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54 lines
1.6 KiB
Bash
54 lines
1.6 KiB
Bash
#!/bin/bash
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#SBATCH --account=ACCOUNT
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#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=4
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#SBATCH --mem=8G
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# Fetch the category we're working with from upstream
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CATEGORY=${1%}
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# Save the folder name we will be saving everything into
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FOLDERNAME="${CATEGORY}-classifier"
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# Load the required modules
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module restore system
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module load swset
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module load miniconda3
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# Start up qiime
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# This code creates errors if run through shellcheck because
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# the shellcheck program doesn't understand miniconda:
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# We'll add a directive to tell it to ignore this error
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# shellcheck disable=SC1091
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source activate qiime2
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# Make sure we have a clean slate to work with
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echo "--^-- X: Creating a classifier model for ${CATEGORY}"
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echo "--^-- X: Clearing previous classifier results..."
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rm -r "$FOLDERNAME"
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echo "--^-- X: Clearing previous classifier results...Done!"
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# Solve the model
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echo "--^-- X: Constructing model..."
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qiime sample-classifier classify-samples \
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--i-table feature-table.qza \
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--m-metadata-file metadata.tsv \
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--m-metadata-column "$CATEGORY" \
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--p-n-jobs 4 \
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--p-missing-samples ignore \
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--p-optimize-feature-selection \
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--output-dir "$FOLDERNAME" \
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--verbose
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echo "--^-- X: Constructing model...Done!"
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# Convert the model output into readable visualizations
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echo "--^-- X: Making visualizations..."
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qiime metadata tabulate \
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--m-input-file "${FOLDERNAME}/feature_importance.qza" \
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--o-visualization "${FOLDERNAME}/feature-importance.qzv"
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qiime metadata tabulate \
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--m-input-file "${FOLDERNAME}/predictions.qza" \
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--m-input-file metadata.tsv \
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--o-visualization "${FOLDERNAME}/predictions.qzv"
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echo "--^-- X: Making visualizations...Done!" |