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chaoszhang / ASTER

Accurate Species Tree EstimatoR series: a family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL)
GNU Affero General Public License v3.0
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astral-pro aborts when using -c #4

Closed edgardomortiz closed 1 year ago

edgardomortiz commented 2 years ago

I was trying to draw quartet support on a tree (not calculated by astral-pro) and got the following errors:

astral-pro -c concat.treefile -o concat_test.tree -t 64 -u 3 -a astral-pro.tsv gene.trees 

Version: v1.3.1.0
#Genetrees: 353
#Duploss: 0
#Species: 375
#Rounds: 16
#Samples: 16
#Threads: 1x64
p = 0.5
Segmentation fault (core dumped)

It also fails with astral-pro_int128:

astral-pro_int128 -c concat.treefile -o concat_test.tree -t 64 -u 3 -a astral-pro.tsv gene.trees 

Version: v1.3.1.0
#Genetrees: 353
#Duploss: 0
#Species: 375
#Rounds: 16
#Samples: 16
#Threads: 1x64
p = 0.5
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
Aborted (core dumped)

Thanks

Edgardo

chaoszhang commented 2 years ago

Sorry for the late response. I just recovered from COVID. For me to replicate your issue, can you send me the files "concat.treefile", "astral-pro.tsv", and "gene.trees"?

2022年6月17日(金) 16:05 Edgardo M. Ortiz @.***>:

I was trying to draw quartet support on a tree (not calculated by astral-pro) and got the following errors:

astral-pro -c concat.treefile -o concat_test.tree -t 64 -u 3 -a astral-pro.tsv gene.trees

Version: v1.3.1.0

Genetrees: 353

Duploss: 0

Species: 375

Rounds: 16

Samples: 16

Threads: 1x64

p = 0.5 Segmentation fault (core dumped)

It also fails with astral-pro_int128:

astral-pro_int128 -c concat.treefile -o concat_test.tree -t 64 -u 3 -a astral-pro.tsv gene.trees

Version: v1.3.1.0

Genetrees: 353

Duploss: 0

Species: 375

Rounds: 16

Samples: 16

Threads: 1x64

p = 0.5 terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively Aborted (core dumped)

Thanks

Edgardo

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edgardomortiz commented 1 year ago

Sorry for the so much delayed reaction to your reply. Here are the relevant files: github_issue.zip

Edgardo

chaoszhang commented 1 year ago

Hi Edgardo,

Thanks for sending me the input. Yes, there is a bug in -c option when input files are rooted on a node instead of a branch, and I am going to fix this issue. Meanwhile, I just rerooted your concat tree on a branch and it worked fine. Attached are the rerooted concat tree, annotated species tree, and freq.csv file. By the way, you just need one thread to annotate a tree.

Best, Chao output.zip

edgardomortiz commented 1 year ago

Excellent, thanks for the help, in the meanwhile I will reroot the trees I need to annotate. Thanks also for the tip about the threads.