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jpayne@69
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1 #!/bin/bash
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2
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3 usage(){
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4 echo "
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5 Written by Brian Bushnell
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6 Last modified December 22, 2021
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7 This script requires at least 17GB RAM.
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8 It is designed for NERSC and uses hard-coded paths.
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9
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10 Description: Removes all reads that map to the human genome with at least 88% identity after quality trimming.
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11 This is more aggressive than removehuman.sh and uses an unmasked human genome reference.
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12 It removes roughly 99.99% of human 2x150bp reads, but may incur false-positive removals.
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13 NOTE! This program uses hard-coded paths and will only run on Nersc systems unless you change the path.
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14
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15 Usage: removehuman.sh in=<input file> outu=<clean output file>
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16
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17 Input may be fasta or fastq, compressed or uncompressed.
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18
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19 Parameters:
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20 threads=auto (t) Set number of threads to use; default is number of logical processors.
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21 overwrite=t (ow) Set to false to force the program to abort rather than overwrite an existing file.
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22 interleaved=auto (int) If true, forces fastq input to be paired and interleaved.
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23 trim=t Trim read ends to remove bases with quality below minq.
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24 Values: t (trim both ends), f (neither end), r (right end only), l (left end only).
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25 untrim=t Undo the trimming after mapping.
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26 minq=4 Trim quality threshold.
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27 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
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28 outm=<file> File to output the reads that mapped to human.
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29 path= Set the path to an indexed human genome.
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30
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31 ***** All BBMap parameters can be used; run bbmap.sh for more details. *****
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32
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33 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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34 "
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35 }
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36
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37 #This block allows symlinked shellscripts to correctly set classpath.
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38 pushd . > /dev/null
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39 DIR="${BASH_SOURCE[0]}"
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40 while [ -h "$DIR" ]; do
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41 cd "$(dirname "$DIR")"
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42 DIR="$(readlink "$(basename "$DIR")")"
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43 done
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44 cd "$(dirname "$DIR")"
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45 DIR="$(pwd)/"
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46 popd > /dev/null
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47
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48 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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49 CP="$DIR""current/"
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50 JNI="-Djava.library.path=""$DIR""jni/"
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51 JNI=""
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52
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53 z="-Xmx16000m"
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54 z2="-Xms16000m"
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55 set=0
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56
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57 calcXmx () {
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58 source "$DIR""/calcmem.sh"
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59 setEnvironment
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60 parseXmx "$@"
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61 }
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62 calcXmx "$@"
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63
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64 function removehuman() {
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65 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 $@"
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66 echo $CMD >&2
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67 eval $CMD
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68 }
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69
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70 removehuman "$@"
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