fragment-insertion sepp command running for more than 24h


I am currently running the following command:

qiime fragment-insertion sepp --i-representative-sequences rep-seqs.qza --i-reference-database sepp-refs-silva-128.qza --o-tree tree-sepp-silva128 --o-placements tree-sepp-silva128-placements --verbose

I understand that the runtime depends on the amount of ASVs, which is 7000 of 250 nt long in my case. I have seen on the qiime2 library site for the fragment-insertion sepp plugin that for 11000 sOTUs with 90 nt long, it took 48 min to complete the analysis. They ran the analysis on four of 32 cores of a Intel(R) Xeon(R) CPU E5-2640 v3 @ 2.60GHz server with 265 GB available RAM.

However, the analysis in my case has been running for more than 24h. I am using a Mac laptop with a 1.6 GHz dual-core intel core i5 processor and 8 GB 1600 MHz DDR3 memory.

Is the runtime normal or is there something wrong?

Best regards,

Hello Pablo,

I think I have discovered your problem:

If this script uses up all your system memory, it will slow down 100x-1000x, going from hours to weeks. I bet that's what happened here.

Do you have a computer with more memory you could use to run this script? Alternately, you could use a program like top to check on your available memory and confirm that it's using too much before looking for a machine with more RAM.

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Hi @colinbrislawn

Thanks a lot for your explanation.

I will try to find a computer with more capacity. Alternatively, I could just build a rooted tree but I am having troubles finding the right tutorial in the qiime2 website. Perhaps you have an idea where I can find that tutorial?


Here you go! Phylogenetic inference with q2-phylogeny — QIIME 2 2021.8.0 documentation

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