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Why clear Deep Sea Ship?
The Deep Sea Ship dungeon is usually farmed for the 
Sunset Rapier, which is an upgrade after the 
Dragon Sword.
The dungeon has two other notable uses.
The first one is farming 
Amulets of Torture for 
FEZ if you don't want farm 
Fierce Devils.
The second one is getting the 
Ancient Sword if you want to save on food. Due to its low drop chance, it's usually done only if you really need it, for instance if you play HCCO.
Gear
Although you can beat the dungeon with any combat style, it is advised to use 
Magic because the final boss 
Kraken has high evasion against 
Melee and 
Ranged.
For instance, your 
HP expenditure per hour with Melee can be a quarter of what Magic spends, but the number of clears with Melee would be half of Magic. Usually for this dungeon, the difference in food is negligible in terms of time needed to produce it, so Magic is recommended.
Check your build with Can I Idle to see if you can idle the dungeon.
As an example, you need 680 HP with 
Auto Eat - Tier II to idle this dungeon without any Damage Resistance.
Clear Statistics
This section will give you the approximate numbers when clearing the dungeon with the following build:
The simulation was done for 78 in all relevant stats and Auto Eat - Tier II.
No 99 cooking mastery or 95% mastery pool.
Fire Surge without Combination Runes was used as the spell of choice.
For the Standard game mode, the only difference is that you spend 172 
Crabs instead of 191.
With the clear speed of 23.5 dungeons per hour, you will need around 4 hours to have a 50% chance of getting Sunset Rapier.
To have a 95% chance, you will need [math]\displaystyle{ ( log_{1-5/641}0.05 ) / 23.5 = 16.2 \text{ hours} }[/math].
Fire Expert Wizard Hat
Fire Expert Wizard Robes
Fire Expert Wizard Bottoms
Fire Expert Wizard Boots
Paladin Gloves
Amulet of Magic
Aorpheat's Signet Ring
Miolite Shield
Combat:
