27 lines
790 B
Bash
27 lines
790 B
Bash
#!/bin/bash
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# run_compleasm_first.sh
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source ~/.bashrc
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conda activate phylo
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# User-specified total CPU threads
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TOTAL_THREADS=TOTAL_THREADS # Replace with total cores you want to use (e.g., 16, 32, 64)
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echo "Processing first genome with ${TOTAL_THREADS} CPU threads to download lineage database..."
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# Create output directory
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mkdir -p 01_busco_results
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# Process FIRST genome only
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first_genome=$(head -n 1 genome_list.txt)
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genome_name=$(basename ${first_genome} .fasta)
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echo "Processing: ${genome_name}"
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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 ${TOTAL_THREADS}
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echo ""
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echo "First genome complete! Lineage database is now cached."
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echo "Now run the parallel script for remaining genomes: bash run_compleasm_parallel.sh"
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