Some genome were not found in the clustering results

[xjhzjucas]

Hi developer, Thank you for this nice tool! I met a problem that I put 577 genomes into dRep using dRep dereplicate ./ -g ./genome577/*.fa -pa 0.99, and it run successfully. I found that only 498 genomes were found to be clustered according to the Primary_clustering_dendrogram.pdf, 79 genomes were not clustered into any cluster, can you tell me why and how to make every genome clustered. And in Cdb.csv, I only got 498 rows too. Thank you so much!

[MrOlm]

They are probably being filtered out by checkM. You can change the checkM filtering chritera, use "cluster" instead of "dereplicate", or add `--ignore_genome_quality" to your command.

Matt

[xjhzjucas]

Thank you for your help！