mirror of
https://github.com/MillironX/cowcalf-rumen-metagenomic-pipeline.git
synced 2024-11-21 22:16:05 +00:00
26 lines
673 B
Bash
26 lines
673 B
Bash
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#!/bin/bash
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#SBATCH --account=cowusda2016
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#SBATCH --nodes=1
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#SBATCH --ntasks-per-node=4
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#SBATCH --cpus-per-task=4
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#SBATCH --mem=16000
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#SBATCH --time="2-00:00:00"
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module restore system
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module load metaxa2
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module load blast-legacy
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R1filename=${1%}
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R2filename="${R1filename/R1/R2}"
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Samplename="${R1filename/_R1_001.fastq.gz/}"
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Samplename="${Samplename/\.\//}"
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# Extract rRNA to files
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metaxa2 -1 "$R1filename" -2 "$R2filename" -o "$Samplename" -f q -cpu 4 \
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--summary F --graphical F --fasta F --taxonomy T
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# Switch modes to extract taxonomy
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INPUT2="${Samplename}.taxonomy.txt"
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# Compile the taxonomy
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metaxa2_ttt -i "$INPUT2" -o "$Samplename" -cpu4 -m 7 -n 7 --summary F
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