GeneRax fails: gene tree leaves not mapped to species, no valid families

[PPrabhu1997]

Hi,
I am trying to run GeneRax on a single orthogroup to do gene tree species tree reconcilation and have created all the necessary files inlcuing the mapping link. However, the programme gives me the following error.

---

WARNING: There was an error initializing an OpenFabrics device.

Local host: node25
Local device: mlx5_0

[00:00:00] GeneRax 2.1.3
Logs will also be printed into no_correction/generax.log
GeneRax was called as follow:
generax --families families.txt --species-tree final_tree.nw --rec-model UndatedDL --prefix no_correction --strategy SPR

General information:

• Output prefix: no_correction
• Families information: families.txt
• Species tree: final_tree.nw
• MPI Ranks: 1
• Random seed: 123
• Reconciliation model: UndatedDL
• DTL rates: global rates
• Infer ML reconciliation: ON
• Unrooted reconciliation likelihood: OFF
• Enforcing gene tree root: OFF
• Prune species tree mode: OFF

Gene tree correction information:

• Gene tree search strategy: SPR
• Max gene SPR radius: 5

[00:00:00] Filtering invalid families...

End of instance initialization
[00:00:00] Starting species tree initialization...
[00:00:00] End of species tree initialization
[00:00:00] Filtering invalid families based on the starting species tree...

[00:00:00] Gathering statistics about the families...
[00:00:00] Input data information:

• Number of gene families: 1
• Number of species: 34
• Total number of genes: 102
• Average number of genes per family: 102
• Maximum number of genes per family: 102
• Species covered with the smallest family coverage: "Leucoagaricus_gongylophorus_Ac12_20141030" (covered by 0/1 families)
• Average (over species) species family coverage: 0

[00:00:00] Reconciliation rates optimization...
D=0.479232, L=0.337269, RecLL= -223.711

[00:00:00] Optimizing gene trees with radius=1...
[00:00:00] JointLL=-29375.6 RecLL=-225.78 LibpllLL=-29149.8

[00:00:00] Reconciliation rates optimization...
D=0.626833, L=1.12785, RecLL= -437.743

[00:00:00] Optimizing gene trees with radius=2...
[00:00:00] JointLL=-29375.6 RecLL=-225.78 LibpllLL=-29149.8

[00:00:00] Reconciliation rates optimization...
D=0.626833, L=1.12785, RecLL= -437.743

[00:00:00] Optimizing gene trees with radius=3...
[00:00:00] JointLL=-29375.6 RecLL=-225.78 LibpllLL=-29149.8

[00:00:00] Reconciliation rates optimization...
D=0.626833, L=1.12785, RecLL= -437.743

[00:00:00] Optimizing gene trees with radius=4...
[00:00:00] JointLL=-29375.6 RecLL=-225.78 LibpllLL=-29149.8

[00:00:00] Reconciliation rates optimization...
D=0.626833, L=1.12785, RecLL= -437.743

[00:00:00] Optimizing gene trees with radius=5...
[00:00:00] JointLL=-29375.6 RecLL=-225.78 LibpllLL=-29149.8

[00:00:00] Reconciling gene trees with the species tree...
[node25:1156123] *** Process received signal ***
[node25:1156123] Signal: Segmentation fault (11)
[node25:1156123] Signal code: Address not mapped (1)
[node25:1156123] Failing at address: (nil)
[node25:1156123] [ 0] /lib64/libpthread.so.0(+0x12d20)[0x7f88146a4d20]
[node25:1156123] [ 1] generax(_ZN8Scenario26savePerSpeciesEventsCountsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb+0xf0)[0x5628501f76f0]
[node25:1156123] [ 2] generax(_ZN8Routines19inferReconciliationERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorI10FamilyInfoSaIS9_EERK15ModelParametersS7_bjb+0x1fb5)[0x56285019b4c5]
[node25:1156123] [ 3] generax(_ZN11GeneRaxCore9reconcileER15GeneRaxInstance+0x143)[0x56285013e5a3]
[node25:1156123] [ 4] generax(_Z12generax_mainiPPcPv+0x232)[0x562850138352]
[node25:1156123] [ 5] /lib64/libc.so.6(__libc_start_main+0xe5)[0x7f88142f67e5]
[node25:1156123] [ 6] generax(+0x5a6a4)[0x5628501366a4]
[node25:1156123] *** End of error message ***
/var/spool/slurm/d/job125098/slurm_script: line 17: 1156123 Segmentation fault (core dumped) generax --families families.txt --species-tree final_tree.nw --rec-model UndatedDL --prefix no_correction --strategy SPR

Any help willbe appreciated.

Cheers,

Prasanth.

[BenoitMorel]

Hello Prasanth, Sorry for the late reply. Could you please send me the mapping file, the alignment, the families file, and the species tree? Best, Benoit Le jeu. 15 janv. 2026 à 17:51, PPrabhu1997 ***@***.***> a écrit :

…

Reopened #77 <#77>. — Reply to this email directly, view it on GitHub <#77 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UOIAHMW2IECZVZ5XVL4G7ARNAVCNFSM6AAAAACRW2MFTCVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMRSGA3TINRVGI2DOMQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[PPrabhu1997]

Hello, Thank you so much for the reply. I have attacehd my input files. Prasanth Prakash Prabhu Ph.D. Candidate Hibbett Lab Clark University Worcester, MA 01610 Personal website :https://sites.google.com/view/prasanth-prakash-prabhu-hehim/about

________________________________ From: BenoitMorel ***@***.***> Sent: 16 January 2026 10:46 To: BenoitMorel/GeneRax ***@***.***> Cc: Prakash Prabhu, Prasanth ***@***.***>; State change ***@***.***> Subject: [EXT] Re: [BenoitMorel/GeneRax] GeneRax fails: gene tree leaves not mapped to species, no valid families (Issue #77) [https://avatars.githubusercontent.com/u/13802961?s=20&v=4]BenoitMorel left a comment (BenoitMorel/GeneRax#77)<#77 (comment)> Hello Prasanth, Sorry for the late reply. Could you please send me the mapping file, the alignment, the families file, and the species tree? Best, Benoit Le jeu. 15 janv. 2026 à 17:51, PPrabhu1997 ***@***.***> a écrit :

Reopened #77 <#77>. — Reply to this email directly, view it on GitHub <#77 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UOIAHMW2IECZVZ5XVL4G7ARNAVCNFSM6AAAAACRW2MFTCVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMRSGA3TINRVGI2DOMQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

— Reply to this email directly, view it on GitHub<#77 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AR56X5ZCEHRV424XDGTZXKL4HEBVRAVCNFSM6AAAAACRW2MFTCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTONRQGY4DANJSGY>. You are receiving this because you modified the open/close state.Message ID: ***@***.***>

[BenoitMorelAmeria]

I don't see them, did I miss anything?

[PPrabhu1997]

Hello,
I tried to install Generax directly from GitHub, and it worked. Earlier i was using the bioconda version and that was giving me the error