contamination or polymorphism!

[jmhallas]

Hello,

My data is low coverage (<1x), and I have a number of assemblies that have the following error -

WARNING: The graph might suffer from contamination or polymorphism!

I am using the follow kmers [21,45,65,85,105]. I am wondering if there are other reasons I may get this error other than contmination? I have removed these individuals from subsequent popgen analyses and would like to include them, but would like a little more information about this error.

Thank you for your advise.

-josh

[JianjunJin]

It may help to troubleshoot the issue by seeing the complete log file and the assembly graph (*fastg or visualized)

[jmhallas]

Here is the log file from one individual.

get_org.log.txt

[JianjunJin]

Sorry for the unintentional slip due to other commitments.
Do you happen to still have the assembly graph for this run? Visualized graph is crucial for troubleshooting.