26 lines
786 B
Bash
26 lines
786 B
Bash
#!/bin/bash
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#SBATCH --job-name=compleasm_parallel
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#SBATCH --array=2-NUM_GENOMES # Start from genome 2 (first genome already processed)
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#SBATCH --cpus-per-task=THREADS_PER_JOB # e.g., 16 for 64-core system with 4 concurrent jobs
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#SBATCH --mem-per-cpu=6G
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#SBATCH --time=48:00:00
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#SBATCH --output=logs/compleasm.%A_%a.out
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#SBATCH --error=logs/compleasm.%A_%a.err
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source ~/.bashrc
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conda activate phylo
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mkdir -p 01_busco_results
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# Get genome for this array task (skipping the first one)
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genome=$(sed -n "${SLURM_ARRAY_TASK_ID}p" genome_list.txt)
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genome_name=$(basename ${genome} .fasta)
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echo "Processing ${genome_name} with ${SLURM_CPUS_PER_TASK} threads..."
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compleasm run \
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-a ${genome} \
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-o 01_busco_results/${genome_name}_compleasm \
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-l LINEAGE \
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-t ${SLURM_CPUS_PER_TASK}
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