booted.

I encountered the following problems while installing however: Mac did not recognize my harddrive. I solved this by using diskutility from the bootable flashdrive to format my hard drive to Mac OS Extended, Journaled.

The next problem was

This was solved by closing the installer, opening terminal (from the installation operating system loaded off the live USB) and typing:

date 1010101015

This sets the clock to Oct 10, 2015, allowing the installation to proceed because the dmg I used was either too old or too new for the code signature to be verified properly. I also read that ntpdate -u time.apple.com works but I assume you need an internet connection for that, and I didn't have one.

Hope this helps

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