21 lines
622 B
Bash
21 lines
622 B
Bash
#! /bin/bash
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set -e
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if [ "$#" -ne 4 ]; then
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echo "Usage: $0 <alignment.fa> <output_prefix> <threads> <outgroup>"
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echo "Run modeltest-ng and raxml-ng on a given alignment"
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exit 1
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fi
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aln=$(readlink -f "$1")
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out=$2
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threads=$3
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outgroup=$4
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outdir=$(dirname "$out")
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mkdir -p "$outdir"
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# run modeltest-ng
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modeltest-ng -p "$threads" -r 12345 --force -i "$aln" -d nt -t ml -o "$out".modeltest
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# run raxml-ng
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cmd=$(grep "raxml-ng" "$out".modeltest.out | tail -n 1 | sed 's/> //')
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params="--all --bs-trees 1000 --outgroup $outgroup --redo --threads $threads --seed 12345 --prefix $out"
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bash -c "$cmd $params" >/dev/null
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