I am currently using GTDB-Tk to classify metagenome-assembled genomes (MAGs), but I am encountering a memory-related issue during the pplacer step.
Specifically, the pipeline reports that approximately 55 GB of RAM is required to run pplacer, which exceeds the available memory on my system (32 GB RAM). As a result, the classification step fails or cannot proceed.
My setup:
· GTDB-Tk
· Database version: [release 214
· System: Linux (Ubuntu)
· RAM: 32 GB
· Core i7
My questions are:
1. Is there a way to run GTDB-Tk (especially pplacer) with lower memory requirements?
2. Are there recommended parameters or flags to reduce RAM usage?
3. Is it acceptable to skip the pplacer step (e.g., using --skip_pplacer), and how would this affect taxonomic accuracy?
4. Are there alternative workflows or tools recommended for systems with limited RAM?
Any suggestions or best practices would be greatly appreciated.
Thank you.