GeneRax error. Could not load open newick file testing_V1/results/Phy003AEDB_CUCME/geneTree.newick

[Benedikt Nuesslein]

Hello,

I am dealing with an issue using the bioconda version of GeneRax v2.1.3 in the Linux shell on my university's HPC cluster, and getting a strange error message that I do not understand. It is happening with my own data, and the example plant data from GitHub (GeneRax/data/plants).

The error message is very similar to the error linked below, but that person's problem was presumably fixed by a new version back in 2021. I tried switching the substitution model anyway, but it always gave the same error (tried LG in the example data, and tried GTR and GTR+G with my own nucleotide data). I also tried switching from -rec-model UndatedDL to UndatedDTL, and from --strategy SPR to --strategy EVAL, but neither changed the error message.
https://groups.google.com/g/generaxusers/c/ycIg-XAO328

The entire terminal output of the command (including the command) is pasted below my email sign-off (with my email replaced by the string "email"). The inputs I used (your example data, with family names added to the filenames) and the results directory (testing_V1) are zipped here as a single file:  

https://drive.google.com/file/d/1bjJvc-W0APopwMJ6G_sjQmD_9xEhAZls/view?usp=sharing  

Thank you for your time, and for making this software accessible to the public.

Best,
Benedikt

(generax_env) [email@p-bc-5426 Testing_Generax_examples]$ mpiexec -np 1 generax --families families_plants.txt --species-tree speciesTree.newick --rec-model UndatedDTL --prefix testing_V1
[00:00:00] GeneRax 2.1.3
Logs will also be printed into testing_V1/generax.log
GeneRax was called as follow:
generax --families families_plants.txt --species-tree speciesTree.newick --rec-model UndatedDTL --prefix testing_V1

General information:
- Output prefix: testing_V1
- Families information: families_plants.txt
- Species tree: speciesTree.newick
- MPI Ranks: 1
- Random seed: 123
- Reconciliation model: UndatedDTL
- 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: 2
- Number of species: 23
- Total number of genes: 54
- Average number of genes per family: 27
- Maximum number of genes per family: 30
- Species covered with the smallest family coverage: "OSTTA" (covered by 0/2 families)
- Average (over species) species family coverage: 1

[00:00:00] Reconciliation rates optimization...
D=0.144177, L=0.0616895, T=0.147367, RecLL= -133.484

[00:00:00] Optimizing gene trees with radius=1...
terminate called after throwing an instance of 'LibpllException'
  what():  Could not load open newick file testing_V1/results/Phy003AEDB_CUCME/geneTree.newick
[p-bc-5426:1507814] *** Process received signal ***
[p-bc-5426:1507814] Signal: Aborted (6)
[p-bc-5426:1507814] Signal code:  (-6)
[00:00:00] JointLL=0 RecLL=0 LibpllLL=0

[00:00:00] Reconciliation rates optimization...
[p-bc-5426:1507814] [ 0] /lib64/libpthread.so.0(+0x12990)[0x150a35f61990]
[p-bc-5426:1507814] [ 1] /lib64/libc.so.6(gsignal+0x10f)[0x150a35bc75af]
[p-bc-5426:1507814] [ 2] /lib64/libc.so.6(abort+0x127)[0x150a35b9aee5]
[p-bc-5426:1507814] [ 3] /storage/work/email/.conda/envs/generax_env/bin/../lib/libstdc++.so.6(+0xb2cd2)[0x150a365a3cd2]
[p-bc-5426:1507814] [ 4] /storage/work/email/.conda/envs/generax_env/bin/../lib/libstdc++.so.6(+0xc5a1a)[0x150a365b6a1a]
[p-bc-5426:1507814] [ 5] /storage/work/email/.conda/envs/generax_env/bin/../lib/libstdc++.so.6(_ZSt10unexpectedv+0x0)[0x150a365a384d]
[p-bc-5426:1507814] [ 6] /storage/work/email/.conda/envs/generax_env/bin/../lib/libstdc++.so.6(+0xc5cb7)[0x150a365b6cb7]
[p-bc-5426:1507814] [ 7] generax(+0x3f87c)[0x55c076ae687c]
[p-bc-5426:1507814] [ 8] generax(_ZN13LibpllParsers20parallelGetTreeSizesERKSt6vectorI10FamilyInfoSaIS1_EE+0xc6)[0x55c076b42cc6]
[p-bc-5426:1507814] [ 9] generax(_ZN16PerCoreGeneTreesC1ERKSt6vectorI10FamilyInfoSaIS1_EEbb+0x153b)[0x55c076b5c1db]
[p-bc-5426:1507814] [10] generax(_ZN8Routines13optimizeRatesEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERK12RecModelInfoRSt6vectorI10FamilyInfoSaISC_EEbR10ParametersRl+0xce)[0x55c076b6145e]
[p-bc-5426:1507814] [11] generax(_ZN11GeneRaxCore25optimizeRatesAndGeneTreesER15GeneRaxInstancebbj+0x66a)[0x55c076b0e43a]
[p-bc-5426:1507814] [12] generax(_ZN11GeneRaxCore19geneTreeJointSearchER15GeneRaxInstance+0x9f)[0x55c076b0f6af]
[p-bc-5426:1507814] [13] generax(_Z12generax_mainiPPcPv+0x229)[0x55c076b03349]
[p-bc-5426:1507814] [14] /lib64/libc.so.6(__libc_start_main+0xe5)[0x150a35bb3865]
[p-bc-5426:1507814] [15] generax(+0x5a6a4)[0x55c076b016a4]
[p-bc-5426:1507814] *** End of error message ***
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec noticed that process rank 0 with PID 1507814 on node p-bc-5426 exited on signal 6 (Aborted).
--------------------------------------------------------------------------

[Benedikt Nuesslein]

I also asked this question on the GeneRax github issues page. The author's reply is here: https://github.com/BenoitMorel/GeneRax/issues/82

Essentially, if the bioconda version of GeneRax is not working, try cloning and building the most recent version from GitHub. It worked for me.

Best,

Benedikt