Initial commit

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

@@ -0,0 +1,28 @@
+#!/bin/bash
+#SBATCH --job-name=compleasm_first
+#SBATCH --cpus-per-task=TOTAL_THREADS  # Replace with total available CPUs (e.g., 64)
+#SBATCH --mem-per-cpu=6G
+#SBATCH --time=24:00:00
+#SBATCH --output=logs/compleasm_first.%j.out
+#SBATCH --error=logs/compleasm_first.%j.err
+
+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 ${SLURM_CPUS_PER_TASK} 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 ${SLURM_CPUS_PER_TASK}
+
+echo "First genome complete! Lineage database is now cached."
+echo "Submit the parallel job for remaining genomes: sbatch run_compleasm_parallel.job"