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SATA drive connected through the extra ports not detected on Mac Pro 1,1 2006

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Hi guys, first-time poster here. Thanks in advance!

I have successfully installed Xubuntu 17.10 (XFCE) following a guide from mattgadient.com on a Mac Pro 1,1 2006. I could confirm that the two SATA port is working as when I put back my drive with MacOS Lion it detects all the drives. But when booted in Xubuntu only the drives in the four bays could be detected.

Xubuntu cannot detect drives at the 2 extra SATA port during installation. If I move the drive with Xubuntu installed to one of the two SATA ports, it will stall at a black screen with a blinking underscore. It will not boot from a Xubuntu installation DVD if the drive is connected to the two SATA ports but boot fine when connected to the bays. A drive with MacOS Lion installed will boot regardless of where it was connected.

I have read online that I should disable IDE or enable AHCI in BIOS, but I don't think it applies to Macs. Since Lion could detect these drives, I'm hoping there are software solutions to it.

My ultimate goal is to revive this old Mac and run ZFS drives on it, therefore would like to make use of the 2 ports. If there is a better way to achieve this, I'm dying to know. For some reason, upgrading to Mountain Lion to reach the minimum requirement for ZFS in Mac isn't successful (perhaps because of that old graphics card) but that would be for another forum.

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