A question about fragment insertion sepp

Hi everyone! I used my data to run fragment insertion sepp. After running more than 10h, there was no error or output. So I want to ask that how long this step usually take?

Here is the code:
time qiime fragment-insertion sepp --i-representative-sequences rep-seqs.qza --i-reference-database sepp-refs-gg-13-8.qza --o-tree tree.qza --o-placements tree_placements.qza --p-threads 15

MacOS
qiime2-2022.2
anaconda3-2019.7

Hello!

There is no good answer to your question. You may run the command with --verbose option to see the progress.
Trees are complicated and obviously, time grows with the number of sequences you're working with. If I remember correctly (didn't keep the log) AGP tree construction with q2-fargment-insertion took around 5 days on my machine with 48 CPUs.
Make sure you have enough space for temporary files in /tmp or change $TMPDIR.

Good luck!
V

5 Likes

Hello!

Thank you for the response! I will try it again!

Thank you!
M