My suspicion is that the input impedance of the 2i2 isn't high enough. I didn't see a spec for the instrument input, but the line input is 10kΩ. I found a spec for the neck pickup of a Squier Affinity Jazz Bass neck pickup, which is 4.6kΩ. I'm no electronics expert, but I'd want the input to be more than just a bit over double the pickup. It's possible that a good active DI would solve your problem. Even a decent passive DI could have twice the input impedance of the 2i2, but an active would be on the order of 100x that.

Boswell

It’s odd. Even with the input turned down down it peaks? The impedance issue usually loads the pickup which results in tonal differences, it would be interesting to see what the waveform looks like on the line input. It will be low, but that playing level is pretty hot. I think a cheap di would be a problem solver, or the DI out of an amp. The clipping indicates and over level issue, but surely this should be controllable? Something a bit odd is going on.

There's no evidence of amplitude overload, simply of too low an impedance. The 2i2 input impedance is 60K Ohm with the button out (line input mode) and 1.5M Ohm with the button in (instrument input mode). Check that you really have the INST button pushed in for the appropriate channel on the front panel.

I agree, that this is very odd. I can confirm that I have the instrument switch selected on the combo input of the 2i2. The pop is not a digital clipping artifact from the DAW, as evidenced by Boswell's screenshot. Something is happening earlier in the signal chain. I did try using a Behringer GDI21, with the amp modeling turned off. Presumably in this scenario it acts as a basic DI box (correct me if I'm wrong) and the issue persists. That's a $30 pedal, so the next step may be a trying a higher quality DI. 

The Zoom B3 mentioned above has volume for the output but not the input, so I'd also like to try a DI with an input pad switch to see if that helps.

Stupid Question? You don't have active pickup electronics on the bass do you?

The bass just has the stock passive pickups. 
 

Not a stupid question. I appreciate the help with troubleshooting this issue. 

It could be that the pre-amp is faithfully reproducing what it is actually seeing at its input. Can you confirm that the bass plays correctly into an amplifier, using the same lead?

The Squier Jazz Bass is a perfectly acceptable instrument, but it is manufactured down to a price, and I'm not being derogatory. I think the model you have is the single-pickup version. I've seen the magnets displace themselves or even fall off the underside of those Squier pickups, and that results in a mangled output. It's worth unscrewing the pickup plate to check.

The bass is very much a possible culprit. I don’t have an amp on hand to compare, so still trying to figure that out. I might take a peak inside, but when not slamming the strings, everything sounds as it should. If the magnets/pickups are not damaged/displaced, are the cheaper electronic components a possible source of the problem? I wouldn’t know where to even start with trying to inspect the wiring and pots. 

I have also considered that I’m just playing too damn hard for direct recording. If all components and parts of the signal chain are in working order, should this popping not be happening, no matter how hard I play? I’m working with a cheaper bass, DI and interface. But even with top of the line equipment, could this problem happen with poor picking technique? 

There is a possibility that it's a transient response issue - but if the pick edge plays mega loud, it should be possible to not overload the input stage. It sounds like clipping but that should be controllable? We have a mystery?

I don't think there's any mystery - just a fault to be found. Plugging the lead into an amplifier rather than into the 2i2 would establish whether the problem is in the Focusrite or in the instrument plus lead. We can see from the waveform that there is no overload problem, simply that the waveform is not correct.

I forgot to ask: you are using a standard guitar lead, aren't you? You could well get this sort of effect if you mistakenly used a TRS (dual conductor plus screen) lead instead of a TS (single conductor plus screen), given that the 2i2 input jack can double as a balanced line input..

First, check to see whether your amplifier's input level is set too high. If it is, down the volume until the clipping stops. Check your amplifier and bass's EQ settings next. Clipping can occur if the EQ is adjusted too high. Reduce the EQ till the sound is clear again. Finally, double-check your bass's and amplifier's gain levels. Clipping can occur if the gain is set too high. Reduce the gain till the sound is clear once more.

I've recently been experiencing some issues with direct bass recording, specifically related to overloading and clipping. I'm fairly new to the recording world and would appreciate some guidance. Whenever I try to record bass directly into my audio interface, I notice that the signal tends to overload and clip, resulting in an unpleasant distorted sound. I've tried adjusting the input gain on my interface, but I still can't seem to get a clean recording without clipping. Here's my setup: I'm using a bass guitar plugged directly into a DI (direct input) box, which is then connected to my audio interface. I'm using a DAW to record and monitor the signal. I've experimented with different input gain settings on both the DI box and the audio interface, but I'm still encountering the same issue. I'm wondering if there are any specific techniques or settings that could help me achieve a clean bass recording without overloading or clipping.