Genome length not within range

[joao1980]

Hi and thanks for the tool.
I have been using staramr on my data but I recently obtaind the follwoing result:

• Genome length is not within the acceptable length range [4000000,6000000]

First, what doesa this mean? and,
Second, should/Can we play around with the default cutoffs?
Best regards,
Joao

[sgsutcliffe]

Hello Joao,
staramr has, slightly restrictive, defaults for genome size range. I believe it was set originally with the Salmonella genome in mind (~5Mbp). You should adjust the default cutoffs to fit with your specific genome. I would try adjusting the
--genome-size-lower-bound and --genome-size-upper-bound parameters and see if that resolves the isssue.
Good luck

[joao1980]

Hi,
Thanks for the reply. Hum...I am setting up the tool to run dynamically so that it can take any microorganism. What would be the implications of creating a higher range (e.g., 1Mbp to 10 Mbp) so that I can provide any prokaryote without having to set the genome upper and lower bounds?
Thanks

[sgsutcliffe]

I think it's largely there as a check for reasonable genome assembly. I think if you trust the assembly then it's fine.