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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 10GB 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 selected common microbial contaminant genomes.
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11 Removes approximately 98.5% of common contaminant reads, with zero false-positives to non-bacteria.
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12 NOTE! This program uses hard-coded paths and will only run on Nersc systems.
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13
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14 Usage: removemicrobes.sh in=<input file> outu=<clean output file>
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15
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16 Input may be fasta or fastq, compressed or uncompressed.
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17
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18 Parameters:
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19 in=<file> Input reads. Should already be adapter-trimmed.
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20 outu=<file> Destination for clean reads.
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21 outm=<file> Optional destination for contaminant reads.
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22 threads=auto (t) Set number of threads to use; default is number of logical processors.
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23 overwrite=t (ow) Set to false to force the program to abort rather than overwrite an existing file.
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24 interleaved=auto (int) If true, forces fastq input to be paired and interleaved.
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25 trim=t Trim read ends to remove bases with quality below minq.
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26 Values: t (trim both ends), f (neither end), r (right end only), l (left end only).
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27 untrim=t Undo the trimming after mapping.
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28 minq=4 Trim quality threshold.
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29 ziplevel=6 (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
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30
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31 build=1 Choses which masking mode was used:
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32 1 is most stringent and should be used for bacteria.
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33 2 uses fewer bacteria for masking (only RefSeq references).
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34 3 is only masked for plastids and entropy, for use on anything except bacteria.
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35 4 is unmasked.
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36
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37 ***** All BBMap parameters can be used; run bbmap.sh for more details. *****
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38
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39 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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40 "
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41 }
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42
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43 #This block allows symlinked shellscripts to correctly set classpath.
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44 pushd . > /dev/null
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45 DIR="${BASH_SOURCE[0]}"
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46 while [ -h "$DIR" ]; do
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47 cd "$(dirname "$DIR")"
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48 DIR="$(readlink "$(basename "$DIR")")"
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49 done
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50 cd "$(dirname "$DIR")"
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51 DIR="$(pwd)/"
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52 popd > /dev/null
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53
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54 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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55 CP="$DIR""current/"
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56 JNI="-Djava.library.path=""$DIR""jni/"
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57 JNI=""
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58
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59 z="-Xmx6000m"
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60 z2="-Xms6000m"
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61 set=0
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62
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63 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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64 usage
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65 exit
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66 fi
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67
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68 calcXmx () {
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69 source "$DIR""/calcmem.sh"
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70 setEnvironment
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71 parseXmx "$@"
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72 }
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73 calcXmx "$@"
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74
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75 function removemicrobes() {
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76 local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBMap strictmaxindel=4 bwr=0.16 bw=12 ef=0.001 minhits=2 path=/global/cfs/cdirs/bbtools/commonMicrobes pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag printunmappedcount ztd=2 kfilter=25 maxsites=1 k=13 minid=0.95 idfilter=0.95 minhits=2 build=1 bloomfilter $@"
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77 echo $CMD >&2
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78 eval $CMD
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79 }
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80
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81 removemicrobes "$@"
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