payamdiba/fastral

A hybrid summary method for reconstructing species tree from gene trees

fastral's Issues

PhyD* was not enabled when compiling ASTRID

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

Local installation problems

I am having problems running FASTRAL after what seems a successful local installation using pip (without sudo). I am not a Python expert, but it seems that FASTRAL assumes that is installed globally and looks for ASTRID's executables in the global dist-packages instead of the local site-packages.