Hi - I am running into two problems running ALEml_undated.
Background:
My species tree is rooted on an outgroup clade that is still in the tree file.
None of the gene trees that are being reconciled to it contain sequences from the outgroup
genomes. The species tree was made using IqTree2
My species tree and gene tree ids are formatted so that it is GenomeName_GeneIdentifier
The GenomeName identifiers are the same in the species tree and gene trees, except that the
outgroup nodes do not exist in the gene trees.
I built an ALE sif file using this command:
singularity build alesuite.sif docker://boussau/alesuite
Iqtree2 was used to make 1000 ufboot replicate trees of gene sequences and this was used
as input to ALE_observe, successfully.
Test Code:
apptainer exec
--bind $PWD:$PWD
--pwd $PWD
../alesuite.sif
ALEml_undated 250930_pca_dsh.strictplus.concat.contree.rooted ./cgc_ale_observe/GC_00827199.ufboot.ale
ALEml_undated using ALE v0.4
Read species tree from: 250930_pca_dsh.strictplus.concat.contree.rooted..
Read summary of tree sample for 1000 trees from: ./cgc_ale_observe/GC_00827199.ufboot.ale..
Reconciliation model initialised, starting DTL rate optimisation..
#optimizing delta rate
#optimizing tau rate
#optimizing lambda rate
#optimizing rates
Optimizing... - 80
ML rates: delta=7.14683e-06; tau=0.053623; lambda=0.338888.
LL=-72.5358
Sampling reconciled gene trees..
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
Results in: GC_00827199.ufboot.ale.uml_rec
Calculating consensus tree.
terminate called after throwing an instance of 'bpp::NodePException'
what(): NodeException: Node::getName: no name associated to this node.(id:1)
Aborted (core dumped)
Results
The results in GC_00827199.ufboot.ale.uml_rec look to be as they should
file GC_00827199.ufboot.ale.ucons_tree is empty except for:
#ALEsample using ALE v0.4 by Szollosi GJ et al.; ssolo@elte.hu; CC BY-SA 3.0;
Second Issue
The same process on a different input file created using the same processes:
Read species tree from: 250930_pca_dsh.strictplus.concat.contree.rooted..
Read summary of tree sample for 1000 trees from: ./cgc_ale_observe/GC_00753123.ufboot.ale..
Reconciliation model initialised, starting DTL rate optimisation..
#optimizing delta rate
#optimizing tau rate
#optimizing lambda rate
#optimizing rates
Optimizing... \ 147
ML rates: delta=0.0927824; tau=1e-06; lambda=0.551988.
LL=-75.1619
Sampling reconciled gene trees..
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
Results in: GC_00753123.ufboot.ale.uml_rec
Calculating consensus tree.
terminate called after throwing an instance of 'bpp::Exception'
what(): Trying to build a tree from incompatible bipartitions
Aborted (core dumped)
This also produces a seemingly fine uml_rec file, but no ucons_tree.
I do not need the ucons_tree files for my analysis, but I am wondering what is wrong and
if my uml_rec files are trustworthy.
Regards
Tim
Hi - I am running into two problems running ALEml_undated.
Background:
My species tree is rooted on an outgroup clade that is still in the tree file.
None of the gene trees that are being reconciled to it contain sequences from the outgroup
genomes. The species tree was made using IqTree2
My species tree and gene tree ids are formatted so that it is GenomeName_GeneIdentifier
The GenomeName identifiers are the same in the species tree and gene trees, except that the
outgroup nodes do not exist in the gene trees.
I built an ALE sif file using this command:
singularity build alesuite.sif docker://boussau/alesuite
Iqtree2 was used to make 1000 ufboot replicate trees of gene sequences and this was used
as input to ALE_observe, successfully.
Test Code:
apptainer exec
--bind $PWD:$PWD
--pwd $PWD
../alesuite.sif
ALEml_undated 250930_pca_dsh.strictplus.concat.contree.rooted ./cgc_ale_observe/GC_00827199.ufboot.ale
ALEml_undated using ALE v0.4
Read species tree from: 250930_pca_dsh.strictplus.concat.contree.rooted..
Read summary of tree sample for 1000 trees from: ./cgc_ale_observe/GC_00827199.ufboot.ale..
Reconciliation model initialised, starting DTL rate optimisation..
#optimizing delta rate
#optimizing tau rate
#optimizing lambda rate
#optimizing rates
Optimizing... - 80
ML rates: delta=7.14683e-06; tau=0.053623; lambda=0.338888.
LL=-72.5358
Sampling reconciled gene trees..
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
Results in: GC_00827199.ufboot.ale.uml_rec
Calculating consensus tree.
terminate called after throwing an instance of 'bpp::NodePException'
what(): NodeException: Node::getName: no name associated to this node.(id:1)
Aborted (core dumped)
Results
The results in GC_00827199.ufboot.ale.uml_rec look to be as they should
file GC_00827199.ufboot.ale.ucons_tree is empty except for:
#ALEsample using ALE v0.4 by Szollosi GJ et al.; ssolo@elte.hu; CC BY-SA 3.0;
Second Issue
The same process on a different input file created using the same processes:
Read species tree from: 250930_pca_dsh.strictplus.concat.contree.rooted..
Read summary of tree sample for 1000 trees from: ./cgc_ale_observe/GC_00753123.ufboot.ale..
Reconciliation model initialised, starting DTL rate optimisation..
#optimizing delta rate
#optimizing tau rate
#optimizing lambda rate
#optimizing rates
Optimizing... \ 147
ML rates: delta=0.0927824; tau=1e-06; lambda=0.551988.
LL=-75.1619
Sampling reconciled gene trees..
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
Results in: GC_00753123.ufboot.ale.uml_rec
Calculating consensus tree.
terminate called after throwing an instance of 'bpp::Exception'
what(): Trying to build a tree from incompatible bipartitions
Aborted (core dumped)
This also produces a seemingly fine uml_rec file, but no ucons_tree.
I do not need the ucons_tree files for my analysis, but I am wondering what is wrong and
if my uml_rec files are trustworthy.
Regards
Tim