Initial commit

skills/phylo_from_buscos/templates/slurm/08a_partition_search.job

@@ -0,0 +1,27 @@
+#!/bin/bash
+#SBATCH --job-name=iqtree_partition
+#SBATCH --cpus-per-task=18
+#SBATCH --mem-per-cpu=4G
+#SBATCH --time=72:00:00
+#SBATCH --output=logs/partition_search.out
+#SBATCH --error=logs/partition_search.err
+
+source ~/.bashrc
+conda activate phylo
+
+cd 06_concatenation  # Use organized directory structure
+
+iqtree \
+  -s FcC_supermatrix.fas \
+  -spp partition_def.txt \
+  -nt ${SLURM_CPUS_PER_TASK} \
+  -safe \
+  -pre partition_search \
+  -m TESTMERGEONLY \
+  -mset MODEL_SET \
+  -msub nuclear \
+  -rcluster 10 \
+  -bb 1000 \
+  -alrt 1000
+
+# Output: partition_search.best_scheme.nex