29 lines
941 B
Bash
29 lines
941 B
Bash
#!/bin/bash
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#SBATCH --job-name=compleasm_first
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#SBATCH --cpus-per-task=TOTAL_THREADS # Replace with total available CPUs (e.g., 64)
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#SBATCH --mem-per-cpu=6G
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#SBATCH --time=24:00:00
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#SBATCH --output=logs/compleasm_first.%j.out
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#SBATCH --error=logs/compleasm_first.%j.err
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source ~/.bashrc
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conda activate phylo
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mkdir -p logs
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mkdir -p 01_busco_results
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# Process FIRST genome only (downloads lineage database)
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first_genome=$(head -n 1 genome_list.txt)
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genome_name=$(basename ${first_genome} .fasta)
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echo "Processing first genome: ${genome_name} with ${SLURM_CPUS_PER_TASK} threads..."
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echo "This will download the BUSCO lineage database for subsequent runs."
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compleasm run \
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-a ${first_genome} \
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-o 01_busco_results/${genome_name}_compleasm \
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-l LINEAGE \
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-t ${SLURM_CPUS_PER_TASK}
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echo "First genome complete! Lineage database is now cached."
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echo "Submit the parallel job for remaining genomes: sbatch run_compleasm_parallel.job"
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