search

PayamDiba / FASTRAL

A hybrid summary method for reconstructing species tree from gene trees
MIT License
9 stars 3 forks source link

PhyD* was not enabled when compiling ASTRID #3

Open kmkocot opened 3 years ago

kmkocot commented 3 years ago

Hello! I'm trying to use FASTRAL on an Ubuntu 18.04 machine, but I'm getting an error related to ASTRID and PhyD: wirenia@wirenia:~/OrthoFinder-2.4.0/2020-09-15_Sacoglossa/OrthoFinder_results/Results_Sep17/Orthogroup_Sequences/phylopypruner_output_min_75_pct/2021-02-27_fastral$ /home/wirenia/.local/bin/fastral --ns 25 --nt 100 --k 1160 --it ./trees.tre --os ./sampled_trees/ --aggregate ./aggregated_species_trees.tre --o ./output_species_tree.tre --time ./time.txt START BUILDING SAMPLES ... START RUNNING ASTRID ... Running ASTRID on sample 0 WARNING: Logging before InitGoogleLogging() is written to STDERR I0227 22:48:30.383447 1428 astrid.cpp:144] Reading trees... I0227 22:48:30.384716 1428 astrid.cpp:150] Read 100 trees Estimating tree Running auto Missing entries in distance matrix, trying to run BioNJ You may have better results adding -u -s to your command line to use UPGMA completion instead. F0227 22:49:53.606385 1428 phydstar.cpp:107] PhyD* was not enabled while compiling ASTRID! Make sure java is set up correctly and try running ASTRID-phydstar Check failure stack trace: Aborted (core dumped) ...

Java is working well enough for other applications and I downloaded PhyDstar.jar and am able to execute it OK with java -jar PhyDstar.jar. Here's what I'm using: wirenia@wirenia:~/OrthoFinder-2.4.0/2020-09-15_Sacoglossa/OrthoFinder_results/Results_Sep17/Orthogroup_Sequences/phylopypruner_output_min_75_pct/2021-02-27_fastral$ java --version openjdk 11.0.10 2021-01-19 OpenJDK Runtime Environment (build 11.0.10+9-Ubuntu-0ubuntu1.18.04) OpenJDK 64-Bit Server VM (build 11.0.10+9-Ubuntu-0ubuntu1.18.04, mixed mode, sharing)

I also tried to just download ASTRID and compile it myself enabling PhyD but despite getting bazel successfully installed and being able to compile ASTRID without PhyD enabled, am getting cryptic errors when I try to compile it with PhyD* enabled.

Any guidance would be greatly appreciated.

Thank you, Kevin

PayamDiba commented 3 years ago

Hi Kevin - I think there is something wrong with Java, especially that the same problem occurred when you tried to compile ASTRID alone. Can you try to re-install / update Java?