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ssolo / ALE

Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.
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Segmentation fault #26

Closed Jigyasa3 closed 1 year ago

Jigyasa3 commented 2 years ago

Hi @ssolo

I am able to run Aleml_undated on most of my trees, but somehow for some trees, the aleml analysis begins but stops in between giving a segmentation fault error.

Code- `#burnin singularity exec /home/j/jigyasa-arora/local/ale.sif ALEobserve symbionttree-d__Bacteria_pFibrobacterotapBacteroidotapUBP14COG0552_tips_2.nwk

run ALEml_undated

singularity exec /home/j/jigyasa-arora/local/ale.sif ALEml_undated 2-hosttree-dBacteria_pFibrobacterotapBacteroidotapUBP14COG0552_tips_2.nwk symbionttree-d__Bacteria_pFibrobacterotapBacteroidotapUBP14__COG0552_tips_2.nwk.ale sample=10 `

Files- species tree , genetree

Error- `Read species tree from: 2-hosttree-dBacteria_pDesulfobacterotapSZUA79pUBA10199COG0552_tips_2.nwk.. Read summary of tree sample for 1 trees from: symbionttree-d__Bacteria_pDesulfobacterotapSZUA79pUBA10199__COG0552_tips_2.nwk.ale.. Reconciliation model initialised, starting DTL rate optimisation..

optimizing delta rate

optimizing tau rate

optimizing lambda rate

optimizing rates

Optimizing... - 46 ML rates: delta=0.108325; tau=0.282899; lambda=0.20712. LL=-103.615 Sampling reconciled gene trees..

0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| **Segmentation fault `

maxemil commented 2 years ago

I've had this problem before as well, but could not figure out how to solve it properly. A workaround for me was to try again (and again) with the same tree. Since the segfault seemed to occur randomly, at some point it would work.... To speed it up, you can specify the ML rates from the first run for the consecutive ones.

Jigyasa3 commented 2 years ago

thank you, @maxemil!

ssolo commented 1 year ago

This should be fixed, please verify.