John started using a DigiTech PDS 1002 Digital Delay during the By The Way tour and continued to use it consistently until his departure from the band. However, since he also used the Line 6 DL4 Delay Modeler during this period, it’s unclear which pedal was used for specific effects or songs.
Notably, this pedal reappeared on John’s 2022 pedalboard for the Unlimited Love tour (see John Frusciante’s 2022 Pedalboard).
he used this on Running Away Into You for the weird vocal effect