28 lines
858 B
Bash
28 lines
858 B
Bash
#!/bin/bash
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#PBS -N compleasm_first
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#PBS -l nodes=1:ppn=TOTAL_THREADS # Replace with total available CPUs (e.g., 64)
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#PBS -l mem=384gb # Adjust based on ppn × 6GB
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#PBS -l walltime=24:00:00
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cd $PBS_O_WORKDIR
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source ~/.bashrc
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conda activate phylo
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mkdir -p logs
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mkdir -p 01_busco_results
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# Process FIRST genome only (downloads lineage database)
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first_genome=$(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 $PBS_NUM_PPN 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 $PBS_NUM_PPN
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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: qsub run_compleasm_parallel.job"
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