agent
e467d67723
- Created `mbblock.txt` for MrBayes configuration. - Implemented `mrbayes.sh` to convert FASTA to Nexus and run MrBayes. - Developed `raxml.sh` to run modeltest-ng and raxml-ng on alignments. - Added `04.filter_ogs.sh` to filter orthologous groups based on taxon count and sequence length. - Implemented `01.run_mrbayes.sh` to execute MrBayes for multiple FASTA files. - Created `02.mbsum.sh` to summarize MrBayes output while skipping high DSF analyses. - Developed `03.run_raxml.sh` to run raxml-ng on filtered alignments.
32 lines
1.0 KiB
Bash
Executable File
32 lines
1.0 KiB
Bash
Executable File
#!/bin/bash
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THREADS=${THREADS:-12}
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MIN_DSF=${MIN_DSF:-0.01}
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if [ "$#" -ne 3 ]; then
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echo "Usage: $0 <mrbayes_output_dir> <mbsum_output_dir> <num_skip>"
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echo "Summarize MrBayes output using mbsum, skipping analyses with high DSF"
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exit 1
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fi
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mb_dir=$(readlink -f "$1")
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mbsum_out_dir=$2
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num_skip=$3
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mkdir -p "$mbsum_out_dir"
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echo -n "" >mbsum.skip.log
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echo -n "" >mbsum.cmds
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for i in "$mb_dir"/*/mrbayes.log; do
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og_dir=$(dirname "$i")
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base=$(basename "$og_dir")
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## skip Average standard deviation of split frequencies > 0.01
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dsf=$(awk '/Average standard deviation of split frequencies:/ {out=$7} END{print out+0}' "$i" 2>/dev/null)
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if awk -v d="$dsf" -v min_dsf="$MIN_DSF" 'BEGIN{if (d >= min_dsf) exit 0; exit 1}'; then
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echo "Skipping ${base} due to high DSF: ${dsf}" >>mbsum.skip.log
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continue
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else
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echo "mbsum ${og_dir}/*.t -n $num_skip -o $mbsum_out_dir/${base}.in >> $og_dir/mbsum.log 2>&1" >>mbsum.cmds
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fi
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done
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xargs -t -P "$THREADS" -I cmd -a mbsum.cmds bash -c "cmd"
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echo "Mbsum all done!"
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