When I run PanEDTA, it seems to rerun EDTA from scratch for each chromosome instead of starting the merging process directly.

[dongaoqian]

Hello, I would like to ask why, when I run the PanEDTA script, it seems that the EDTA for each genome is being rerun instead of directly merging the EDTA results for each chromosome?

My command is as follows: panEDTA.sh -g PanEDTA_genome.list -c sample.cds.fna -t 20.

The output directory and the contents of genome.list are as follows:

[oushujun]

Hello @dongaoqian, sorry for the delayed response. Your PanEDTA_genome.list should contain genome files pointing to the directory that contains existing runs, otherwise it will regenerate them.

Thanks!
Shujun