GTDB Forum

Pplacer requirements

Hi all!
I installed the new version of gtdb v1.3.0 and database release 95! I tried to run the gtdb program with 4 genomes (but I have 130 genomes :smiley: ) and I received the following messagge:

WARNING: pplacer requires ~152 GB of RAM to fully load the bacterial tree into memory. However, 131.97GB was detected. This may affect pplacer performance, or fail if there is insufficient scratch space.

I would like to know the impact of this error in my analysis

Thank you!!

Hello,

Because your server has less than the required RAM (131/152GB) , GTDB-Tk will need to use scratch space. If program cant access the scratch space, it will crash and not return any results for the classify step.
Having less than the recommended amount of RAM doesnโ€™t affect the accuracy of the tool but instead increases the risk it crashing.
To reduce the memory usage, you can use the --scratch_dir flag ( see https://ecogenomics.github.io/GTDBTk/commands/index.html ) .

Hope this helps.

Regards,
Pierre