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skills/phylo_from_buscos/templates/pbs/02_compleasm_first.job

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+#!/bin/bash
+#PBS -N compleasm_first
+#PBS -l nodes=1:ppn=TOTAL_THREADS  # Replace with total available CPUs (e.g., 64)
+#PBS -l mem=384gb  # Adjust based on ppn × 6GB
+#PBS -l walltime=24:00:00
+
+cd $PBS_O_WORKDIR
+source ~/.bashrc
+conda activate phylo
+
+mkdir -p logs
+mkdir -p 01_busco_results
+
+# Process FIRST genome only (downloads lineage database)
+first_genome=$(head -n 1 genome_list.txt)
+genome_name=$(basename ${first_genome} .fasta)
+echo "Processing first genome: ${genome_name} with $PBS_NUM_PPN threads..."
+echo "This will download the BUSCO lineage database for subsequent runs."
+
+compleasm run \
+  -a ${first_genome} \
+  -o 01_busco_results/${genome_name}_compleasm \
+  -l LINEAGE \
+  -t $PBS_NUM_PPN
+
+echo "First genome complete! Lineage database is now cached."
+echo "Submit the parallel job for remaining genomes: qsub run_compleasm_parallel.job"