--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/removecatdogmousehuman.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,76 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified December 22, 2021
+This script requires at least 52GB RAM.
+It is designed for NERSC and uses hard-coded paths.
+
+Description:  Removes all reads that map to the cat, dog, mouse, or human genome with at least 95% identity after quality trimming.
+Removes approximately 98.6% of human 2x150bp reads, with zero false-positives to non-animals.
+NOTE!  This program uses hard-coded paths and will only run on Nersc systems.
+
+Usage:  removecatdogmousehuman.sh in=<input file> outu=<clean output file>
+
+Input may be fasta or fastq, compressed or uncompressed.
+
+Parameters:
+threads=auto        (t) Set number of threads to use; default is number of logical processors.
+overwrite=t         (ow) Set to false to force the program to abort rather than overwrite an existing file.
+interleaved=auto    (int) If true, forces fastq input to be paired and interleaved.
+trim=t              Trim read ends to remove bases with quality below minq.
+                    Values: t (trim both ends), f (neither end), r (right end only), l (left end only).
+untrim=t            Undo the trimming after mapping.
+minq=4              Trim quality threshold.
+ziplevel=2          (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
+outm=<file>         File to output the reads that mapped to human.
+
+***** All BBMap parameters can be used; run bbmap.sh for more details. *****
+
+Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
+"
+}
+
+#This block allows symlinked shellscripts to correctly set classpath.
+pushd . > /dev/null
+DIR="${BASH_SOURCE[0]}"
+while [ -h "$DIR" ]; do
+  cd "$(dirname "$DIR")"
+  DIR="$(readlink "$(basename "$DIR")")"
+done
+cd "$(dirname "$DIR")"
+DIR="$(pwd)/"
+popd > /dev/null
+
+#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
+CP="$DIR""current/"
+JNI="-Djava.library.path=""$DIR""jni/"
+JNI=""
+
+z="-Xmx50g"
+z2="-Xms50g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+}
+calcXmx "$@"
+
+function removecatdogmousehuman() {
+	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBMap minratio=0.9 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 path=/global/cfs/cdirs/bbtools/mousecatdoghuman/ pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag usemodulo printunmappedcount ztd=2 kfilter=25 maxsites=1 k=14 bloomfilter $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+removecatdogmousehuman "$@"