In detail you mentioned Apalis iMX6Q, but from the logs it seems you are using Apalis iMX8.
Kindly provide complete detail of the setup you are testing and interface attaching. From logs your device is not detected on PCIe.
Are you testing with custom baseboard ?
What is version of module and hardware you are using?
What are the changes done in image?
Can you try with default Toradex image?
Are you using any evaluation board for the PCie to SATA adapter?
Please check known issue below concerning to PCIe and iMX8
Since we do not have hardware(PCIe to SATA) to test, it is hard to tell from here what went wrong. So kindly share complete details in order provide any help.