You can always file Married Filing Separately. However, you would definitely want to select Head of Household if that's an option for you. HOH requires that you "keep up a home" for a qualifying person, such as a child. Because you didn't live with your spouse for the last 6 months of the year, this may be an option for you.

Please see FAQ on Head of Household below:

https://ttlc.intuit.com/questions/1894553-do-i-qualify-for-head-of-household

If you don't qualify for HOH due to not have a child, not paying over 1/2 the costs of your home, etc.. you may not want to rule out a joint return if its feasible. Married Filing Separate is sometimes a disadvantageous status.