Using the SILVA classifier directly?

[Nicholas_Bokulich]

@mihcir

Is there a way to further reduce the memory requirement, or do you think from the full error log that perhaps I have a different problem?

Definitely a memory error.

See recommendations here.

Use greengenes instead of SILVA — that should help a lot. You can also adjust the reads-per-batch parameter (e.g. try 2000) to have a longer but lower memory job.