Slow runtime with large metagenomic FASTA in Flye consensus assembly

[apacon90]

Hi!!!!
Thank you very much for your tool!

I’m currently working with metagenomic reads, and now, with my FASTA files grouped by species, I’m trying to generate a consensus assembly with Flye (since afterwards I want to map my reads back to the consensus — my project is focused on genetic variability). However, I’ve been running into some issues, and I would really appreciate your advice.

For example, one of my FASTA files for a given species has around 309,160 reads (which is quite a lot). I have been using the following command:

nohup flye --nano-raw Akkermansia_muciniphila.reads.fa
--out-dir flye_1_octubre
--threads 32
--genome-size 6k
--meta > flye_1_octubre.log 2>&1 &

With this command, the process is taking a very long time. Is this expected, or would you have any suggestions to improve it?

I would love to hear your recommendations. Thank you in advance!

[mikolmogorov]

How slow does it run and what are your expectations in this case? Could you tell more about the input dataset and post full flye.log? Does the performance disagree with the performance tables in the manual?