terminate called after throwing an instance of 'LibpllException'

[Alessandra Aleotti]

Hello,

I am having a situation in which some of my generax runs are being aborted. 

After successfully passing the Filtering of invalid families step and after starting the reconciliation rates optimization, after a while I get the following message:

[00:00:00] Optimizing gene trees with radius=1...

sh: line 1: 32432 Segmentation fault      generax optimizeGeneTrees INAD.ete.newick.newick NONE INAD.extracted.ordered.reduced.cdhit97.mafft.trimal INAD_Results/inferred_species_tree.newick LG+F+R7 INAD_Results/gene_optimization_0/dtl_rates.txt 0 0 0 1 -1 1 1 1 1 INAD_Results/results/INAD/geneTree.newick INAD_Results/results/INAD/stats.txt > INAD_Results/gene_optimization_0/per_job_logs/INAD_out.txt

        JointLL=0 RecLL=0 LibpllLL=0

[00:02:49] Reconciliation rates optimization...

terminate called after throwing an instance of 'LibpllException'

  what():  Could not load open newick file INAD_Results/results/INAD/geneTree.newick

[alice04:32413] *** Process received signal ***

[alice04:32413] Signal: Aborted (6)

[alice04:32413] Signal code:  (-6)

[alice04:32413] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2aaaab359630]

[alice04:32413] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2aaaab59c387]

[alice04:32413] [ 2] /lib64/libc.so.6(abort+0x148)[0x2aaaab59da78]

[alice04:32413] [ 3] /lustre/ahome3/a/aa1176/miniconda3/envs/generax_env/bin/../lib/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0xbc)[0x2aaaaaf81892]

[alice04:32413] [ 4] /lustre/ahome3/a/aa1176/miniconda3/envs/generax_env/bin/../lib/libstdc++.so.6(+0xacf69)[0x2aaaaaf7ff69]

[alice04:32413] [ 5] /lustre/ahome3/a/aa1176/miniconda3/envs/generax_env/bin/../lib/libstdc++.so.6(+0xacfab)[0x2aaaaaf7ffab]

[alice04:32413] [ 6] /lustre/ahome3/a/aa1176/miniconda3/envs/generax_env/bin/../lib/libstdc++.so.6(__cxa_rethrow+0x0)[0x2aaaaaf80194]

[alice04:32413] [ 7] generax(_ZN13LibpllParsers18readNewickFromFileERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x465)[0x5555555c32e5]

[alice04:32413] [ 8] generax(_ZN13LibpllParsers20parallelGetTreeSizesERKSt6vectorI10FamilyInfoSaIS1_EE+0xd0)[0x5555555c41d0]

[alice04:32413] [ 9] generax(_ZN16PerCoreGeneTreesC2ERKSt6vectorI10FamilyInfoSaIS1_EE+0x70)[0x5555555f9b80]

[alice04:32413] [10] generax(_ZN8Routines13optimizeRatesEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE8RecModelbbRSt6vectorI10FamilyInfoSaISA_EEbR10ParametersRl+0xcb)[0x5555556001db]

[alice04:32413] [11] generax(_ZN11GeneRaxCore25optimizeRatesAndGeneTreesER15GeneRaxInstancebbj+0x6ba)[0x5555555924ca]

[alice04:32413] [12] generax(_ZN11GeneRaxCore19geneTreeJointSearchER15GeneRaxInstance+0xbb)[0x5555555933fb]

[alice04:32413] [13] generax(_Z12generax_mainiPPcPv+0x398)[0x55555558a808]

[alice04:32413] [14] generax(_Z13internal_mainiPPcPv+0x3c)[0x55555558b50c]

[alice04:32413] [15] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2aaaab588555]

[alice04:32413] [16] generax(+0x35bc1)[0x555555589bc1]

[alice04:32413] *** End of error message ***

Aborted

What could the problem be? Is there a problem with the gene trees? My gene trees are in newick format and I have checked for multifurcations, I have also tried using both rooted and unrooted versions. What else can I try?

The species tree I am using has worked fine for other gene families I have previously run. 

Thank you very much!

Alessandra

[Benoit Morel]

Dear Alessandra,

Sorry, I just realized that I replied in private to the previous messages.

I managed to reproduce the issue with your data. There is a bug in GeneRax that is triggered by the use of free rates in the substitution model (here LG+F+R7). I will release a new version with the fix, hopefully tomorrow. I think that you installed GeneRax with BioConda, so you might have to wait a few more days before the conda package gets updated. I will tell you when it' available.

Many thanks for the report,

Benoit