34 lines
958 B
Bash
34 lines
958 B
Bash
#!/bin/bash
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# run_compleasm_parallel.sh
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source ~/.bashrc
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conda activate phylo
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# Threading configuration (adjust based on your system)
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TOTAL_THREADS=TOTAL_THREADS # Total cores to use (e.g., 64)
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THREADS_PER_JOB=THREADS_PER_JOB # Threads per genome (e.g., 16)
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CONCURRENT_JOBS=$((TOTAL_THREADS / THREADS_PER_JOB)) # Calculated automatically
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echo "Configuration:"
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echo " Total threads: ${TOTAL_THREADS}"
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echo " Threads per genome: ${THREADS_PER_JOB}"
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echo " Concurrent genomes: ${CONCURRENT_JOBS}"
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echo ""
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# Create output directory
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mkdir -p 01_busco_results
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# Process remaining genomes (skip first one) in parallel
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tail -n +2 genome_list.txt | parallel -j ${CONCURRENT_JOBS} '
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genome_name=$(basename {} .fasta)
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echo "Processing ${genome_name} with THREADS_PER_JOB threads..."
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compleasm run \
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-a {} \
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-o 01_busco_results/${genome_name}_compleasm \
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-l LINEAGE \
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-t THREADS_PER_JOB
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'
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echo ""
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echo "All genomes processed!"
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