If you do not have her SIN and cannot obtain, file your return with 000 000 000 as her SIN number. Be sure you enter your date of separation and CRA should be able to match your information from previously filed returns.
It's important that you do not claim a Spousal Tax Credit for your spouse in error if you do not know your spouse's income. You do not want to claim a credit and then repay this amount to CRA if her income exceeded $15,000 during the year.
Here's some helpful information from TurboTax: What do I do if I don’t know my spouse’s income?
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