jpayne@69: #!/bin/bash
jpayne@69:
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified December 22, 2021
jpayne@69: This script requires at least 17GB RAM.
jpayne@69: It is designed for NERSC and uses hard-coded paths.
jpayne@69:
jpayne@69: Description: Removes all reads that map to the human genome with at least 88% identity after quality trimming.
jpayne@69: This is more aggressive than removehuman.sh and uses an unmasked human genome reference.
jpayne@69: It removes roughly 99.99% of human 2x150bp reads, but may incur false-positive removals.
jpayne@69: NOTE! This program uses hard-coded paths and will only run on Nersc systems unless you change the path.
jpayne@69:
jpayne@69: Usage: removehuman.sh in= outu=
jpayne@69:
jpayne@69: Input may be fasta or fastq, compressed or uncompressed.
jpayne@69:
jpayne@69: Parameters:
jpayne@69: threads=auto (t) Set number of threads to use; default is number of logical processors.
jpayne@69: overwrite=t (ow) Set to false to force the program to abort rather than overwrite an existing file.
jpayne@69: interleaved=auto (int) If true, forces fastq input to be paired and interleaved.
jpayne@69: trim=t Trim read ends to remove bases with quality below minq.
jpayne@69: Values: t (trim both ends), f (neither end), r (right end only), l (left end only).
jpayne@69: untrim=t Undo the trimming after mapping.
jpayne@69: minq=4 Trim quality threshold.
jpayne@69: ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
jpayne@69: outm= File to output the reads that mapped to human.
jpayne@69: path= Set the path to an indexed human genome.
jpayne@69:
jpayne@69: ***** All BBMap parameters can be used; run bbmap.sh for more details. *****
jpayne@69:
jpayne@69: Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69: "
jpayne@69: }
jpayne@69:
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69:
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: JNI="-Djava.library.path=""$DIR""jni/"
jpayne@69: JNI=""
jpayne@69:
jpayne@69: z="-Xmx16000m"
jpayne@69: z2="-Xms16000m"
jpayne@69: set=0
jpayne@69:
jpayne@69: calcXmx () {
jpayne@69: source "$DIR""/calcmem.sh"
jpayne@69: setEnvironment
jpayne@69: parseXmx "$@"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69:
jpayne@69: function removehuman() {
jpayne@69: local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBMap minratio=0.75 maxindel=8 bwr=0.22 bw=26 minhits=1 path=/global/cfs/cdirs/bbtools/hg19 build=2 pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag usemodulo printunmappedcount ztd=2 maxsites=1 k=14 tipsearch=0 kfilter=25 bloomfilter $@"
jpayne@69: echo $CMD >&2
jpayne@69: eval $CMD
jpayne@69: }
jpayne@69:
jpayne@69: removehuman "$@"