Hi! I'm trying to run generax to try reconciliating a single gene tree (with multiple gains and losses) to a species tree. However, I am getting the following error message:
[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: 76
- Total number of genes: 210
- Average number of genes per family: 210
- Maximum number of genes per family: 210
- Species covered with the smallest family coverage: "Polypedilumvanderplanki" (covered by 1/1 families)
- Average (over species) species family coverage: 1
[00:00:00] Optimizing DTL rates before the reconciliation...
[00:00:00] ll=-569.502
[00:00:00] Optimizing the phylogenetic likelihood...
[00:00:00] Reconciling gene trees with the species tree...
[IBIO-DRW7N0JQY0:04079] *** Process received signal ***
[IBIO-DRW7N0JQY0:04079] Signal: Segmentation fault: 11 (11)
[IBIO-DRW7N0JQY0:04079] Signal code: Invalid permissions (2)
[IBIO-DRW7N0JQY0:04079] Failing at address: 0x0
[IBIO-DRW7N0JQY0:04079] [ 0] 0 libsystem_platform.dylib 0x0000000188dcea24 _sigtramp + 56
[IBIO-DRW7N0JQY0:04079] [ 1] 0 generax 0x0000000100b2362c _ZN8Scenario26savePerSpeciesEventsCountsERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEEb + 88
[IBIO-DRW7N0JQY0:04079] [ 2] 0 generax 0x0000000100ad9d50 _ZN8Routines19inferReconciliationERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEERNS0_6vectorI10FamilyInfoNS4_ISA_EEEERK15ModelParametersS8_bjb + 1916
[IBIO-DRW7N0JQY0:04079] [ 3] 0 generax 0x0000000100a57640 _ZN11GeneRaxCore9reconcileER15GeneRaxInstance + 1448
[IBIO-DRW7N0JQY0:04079] [ 4] 0 generax 0x0000000100a4e99c _Z12generax_mainiPPcPv + 544
[IBIO-DRW7N0JQY0:04079] [ 5] 0 generax 0x0000000100a4f1e0 main + 92
[IBIO-DRW7N0JQY0:04079] [ 6] 0 dyld 0x0000000188a47fd8 start + 2412
[IBIO-DRW7N0JQY0:04079] *** End of error message ***
zsh: segmentation fault generax --families NHA_family_input.txt --species-tree --rec-model UndatedDL
My gene tree does not contain any polytomies and the program has not described any inconsistencies in labels between my mapping file, the gene tree and the species tree. This command took less than a minute to run. Could you help me troubleshoot this? I'm not sure what exactly generax is struggling with.
Hi! I'm trying to run generax to try reconciliating a single gene tree (with multiple gains and losses) to a species tree. However, I am getting the following error message:
My gene tree does not contain any polytomies and the program has not described any inconsistencies in labels between my mapping file, the gene tree and the species tree. This command took less than a minute to run. Could you help me troubleshoot this? I'm not sure what exactly generax is struggling with.