Assessing Chrysanthemum lavandulifolium genome assembly

[zhangdeng1992]

Dear Shujun,

We're using LTR_retriever to assess a genome assembly for Chrysanthemum lavandulifolium. Because the genome is very large and a single chromosome's size exceeds 300 MB. I have been running the program on the server for over 30 days with -threads 30, and there are still no results. The program has been stuck at this step （“Module 6: Start to remove nested insertions in internal regions...”）for more than 20 days. Even when I split the genome and only run it on one chromosome, the issue persists. I'd like to ask if it's normal for this step to take such a long time, and how I can solve this problem？

Thank you very much for you time.
Regards,
Zhangdeng

[oushujun]

Hello, Zhangdeng,

It seems odd to me. The genome size of Chrysanthemum lavandulifolium is like 2.6Gb? It should be done in a few days with 30 threads. You may need to isolate the script that get stalled and run it manually with a subset of the original input of that step. In this case you may find any abnormal behavior of the step and start to debug.

Shujun

[zhangdeng1992]

Thanks for the reply, Shujun. Okay, I'll try to isolate the script that get stalled and run it manually with a subset of the original input of that step.