Cecilio Jimenes - 2019-01-18

Hi,
I want to run BBMap_38.34 on a win10 (education) laptop 16GB RAM, i7 processor.

I have java:
java version "1.8.0_191"
Java(TM) SE Runtime Environment (build 1.8.0_191-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.191-b12, mixed mode)

I attempeted to run bbmap with the following command:

C:\bbamp\mapPacBio.sh -Xmx20g k=7 in=m54092_180523_205249.subreadsFQ.fastq ref=Moellerella_wisconsensis.fasta maxlen=1000 minlen=200 idtag ow int=f qin=33 out=Kurthiamapped1.sam minratio=0.15 ignorequality slow ordered maxindel1=40 maxindel2=400

I get the following error:

!/bin/bash

See bbmap.sh for documentation.

usage(){
bash "$DIR"bbmap.sh
}

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="$DIR""current/"
NATIVELIBDIR="$DIR""jni/"

z="-Xmx1g"
z2="-Xms1g"
EA="-ea"
EOOM=""
set=0

if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi

calcXmx () {
source "$DIR""/calcmem.sh"
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 3200m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"

mapPacBio() {
if [[ $SHIFTER_RUNTIME == 1 ]]; then
#Ignore NERSC_HOST
shifter=1
elif [[ $NERSC_HOST == genepool ]]; then
module unload oracle-jdk
module load oracle-jdk/1.8_144_64bit
module load samtools/1.4
module load pigz
elif [[ $NERSC_HOST == denovo ]]; then
module unload java
module load java/1.8.0_144
module load PrgEnv-gnu/7.1
module load samtools/1.4
module load pigz
elif [[ $NERSC_HOST == cori ]]; then
module use /global/common/software/m342/nersc-builds/denovo/Modules/jgi
module use /global/common/software/m342/nersc-builds/denovo/Modules/usg
module unload java
module load java/1.8.0_144
module unload PrgEnv-intel
module load PrgEnv-gnu/7.1
module load samtools/1.4
module load pigz
fi

#local CMD="java -Djava.library.path=$NATIVELIBDIR $EA $z -cp $CP align2.BBMapPacBio build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambiguous=best minscaf=100 startpad=10000 stoppad=10000 midpad=6000 $@"

local CMD="java $EA $z -cp $CP align2.BBMapPacBio build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambiguous=best minscaf=100 startpad=10000 stoppad=10000 midpad=6000 $@"
echo $CMD >&2
eval $CMD

}

mapPacBio "$@"

Can someone tell me waht I am doing worng?

Regards,

Cecilio1