Roary 3.5.8 works with -i 80 switch, but not with -i 90 or higher with large datasets? #234

dutchscientist · 2016-02-15T23:26:27Z

I am rerunning a dataset done with an earlier version of Roary, now with 3.5.8, and suddenly it refuses to do the whole set (497 genomes) with the -i 90 or higher setting. It works fine until the generation of the tree with the accessory genes, and then it stops. After 3 days still no movement, whereas it was previously done in <6h.

When I make the dataset smaller, it works fine again, and all the GFF files individually work fine. When using -i 70 or -i 60, it works fine.

Tried it both on a server (double Xeon, 64 Gb RAM etc) and the Sanger Pathogens VM, same result. Any thoughts?

Haven't tried going back to the previous version yet, is that easy with cpan?

dutchscientist · 2016-02-17T00:52:13Z

Update: have downgraded to 3.5.7 via:
sudo cpanm -f AJPAGE/Bio-Roary-3.5.7

And then it works without a hitch again. Hence I think there is a bug somewhere in 3.5.8, I just don't know what it is!

andrewjpage · 2016-02-18T15:15:00Z

Hi,
I have rolled back the changes and pushed it out as version 3.5.9.
In 3.5.8 the entire accessory genome was used to create a binary tree & clusters, however it now goes back to its previous behaviour where its limited to 4000 genes (with the top and bottom % removed).

dutchscientist · 2016-02-19T00:02:27Z

Thanks, glad it's working again :)

tseemann · 2016-02-20T03:25:32Z

Can this be made an option? As we need the true pan-genome binary tree.

andrewjpage closed this as completed Feb 18, 2016

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Roary 3.5.8 works with -i 80 switch, but not with -i 90 or higher with large datasets? #234

Roary 3.5.8 works with -i 80 switch, but not with -i 90 or higher with large datasets? #234

Roary 3.5.8 works with -i 80 switch, but not with -i 90 or higher with large datasets? #234

Roary 3.5.8 works with -i 80 switch, but not with -i 90 or higher with large datasets? #234

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