Memory issue when indexing database

[Former user]

Hi team,

I am trying to kma index a database (fna.gz) to apply CCMetagen; I however continuously run into memory issues despite providing 1Tb. I use kma v1.3 and the kma index command. My database contains all bacterial and fungal sequences from RefSeq - which is admittedly quite large, but given the purpose of CCMetagen, it should work. Please let me know if you have any suggestion.

Thank you very much!

Best regards, Lara

[ptlcc]

Hi Lara

I have not checked the current size of RefSeq, but 1 Tb might not be sufficient. Have you tried adding the option “-Sparse TG“ to the indexing cmd.

Best,
Philip