Simulated outputs: astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/.astralx.success

@@ -0,0 +1,2 @@
+exit_code=0
+output=/root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/out-astralx.command

@@ -0,0 +1,20 @@
+# ASTRAL-X run command (written by run-astralx-with-monitor.sh)
+# date:         2026-09-12T03:38:42+0000
+# host:         c71e672efb9c
+# astralx_root: /root/phylogeny/ASTRAL-X
+# git_commit:   2fae126 (with uncommitted changes)
+# input:        /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre
+# output:       /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre
+# wrapper:      /root/phylogeny/ASTRAL-X/run-astralx-with-monitor.sh -i /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre -o /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre --astralx-root /root/phylogeny/ASTRAL-X --no-notify --opts --search-space\ S1\ --intersection-method\ I1
+# exact ASTRAL-X invocation (run from astralx_root):
+cd /root/phylogeny/ASTRAL-X && ./run.sh --input /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre --output /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre --search-space S1 --intersection-method I1
+# exit_code:    0
+# running_time: 2181.263s
+# --- simulated-run context (test-astralx-simulated.sh) ---
+# dataset:      t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000
+# replicate:    R1
+# setting:      search-space_S1__intersection-method_I1
+# true tree:    /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/s_tree.trees
+# rf_rate:      0.0064
+# invoked as:   /root/phylogeny/ASTRAL-X/test-astralx-simulated.sh -r R1 --simphy-data-dir /root/phylogeny/data/simphy/data --simphy-outputs-dir /root/phylogeny/data/outputs/simphy -t 75000 -g 1000 --sb 0.000001 --spmin 100000 --spmax 200000 --opts --search-space\ S1\ --intersection-method\ I1
+# wrapper cmd:  /root/phylogeny/ASTRAL-X/run-astralx-with-monitor.sh -i /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre -o /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre --astralx-root /root/phylogeny/ASTRAL-X --no-notify --opts --search-space\ S1\ --intersection-method\ I1

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/out-astralx_stats.csv

@@ -0,0 +1,2 @@
+algorithm,input_file,output_file,running_time_s,max_cpu_mb,max_gpu_mb,optimal_quartet_score,rf_rate,exit_code
+astral-x,all_gt.tre,out-astralx.tre,2181.263,61254.516,1296.384,1704391291738740098290,NA,0

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/stat-astralx.csv

@@ -0,0 +1,2 @@
+alg,setting,num-taxa,gene-trees,replicate,sb,spmin,spmax,rf-rate,optimal-quartet-score,running-time-s,max-cpu-mb,max-gpu-mb
+astralx,search-space_S1__intersection-method_I1,75000,1000,R1,0.000001,100000,200000,0.0064,1704391291738740098290,2181.263,61254.516,1296.384

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/search-space_S1__intersection-method_I1/.astralx.success

@@ -0,0 +1,2 @@
+exit_code=0
+output=/root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/search-space_S1__intersection-method_I1/out-astralx.command

@@ -0,0 +1,20 @@
+# ASTRAL-X run command (written by run-astralx-with-monitor.sh)
+# date:         2026-09-12T04:15:56+0000
+# host:         c71e672efb9c
+# astralx_root: /root/phylogeny/ASTRAL-X
+# git_commit:   2fae126 (with uncommitted changes)
+# input:        /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre
+# output:       /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre
+# wrapper:      /root/phylogeny/ASTRAL-X/run-astralx-with-monitor.sh -i /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre -o /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre --astralx-root /root/phylogeny/ASTRAL-X --no-notify --opts --search-space\ S1\ --intersection-method\ I1
+# exact ASTRAL-X invocation (run from astralx_root):
+cd /root/phylogeny/ASTRAL-X && ./run.sh --input /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre --output /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre --search-space S1 --intersection-method I1
+# exit_code:    0
+# running_time: 946.557s
+# --- simulated-run context (test-astralx-simulated.sh) ---
+# dataset:      t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000
+# replicate:    R2
+# setting:      search-space_S1__intersection-method_I1
+# true tree:    /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/s_tree.trees
+# rf_rate:      0.0057
+# invoked as:   /root/phylogeny/ASTRAL-X/test-astralx-simulated.sh -r R2 --simphy-data-dir /root/phylogeny/data/simphy/data --simphy-outputs-dir /root/phylogeny/data/outputs/simphy -t 75000 -g 1000 --sb 0.000001 --spmin 100000 --spmax 200000 --opts --search-space\ S1\ --intersection-method\ I1
+# wrapper cmd:  /root/phylogeny/ASTRAL-X/run-astralx-with-monitor.sh -i /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre -o /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre --astralx-root /root/phylogeny/ASTRAL-X --no-notify --opts --search-space\ S1\ --intersection-method\ I1

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/search-space_S1__intersection-method_I1/out-astralx_stats.csv

@@ -0,0 +1,2 @@
+algorithm,input_file,output_file,running_time_s,max_cpu_mb,max_gpu_mb,optimal_quartet_score,rf_rate,exit_code
+astral-x,all_gt.tre,out-astralx.tre,946.557,53631.555,1253.376,2595714225458406131860,NA,0

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/search-space_S1__intersection-method_I1/stat-astralx.csv

@@ -0,0 +1,2 @@
+alg,setting,num-taxa,gene-trees,replicate,sb,spmin,spmax,rf-rate,optimal-quartet-score,running-time-s,max-cpu-mb,max-gpu-mb
+astralx,search-space_S1__intersection-method_I1,75000,1000,R2,0.000001,100000,200000,0.0057,2595714225458406131860,946.557,53631.555,1253.376

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/search-space_S1__intersection-method_I1/.astralx.success

@@ -0,0 +1,2 @@
+exit_code=0
+output=/root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/search-space_S1__intersection-method_I1/out-astralx.command

@@ -0,0 +1,20 @@
+# ASTRAL-X run command (written by run-astralx-with-monitor.sh)
+# date:         2026-09-12T04:32:35+0000
+# host:         c71e672efb9c
+# astralx_root: /root/phylogeny/ASTRAL-X
+# git_commit:   2fae126 (with uncommitted changes)
+# input:        /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre
+# output:       /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre
+# wrapper:      /root/phylogeny/ASTRAL-X/run-astralx-with-monitor.sh -i /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre -o /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre --astralx-root /root/phylogeny/ASTRAL-X --no-notify --opts --search-space\ S1\ --intersection-method\ I1
+# exact ASTRAL-X invocation (run from astralx_root):
+cd /root/phylogeny/ASTRAL-X && ./run.sh --input /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre --output /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre --search-space S1 --intersection-method I1
+# exit_code:    0
+# running_time: 876.703s
+# --- simulated-run context (test-astralx-simulated.sh) ---
+# dataset:      t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000
+# replicate:    R3
+# setting:      search-space_S1__intersection-method_I1
+# true tree:    /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/s_tree.trees
+# rf_rate:      0.0053
+# invoked as:   /root/phylogeny/ASTRAL-X/test-astralx-simulated.sh -r R3 --simphy-data-dir /root/phylogeny/data/simphy/data --simphy-outputs-dir /root/phylogeny/data/outputs/simphy -t 75000 -g 1000 --sb 0.000001 --spmin 100000 --spmax 200000 --opts --search-space\ S1\ --intersection-method\ I1
+# wrapper cmd:  /root/phylogeny/ASTRAL-X/run-astralx-with-monitor.sh -i /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre -o /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre --astralx-root /root/phylogeny/ASTRAL-X --no-notify --opts --search-space\ S1\ --intersection-method\ I1

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/search-space_S1__intersection-method_I1/out-astralx_stats.csv

@@ -0,0 +1,2 @@
+algorithm,input_file,output_file,running_time_s,max_cpu_mb,max_gpu_mb,optimal_quartet_score,rf_rate,exit_code
+astral-x,all_gt.tre,out-astralx.tre,876.703,53240.008,1243.136,2465924413947402358446,NA,0

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/search-space_S1__intersection-method_I1/stat-astralx.csv

@@ -0,0 +1,2 @@
+alg,setting,num-taxa,gene-trees,replicate,sb,spmin,spmax,rf-rate,optimal-quartet-score,running-time-s,max-cpu-mb,max-gpu-mb
+astralx,search-space_S1__intersection-method_I1,75000,1000,R3,0.000001,100000,200000,0.0053,2465924413947402358446,876.703,53240.008,1243.136

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/search-space_S1__intersection-method_I1/.astralx.success

@@ -0,0 +1,2 @@
+exit_code=0
+output=/root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/search-space_S1__intersection-method_I1/out-astralx.command

@@ -0,0 +1,20 @@
+# ASTRAL-X run command (written by run-astralx-with-monitor.sh)
+# date:         2026-09-12T04:48:05+0000
+# host:         c71e672efb9c
+# astralx_root: /root/phylogeny/ASTRAL-X
+# git_commit:   2fae126 (with uncommitted changes)
+# input:        /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre
+# output:       /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre
+# wrapper:      /root/phylogeny/ASTRAL-X/run-astralx-with-monitor.sh -i /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre -o /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre --astralx-root /root/phylogeny/ASTRAL-X --no-notify --opts --search-space\ S1\ --intersection-method\ I1
+# exact ASTRAL-X invocation (run from astralx_root):
+cd /root/phylogeny/ASTRAL-X && ./run.sh --input /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre --output /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre --search-space S1 --intersection-method I1
+# exit_code:    0
+# running_time: 381.345s
+# --- simulated-run context (test-astralx-simulated.sh) ---
+# dataset:      t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000
+# replicate:    R4
+# setting:      search-space_S1__intersection-method_I1
+# true tree:    /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/s_tree.trees
+# rf_rate:      0.0036
+# invoked as:   /root/phylogeny/ASTRAL-X/test-astralx-simulated.sh -r R4 --simphy-data-dir /root/phylogeny/data/simphy/data --simphy-outputs-dir /root/phylogeny/data/outputs/simphy -t 75000 -g 1000 --sb 0.000001 --spmin 100000 --spmax 200000 --opts --search-space\ S1\ --intersection-method\ I1
+# wrapper cmd:  /root/phylogeny/ASTRAL-X/run-astralx-with-monitor.sh -i /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre -o /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre --astralx-root /root/phylogeny/ASTRAL-X --no-notify --opts --search-space\ S1\ --intersection-method\ I1

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/search-space_S1__intersection-method_I1/out-astralx_stats.csv

@@ -0,0 +1,2 @@
+algorithm,input_file,output_file,running_time_s,max_cpu_mb,max_gpu_mb,optimal_quartet_score,rf_rate,exit_code
+astral-x,all_gt.tre,out-astralx.tre,381.345,66220.828,1148.928,2552707719952835421770,NA,0

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/search-space_S1__intersection-method_I1/stat-astralx.csv

@@ -0,0 +1,2 @@
+alg,setting,num-taxa,gene-trees,replicate,sb,spmin,spmax,rf-rate,optimal-quartet-score,running-time-s,max-cpu-mb,max-gpu-mb
+astralx,search-space_S1__intersection-method_I1,75000,1000,R4,0.000001,100000,200000,0.0036,2552707719952835421770,381.345,66220.828,1148.928

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000.command

@@ -0,0 +1 @@
+/root/phylogeny/STELAR-X-2/simphy/simphy_lnx64 -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:1000 -rg 1 -o /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:75000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42 

ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000.params

@@ -0,0 +1,40 @@
+
+Global settings:
+--------------------
+
+Trees:
+	-Species trees: 5 Birth-death simulations
+		-Speciation rate: Fixed 1.000000e-06,
+		-Extinction rate: Fixed 0.000000e+00,
+		-Outgroup addition: No addition
+		-Stopping rules:
+			-Number of leaves: Fixed 75000,
+			-Generations: LogN(1.620000e+01,1)
+	-Locus trees: Fixed 1000, directly obtained from each species tree (no birth-death process)
+
+	-Gene trees: 1 multilocus coalescent simulations
+
+Parameters:
+	-Haploid efective population size: Uniform[100000,200000]
+	-Generation time: Fixed 1,
+	-Global substitution rate: LogN(-1.727461e+01,6.931472e-01)
+	-Substitution rate heterogeneities
+		-Lineage (species) specific rate heterogeneity gamma shape: No heterogeneity
+		-Gene family (locus tree) specific rate heterogeneity gamma shape: No heterogeneity
+		-Gene tree branch specific rate heterogeneity gamma shape: Genome-wide parameter (hyperhyperparameter) No heterogeneity, locus-tree related parameter No heterogeneity, Gamma parameter(gene-tree related) No heterogeneity
+	-Individuals per species: Fixed 1,
+
+Misc parameters:
+	-Rooting method epsilon: 0.000001
+	-Seed: 42
+
+I/O options:
+	-Output files prefix: /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000
+	-Verbosity: 2
+	-Stats file: OFF
+	-Mapping: ON
+	-Database: ON
+	-Parameterization: ON 
+	-Command-line arguments: ON
+	-Bounded locus subtrees: ON
+	-Output trees with internal node labels: OFF