mirror of
https://github.com/MillironX/cowcalf-rumen-metagenomic-pipeline.git
synced 2024-11-23 22:49:55 +00:00
26 lines
673 B
Bash
26 lines
673 B
Bash
|
#!/bin/bash
|
||
|
|
#SBATCH --account=cowusda2016
|
||
|
|
#SBATCH --nodes=1
|
||
|
|
#SBATCH --ntasks-per-node=4
|
||
|
|
#SBATCH --cpus-per-task=4
|
||
|
|
#SBATCH --mem=16000
|
||
|
|
#SBATCH --time="2-00:00:00"
|
||
|
|
|
||
|
|
module restore system
|
||
|
|
module load metaxa2
|
||
|
|
module load blast-legacy
|
||
|
|
|
||
|
|
R1filename=${1%}
|
||
|
|
R2filename="${R1filename/R1/R2}"
|
||
|
|
Samplename="${R1filename/_R1_001.fastq.gz/}"
|
||
|
|
Samplename="${Samplename/\.\//}"
|
||
|
|
|
||
|
|
# Extract rRNA to files
|
||
|
|
metaxa2 -1 "$R1filename" -2 "$R2filename" -o "$Samplename" -f q -cpu 4 \
|
||
|
|
--summary F --graphical F --fasta F --taxonomy T
|
||
|
|
|
||
|
|
# Switch modes to extract taxonomy
|
||
|
|
INPUT2="${Samplename}.taxonomy.txt"
|
||
|
|
|
||
|
|
# Compile the taxonomy
|
||
|
|
metaxa2_ttt -i "$INPUT2" -o "$Samplename" -cpu4 -m 7 -n 7 --summary F
|