Assertion `internal_index == p->nodes_number' failed.

[Jed G]

I have successfully run GeneRax before, but I am now stymied by a new error, and I'm hoping it's something simple to fix.

GeneRax 2.1.3

generax -s generax_species_tree.braflo.new.tre -f 251218.nohag.families --geneSearchStrategy EVAL -p 251218.test -r UndatedDL --enforce-gene-tree-root

[00:00:00] Filtering invalid families...
generax: /root/GeneRax/ext/GeneRaxCore/src/IO/RootedNewickParser.cpp:293: corax_rtree_t* build_rtree(RTreeParser*): Assertion `internal_index == p->nodes_number' failed.
Aborted

ML tree produced by RAxML (BestTree)

Species tree:

(((((((((((Human_Homsap,Cow_Bostau),Gray_Opposum_Mondom),Platypus_Ornana),Chicken_Galgal),Newt_Plewal),Coelacanth),(((((Bowfin_Amioce,Gar_Lepocu),Zebra
fish_Danrer)),Sterlet_Acirut),Gray_bichir_Polsen)),((Sawfish_Pripec,Sawshark_Prijap),Makorepe_Calmil)),(Hagfish_Eptata,Lamprey_Petmar)),Tunicate_Cioint
),Amphioxus_Braflo);

Happy to send additional files.

Jed

[Benoit Morel]

Hi Jed,

Apparently, generax expects a rooted binary tree at some place and finds something else (either an unrooted tree or a non-binary tree)

Can you:

- double check the species tree (but it looks fine)
- try without --enforce-gene-tree-root 

- check your gene trees (maybe only run this on one single gene family to check if at least some gene families are working)

Best,

Benoit

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[Stefan Flaumberg]

Hi Jed,

Looks like your species tree has an extra node (monofurcation) before the clade of Neopterygii, it can be visualized in the iTOL tree viewer by displaying internal nodes. As RaxML reconstructs only unrooted trees, I guess the problem originated due to manual rooting. Try out etetoolkit (ete3 or ete4 python packages) to avoid such problems in future.

GeneRax and AleRax can use only strictly bifurcating trees, so please try the refined tree from below, in which I removed an extra pair of parentheses:

(((((((((((Human_Homsap,Cow_Bostau),Gray_Opposum_Mondom),Platypus_Ornana),Chicken_Galgal),Newt_Plewal),Coelacanth),((((Bowfin_Amioce,Gar_Lepocu),Zebrafish_Danrer),Sterlet_Acirut),Gray_bichir_Polsen)),((Sawfish_Pripec,Sawshark_Prijap),Makorepe_Calmil)),(Hagfish_Eptata,Lamprey_Petmar)),Tunicate_Cioint),Amphioxus_Braflo);

Best,

Stefan

[Benoit Morel]

Stefan is most likely right ;-)

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[Jed G]

<Head-slap> That's the problem. Generax seems to be working now.

Thank you, I thought I'd edited those out, but my (older) tree-viewer seems to have hidden them. 

Jed