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Guidance

Guidance is a tool for assigning a confidence score for each residue, column, and sequence in an alignment and for projecting these scores onto the Multiple Sequence Alignment (MSA).

Guidance is available as a module on Apocrita.

Usage

To run the latest installed version of Guidance, simply load the guidance module:

module load guidance

GUIDANCE_CMD

${GUIDANCE_CMD} points to the guidance.pl file

then run guidance via perl:

perl ${GUIDANCE_CMD} \
    --program GUIDANCE \
    --seqFile /data/abc123/example_input.fa \
    --msaProgram MUSCLE \
    --seqType codon \
    --outDir ${TMPDIR}/example_output \
    --bootstraps 100

mv ${TMPDIR}/example_output /data/home/abc123/example_output

Absolute file paths

Guidance requires absolute file paths for both input and output eg. /data/abc123/file vs file.

Example jobs

Using ${TMPDIR}

Guidance is I/O intensive and when run in large batches may severely affect GPFS, in order to avoid this and improve guidance performance ${TMPDIR} should be used as the --outDir and results copied onto GPFS after completion.

All examples on this page use ${TMPDIR} and further information is available.

Serial job

Here is an example job running on 1 cores and using ${TMPDIR}.

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load guidance

INPUTFILE=/data/home/abc123/example_input.fa
OUTPUTDIR=/data/home/abc123/example_output

perl ${GUIDANCE_CMD} \
    --program GUIDANCE \
    --seqFile ${INPUTFILE} \
    --msaProgram MUSCLE \
    --seqType codon \
    --outDir ${TMPDIR}/example_output \
    --bootstraps 100

mv ${TMPDIR}/example_output ${OUTPUTDIR}

References