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dDocentHPC.bash
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dDocentHPC.bash
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#!/usr/bin/env bash
VERSION=4.1
#This script serves as an interactive bash wrapper to QC, assemble, map, and call SNPs from double digest RAD (SE or PE), ezRAD (SE or PE) data, or SE RAD data.
#It requires that your raw data are split up by tagged individual and follow the naming convention of:
#Pop_Sample1.F.fq and Pop_Sample1.R.fq
#Prints out title and contact info
echo; echo -e "\n* dDocentHPC v$VERSION Forked by [email protected] * \n"
#echo -e "Contact [email protected] with any problems \n\n "
#Determine which functions to run
#demultiplexFQ trimFQ mkREF mkBAM fltrBAM mkVCF fltrVCF
if [ -n "$1" ]; then
#getting functions from command line
FUNKTION=$(echo $1)
echo; echo "Running dDocentHPC $FUNKTION..."
else
echo ""; echo `date` "ERROR: dDocentHPC must be run with 2 arguments, "
echo " dDocentHPC.bash [function] [config file]"
echo " functions: trimFQ, mkREF, mkBAM, fltrBAM, mkVCF, fltrVCF"
exit
fi
#load variables from config file
if [ -n "$2" ]; then
echo " "
echo `date` "Files output to: " $(pwd)
echo ""; echo `date` "Reading config file... "
echo " "
#echo "BEGIN*CONFIG*FILE*****************************************************************************************"
# cat $1
cat $2
#echo "*********END*CONFIG*FILE*******************************************************************************************"
echo ""; echo `date` "Reading in variables from config file..."
CONFIG=$2
NUMProc=$(grep 'Number of Processors (Auto, 1, 2, 3,' $CONFIG | awk '{print $1;}')
MAXMemory=$(grep 'Maximum Memory (1G,2G,' $CONFIG | awk '{print $1;}')
#TRIM=$(grep -A1 Trim $CONFIG | tail -1)
TRIM="RemoveThisVar"
TRIM_LENGTH_ASSEMBLY=$(grep 'trimmomatic MINLEN (integer, mkREF only)' $CONFIG | awk '{print $1;}')
SEED_ASSEMBLY=$(grep 'trimmomatic ILLUMINACLIP:<seed mismatches> (integer)' $CONFIG | awk '{print $1;}')
PALIMDROME_ASSEMBLY=$(grep 'trimmomatic ILLUMINACLIP:<palindrome clip thresh> (integer)' $CONFIG | awk '{print $1;}')
SIMPLE_ASSEMBLY=$(grep 'trimmomatic ILLUMINACLIP:<simple clip thresh> (integer)' $CONFIG | awk '{print $1;}')
windowSize_ASSEMBLY=$(grep 'trimmomatic SLIDINGWINDOW:<windowSize> (integer)' $CONFIG | awk '{print $1;}')
windowQuality_ASSEMBLY=$(grep 'trimmomatic SLIDINGWINDOW:<windowQuality> (integer)' $CONFIG | awk '{print $1;}')
TRAILING_ASSEMBLY=$(grep 'trimmomatic TRAILING:<quality> (integer, mkREF only)' $CONFIG | awk '{print $1;}')
TRIM_LENGTH_MAPPING=$(grep 'trimmomatic MINLEN (integer, mkBAM only)' $CONFIG | awk '{print $1;}')
LEADING_MAPPING=$(grep 'trimmomatic LEADING:<quality> (integer, mkBAM only)' $CONFIG | awk '{print $1;}')
TRAILING_MAPPING=$(grep 'trimmomatic TRAILING:<quality> (integer, mkBAM only)' $CONFIG | awk '{print $1;}')
HEADCROP=$(grep 'HEADCROP:<length> (integer, only Read1 for ezRAD)' $CONFIG | awk '{print $1;}')
FixStacks=$(grep 'FixStacks (yes,no)' $CONFIG | awk '{print $1;}')
ASSEMBLY="RemoveThisVar"
ATYPE=$(grep 'Type of reads for assembly (PE, SE, OL, RPE)' $CONFIG | awk '{print $1;}')
simC=$(grep 'cdhit Clustering_Similarity_Pct (0-1)' $CONFIG | awk '{print $1;}')
HPC=$(grep 'Get graphs for cutoffs, then stop? (yes or no)' $CONFIG | awk '{print $1;}')
MANCUTOFF=$(grep 'Manually set cutoffs? (yes or no)' $CONFIG | awk '{print $1;}')
if [ "$MANCUTOFF" = "no" ]; then
CUTOFF=$(grep 'Cutoff1 (integer)' $CONFIG | awk '{print $1;}')
CUTOFF2=$(grep 'Cutoff2 (integer)' $CONFIG | awk '{print $1;}')
#echo ""; echo `date` " CUTOFF=" $CUTOFF
#echo ""; echo `date` " CUTOFF2=" $CUTOFF2
else
echo ""; echo `date` " ERROR: This is the HPC version of dDocent. Manual cutoffs are not possible. Please change config file settings."
echo " Aborting dDocentHPC"
exit
fi
MAP="RemoveThisVar"
optA=$(grep 'bwa mem -A Mapping_Match_Value (integer)' $CONFIG | awk '{print $1;}')
optB=$(grep 'bwa mem -B Mapping_MisMatch_Value (integer)' $CONFIG | awk '{print $1;}')
optO=$(grep 'bwa mem -O Mapping_GapOpen_Penalty (integer)' $CONFIG | awk '{print $1;}')
MAPPING_MIN_ALIGNMENT_SCORE=$(grep 'bwa mem -T Mapping_Minimum_Alignment_Score (integer)' $CONFIG | awk '{print $1;}')
MAPPING_CLIPPING_PENALTY=$(grep 'bwa mem -L Mapping_Clipping_Penalty (integer,integer)' $CONFIG | awk '{print $1;}')
FILTERMAP="RemoveThisVar"
MAPPING_MIN_QUALITY=$(grep 'Mapping_Min_Quality (integer)' $CONFIG | awk '{print $1;}')
SAMTOOLS_VIEW_F4=$(grep 'Remove_unmapped_reads? (yes,no)' $CONFIG | awk '{print $1;}')
SAMTOOLS_VIEW_F8=$(grep 'Remove_read_pair_if_one_is_unmapped? (yes,no)' $CONFIG | awk '{print $1;}')
SAMTOOLS_VIEW_F256=$(grep 'Remove_secondary_alignments? (yes,no)' $CONFIG | awk '{print $1;}')
SAMTOOLS_VIEW_F512=$(grep 'Remove_reads_not_passing_platform_vendor_filters (yes,no)' $CONFIG | awk '{print $1;}')
SAMTOOLS_VIEW_F1024=$(grep 'Remove_PCR_or_optical_duplicates? (yes,no)' $CONFIG | awk '{print $1;}')
SAMTOOLS_VIEW_F2048=$(grep 'Remove_supplementary_alignments? (yes,no)' $CONFIG | awk '{print $1;}')
SAMTOOLS_VIEW_f2=$(grep 'Keep_only_properly_aligned_read_pairs? (yes,no)' $CONFIG | awk '{print $1;}')
if [ "$SAMTOOLS_VIEW_F4" == "yes" ]; then
F4=4
else
F4=0
fi
if [ "$SAMTOOLS_VIEW_F8" == "yes" ]; then
F8=8
else
F8=0
fi
if [ "$SAMTOOLS_VIEW_F256" == "yes" ]; then
F256=256
else
F256=0
fi
if [ "$SAMTOOLS_VIEW_F512" == "yes" ]; then
F512=512
else
F512=0
fi
if [ "$SAMTOOLS_VIEW_F1024" == "yes" ]; then
F1024=1024
else
F1024=0
fi
if [ "$SAMTOOLS_VIEW_F2048" == "yes" ]; then
F2048=2048
else
F2048=0
fi
SAMTOOLS_VIEW_F=$(($F4+$F8+$F256+$F512+$F1024+$F2048))
if [ "$SAMTOOLS_VIEW_f2" == "yes" ]; then
SAMTOOLS_VIEW_f=2
else
SAMTOOLS_VIEW_f=0
fi
SAMTOOLS_VIEW_Fcustom=$(grep 'Custom_samtools_view_F_bit_value? (integer)' $CONFIG | awk '{print $1;}')
SAMTOOLS_VIEW_fcustom=$(grep 'Custom_samtools_view_f_bit_value? (integer)' $CONFIG | awk '{print $1;}')
SOFT_CLIP_CUT=$(grep 'Remove_reads_with_excessive_soft_clipping? (no, integers by 10s)' $CONFIG | awk '{print $1;}')
SOFT_CLIP_CUTOFF=$((($SOFT_CLIP_CUT+9)/10))
FILTER_MIN_AS=$(grep 'Remove_reads_with_alignment_score_below (integers by 10s)' $CONFIG | awk '{print $1;}')
FILTER_ORPHANS=$(grep 'Remove_reads_orphaned_by_filters? (yes,no)' $CONFIG | awk '{print $1;}')
SNP="RemoveThisVar"
POOLS=$(grep 'freebayes -J --pooled-discrete (yes or no)' $CONFIG | awk '{print $1;}')
POOL_PLOIDY_FILE=$(grep 'freebayes -A --cnv-map (filename.bed or no)' $CONFIG | awk '{print $1;}')
PLOIDY=$(grep 'freebayes -p --ploidy (integer)' $CONFIG | awk '{print $1;}')
BEST_N_ALLELES=$(grep 'freebayes -n --use-best-n-alleles (integer)' $CONFIG | awk '{print $1;}')
MIN_MAPPING_QUAL=$(grep 'freebayes -m --min-mapping-quality (integer)' $CONFIG | awk '{print $1;}')
MIN_BASE_QUAL=$(grep 'freebayes -q --min-base-quality (integer)' $CONFIG | awk '{print $1;}')
HAPLOTYPE_LENGTH=$(grep 'freebayes -E --haplotype-length (-1, 3, or integer)' $CONFIG | awk '{print $1;}')
MIN_REPEAT_ENTROPY=$(grep 'freebayes --min-repeat-entropy (0, 1, or integer)' $CONFIG | awk '{print $1;}')
MIN_COVERAGE=$(grep 'freebayes --min-coverage (integer)' $CONFIG | awk '{print $1;}')
MIN_ALT_FRACTION=$(grep 'freebayes -F --min-alternate-fraction' $CONFIG | awk '{print $1;}')
FREEBAYES_z=$(grep 'freebayes -z --read-max-mismatch-fraction' $CONFIG | awk '{print $1;}')
FREEBAYES_C=$(grep 'freebayes -C --min-alternate-count' $CONFIG | awk '{print $1;}')
FREEBAYES_3=$(grep 'freebayes ~3 ~~min-alternate-qsum' $CONFIG | awk '{print $1;}'); FREEBAYES_3=$((FREEBAYES_3 * FREEBAYES_C))
FREEBAYES_G=$(grep 'freebayes -G --min-alternate-total' $CONFIG | awk '{print $1;}')
FREEBAYES_Q=$(grep 'freebayes -Q --mismatch-base-quality-threshold' $CONFIG | awk '{print $1;}')
FREEBAYES_U=$(grep 'freebayes -U --read-mismatch-limit' $CONFIG | awk '{print $1;}')
FREEBAYES_DOLLAR=$(grep 'freebayes -\$ --read-snp-limit' $CONFIG | awk '{print $1;}')
FREEBAYES_e=$(grep 'freebayes -e --read-indel-limit' $CONFIG | awk '{print $1;}')
FREEBAYES_w=$(grep 'freebayes -w --hwe-priors-off' $CONFIG | awk '{print $1;}'); if [ $FREEBAYES_w == "no" ]; then FREEBAYES_w=""; else FREEBAYES_w="-w "; fi
FREEBAYES_V=$(grep 'freebayes -V --binomial-obs-priors-off' $CONFIG | awk '{print $1;}'); if [ $FREEBAYES_V == "no" ]; then FREEBAYES_V=""; else FREEBAYES_V="-V "; fi
FREEBAYES_a=$(grep 'freebayes -a --allele-balance-priors-off' $CONFIG | awk '{print $1;}'); if [ $FREEBAYES_a == "no" ]; then FREEBAYES_a=""; else FREEBAYES_a="-a "; fi
FREEBAYES_no_partial_observations=$(grep 'freebayes --no-partial-observations' $CONFIG | awk '{print $1;}'); if [ ${FREEBAYES_no_partial_observations} == "no" ]; then FREEBAYES_no_partial_observations=""; else FREEBAYES_no_partial_observations="--no-partial-observations "; fi
MAIL=$(grep -A1 Email $CONFIG | tail -1)
CUTOFFS=$CUTOFF.$CUTOFF2
else
echo ""; echo `date` "ERROR: dDocentHPC must be run with 2 arguments, "
echo " dDocentHPC.bash [function] [config file]"
echo " functions: trimFQ, mkREF, mkBAM, fltrBAM, mkVCF, fltrVCF"
echo " the default config file is called config.*"
exit
fi
####################################################################################################
###Function to check for the required software for dDocent
####################################################################################################
CheckDependencies(){
echo ""; echo " Running CheckDependencies Function..."
DEP=$1
EXIT_IF_DEP_MISSING=$2
dDocentFUNCTION=$3
NUMDEP=0
for i in "${DEP[@]}"
do
if which $i &> /dev/null; then
echo ""; echo " The dependency $i is installed!"
else
echo ""; echo " The dependency" $i "is not installed or is not in your" '$PATH'"."
NUMDEP=$(($NUMDEP + 1))
fi
if [ "$i" == "freebayes" ]; then
FREEB=(`freebayes | grep -oh 'v[0-9].*' | cut -f1 -d "." | sed 's/v//' `)
if [ "$FREEB" != "1" ]; then
echo " The version of FreeBayes installed in your" '$PATH' "is not optimized for dDocent."
echo " Please install at least version 1.0.0"
NUMDEP=$(($NUMDEP + 1))
fi
#elif [ "$i" == "mawk" ]; then
elif [ "$i" == "bwa" ]; then
BWAV=$( bwa 2>&1 | mawk '/Versi/' | sed 's/Version: //g' | sed 's/0.7.//g' | sed 's/-.*//g' | cut -c 1-2 )
if [ "$BWAV" -lt "13" ]; then
echo " The version of bwa installed in your" '$PATH' "is not optimized for dDocent."
echo " Please install at least version 0.7.13"
NUMDEP=$(($NUMDEP + 1))
fi
elif [ "$i" == "samtools" ]; then
SAMV1=$(samtools 2>&1 >/dev/null | grep Ver | sed -e 's/Version://' | cut -f2 -d " " | sed -e 's/-.*//' | cut -c1)
SAMV2=$(samtools 2>&1 >/dev/null | grep Ver | sed -e 's/Version://' | cut -f2 -d " " | sed -e 's/-.*//' | cut -c3)
if [ "$SAMV1" -ge "1" ]; then
if [ "$SAMV2" -lt "3" ]; then
echo " The version of Samtools installed in your" '$PATH' "is not optimized for dDocent."
echo " Please install at least version 1.3.0"
NUMDEP=$(($NUMDEP + 1))
fi
else
echo " The version of Samtools installed in your" '$PATH' "is not optimized for dDocent."
echo " Please install at least version 1.3.0"
NUMDEP=$(($NUMDEP + 1))
fi
elif [ "$i" == "vcftools" ]; then
VCFTV=$(vcftools | grep 'VCF' | sed -e 's/VCFtools (//' | sed -e 's/)//')
if [[ "$VCFTV" != 0.1.[1-9][0-9] ]]; then
echo " The version of VCFtools installed in your" '$PATH' "is not optimized for dDocent."
echo " Please install only version 0.1.11"
NUMDEP=$(($NUMDEP + 1))
fi
elif [ "$i" == "rainbow" ]; then
RAINV=(`rainbow | head -1 | cut -f2 -d' ' `)
if [[ "$RAINV" != "2.0.2" && "$RAINV" != "2.0.3" && "$RAINV" != "2.0.4" ]]; then
echo " The version of Rainbow installed in your" '$PATH' "is not optimized for dDocent."
echo " Please install a version newer than 2.0.2"
NUMDEP=$(($NUMDEP + 1))
fi
#elif [ "$i" == "gnuplot" ]; then
#elif [ "$i" == "gawk" ]; then
#elif [ "$i" == "seqtk" ]; then
#elif [ "$i" == "cd-hit-est" ]; then
#elif [ "$i" == "bamToBed" ]; then
elif [ "$i" == "bedtools" ]; then
BTC=$(bedtools --version | mawk '{print $2}' | sed 's/v//g' | cut -f1,2 -d"." )
if [[ "$BTC" != 2.[2-9][0-9] ]]; then
echo " The version of bedtools installed in your" '$PATH' "is not optimized for dDocent."
echo " Please install only version 2.xx.0"
NUMDEP=$(($NUMDEP + 1))
fi
BTC=$( bedtools --version | mawk '{print $2}' | sed 's/v//g' | cut -f1,2 -d"." | sed 's/2\.//g' )
if [ "$BTC" -ge "26" ]; then
BEDTOOLSFLAG="NEW"
elif [ "$BTC" == "23" ]; then
BEDTOOLSFLAG="OLD"
elif [ "$BTC" != "23" ]; then
echo " The version of bedtools installed in your" '$PATH' "is not optimized for dDocent."
echo " Please install version 2.23.0 or version 2.26.0 and above"
NUMDEP=$(($NUMDEP + 1))
fi
#elif [ "$i" == "coverageBed" ]; then
#elif [ "$i" == "parallel" ]; then
#elif [ "$i" == "vcfcombine" ]; then
#elif [ "$i" == "bamtools" ]; then
#elif [ "$i" == "pearRM" ]; then
elif [ "$i" == "trimmomatic" ]; then
if find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null| grep -q 'trim' ; then
TRIMMOMATIC=$(find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null | head -1)
else
echo " The dependency trimmomatic is not installed or is not in your" '$PATH'"."
NUMDEP=$(($NUMDEP + 1))
fi
if find ${PATH//:/ } -maxdepth 2 -name TruSeq3-PE-2.fa 2> /dev/null | grep -q 'Tru' ; then
ADAPTERS=$(find ${PATH//:/ } -maxdepth 2 -name TruSeq3-PE-2.fa 2> /dev/null | head -1)
else
echo " The file listing adapters (included with trimmomatic) is not installed or is not in your" '$PATH'"."
NUMDEP=$(($NUMDEP + 1))
fi
fi
done
if [[ $NUMDEP -gt 0 && $EXIT_IF_DEP_MISSING == "TRUE" ]]; then
echo -e "\n ERROR: Please install all required software then try again."
exit 1
elif [[ $NUMDEP -gt 0 && $EXIT_IF_DEP_MISSING == "FALSE" ]]; then
echo -e "\n ERROR: Some software is not installed but $dDocentFUNCTION . Please install all required software for full functionality"
else
echo -e "\n All dependencies are installed and up to date!"
fi
}
echo ""; echo `date` "Checking for all required dDocent software..."
DEP=(freebayes mawk bwa samtools vcftools rainbow gnuplot gawk seqtk cd-hit-est bamToBed bedtools coverageBed parallel vcfcombine bamtools pearRM)
CheckDependencies $DEP "FALSE" "dDocentHPC will continue to run with limited functionality"
if ! awk --version | fgrep -v GNU &>/dev/null; then
awk=gawk
else
awk=awk
fi
#This code checks for individual fastq files follow the correct naming convention and are gziped
TEST=$(ls *.fq 2> /dev/null | wc -l )
if [ "$TEST" -gt 0 ]; then
echo -e "\ndDocent is now configured to work on compressed sequence files. Please run gzip to compress your files."
echo "This is as simple as 'gzip *.fq'"
echo "Please rerun dDocent after compressing files."
echo $TEST
exit 1
fi
###############################################################################################
#Wrapper for main program functions. This allows the entire file to be read first before execution
main(){
echo "";echo ""; echo `date` " Begin main ddocent function"
##########User Input Section##########
#This code gets input from the user and assigns variables
######################################
#RMH added ALL variables
# echo "";echo " Loading variable values..."
# echo " FUNKTION= ${55}"
# echo " NUMProc= $1"
# echo " MAXMemory= $2"
# echo " TRIM= $3"
# echo " TRIM_LENGTH_ASSEMBLY= $4"
# echo " SEED_ASSEMBLY= $5"
# echo " PALIMDROME_ASSEMBLY= $6"
# echo " SIMPLE_ASSEMBLY= $7"
# echo " windowSize_ASSEMBLY= $8"
# echo " windowQuality_ASSEMBLY= $9"
# echo " TRAILING_ASSEMBLY= ${10}"
# echo " TRIM_LENGTH_MAPPING= ${11}"
# echo " LEADING_MAPPING= ${12}"
# echo " TRAILING_MAPPING= ${13}"
# echo " HEADCROP= ${56}"
# echo " FixStacks= ${14}"
# echo " ASSEMBLY= ${15}"
# echo " ATYPE= ${16}"
# echo " simC= ${17}"
# echo " HPC= ${18}"
# echo " MANCUTOFF= ${19}"
# echo " CUTOFF= ${20}"
# echo " CUTOFF2= ${21}"
# echo " MAP= ${22}"
# echo " optA= ${23}"
# echo " optB= ${24}"
# echo " optO= ${25}"
# echo " MAPPING_MIN_ALIGNMENT_SCORE= ${26}"
# echo " MAPPING_CLIPPING_PENALTY= ${27}"
# echo " FILTERMAP= ${45}"
# echo " MAPPING_MIN_QUALITY= ${28}"
# echo " SAMTOOLS_VIEW_f= ${46}"
# echo " SAMTOOLS_VIEW_F= ${29}"
# echo " SAMTOOLS_VIEW_Fcustom= ${47}"
# echo " SAMTOOLS_VIEW_fcustom= ${48}"
# echo " SOFT_CLIP_CUTOFF= ${49}"
# echo " FILTER_MIN_AS= ${52}"
# echo " FILTER_ORPHANS= ${50}"
# echo " SNP= ${30}"
# echo " POOLS= ${31}"
# echo " POOL_PLOIDY_FILE= ${32}"
# echo " PLOIDY= ${33}"
# echo " BEST_N_ALLELES= ${34}"
# echo " MIN_MAPPING_QUAL= ${35}"
# echo " MIN_BASE_QUAL= ${36}"
# echo " HAPLOTYPE_LENGTH= ${37}"
# echo " MIN_REPEAT_ENTROPY= ${38}"
# echo " MIN_COVERAGE= ${39}"
# echo " MIN_ALT_FRACTION= ${40}"
# echo " FREEBAYES_C= ${41}"
# echo " FREEBAYES_G= ${42}"
# echo " FREEBAYES_z= ${43}"
# echo " FREEBAYES_Q= ${53}"
# echo " FREEBAYES_U= ${54}"
# echo " freebayes -3 $FREEBAYES_3"
# echo " freebayes -\$ $FREEBAYES_DOLLAR"
# echo " freebayes -e $FREEBAYES_e"
# if [[ $FREEBAYES_w != "" ]]; then echo " freebayes ${FREEBAYES_w}"; fi
# if [[ $FREEBAYES_V != "" ]]; then echo " freebayes ${FREEBAYES_V}"; fi
# if [[ $FREEBAYES_a != "" ]]; then echo " freebayes ${FREEBAYES_a}"; fi
# if [[ $FREEBAYES_no_partial_observations != "" ]]; then echo " freebayes ${FREEBAYES_no_partial_observations}"; fi
# echo " MAIL= ${44}"
# echo " BEDTOOLSFLAG= ${51}"
#Load config arguments into variables
# RMH added ALL variables
# FUNKTION=${55}
# NUMProc=$1
# MAXMemory=$2
# TRIM=$3
# TRIM_LENGTH_ASSEMBLY=$4
# SEED_ASSEMBLY=$5
# PALIMDROME_ASSEMBLY=$6
# SIMPLE_ASSEMBLY=$7
# windowSize_ASSEMBLY=$8
# windowQuality_ASSEMBLY=$9
# TRAILING_ASSEMBLY=${10}
# TRIM_LENGTH_MAPPING=${11}
# LEADING_MAPPING=${12}
# TRAILING_MAPPING=${13}
# HEADCROP=${56}
# FixStacks=${14}
# ASSEMBLY=${15}
# ATYPE=${16}
# simC=${17}
# HPC=${18}
# MANCUTOFF=${19}
# CUTOFF=${20}
# CUTOFF2=${21}
# MAP=${22}
# optA=${23}
# optB=${24}
# optO=${25}
# MAPPING_MIN_ALIGNMENT_SCORE=${26}
# MAPPING_CLIPPING_PENALTY=${27}
# FILTERMAP=${45}
# MAPPING_MIN_QUALITY=${28}
# SAMTOOLS_VIEW_f=${46}
# SAMTOOLS_VIEW_F=${29}
# SAMTOOLS_VIEW_Fcustom=${47}
# SAMTOOLS_VIEW_fcustom=${48}
# SOFT_CLIP_CUTOFF=${49}
# FILTER_MIN_AS=${52}
# FILTER_ORPHANS=${50}
# SNP=${30}
# POOLS=${31}
# POOL_PLOIDY_FILE=${32}
# PLOIDY=${33}
# BEST_N_ALLELES=${34}
# MIN_MAPPING_QUAL=${35}
# MIN_BASE_QUAL=${36}
# HAPLOTYPE_LENGTH=${37}
# MIN_REPEAT_ENTROPY=${38}
# MIN_COVERAGE=${39}
# MIN_ALT_FRACTION=${40}
# FREEBAYES_C=${41}
# FREEBAYES_G=${42}
# FREEBAYES_z=${43}
# FREEBAYES_Q=${53}
# FREEBAYES_U=${54}
# MAIL=${44}
# BEDTOOLSFLAG=${51}
#$$$$$$$$$$$$$$$$$$$$$CEB$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
#Count number of individuals in current directory
#this alerts user to fastq file naming conventions
echo "";echo " The HPC version of dDocent will only digest files with particular extensions for particular tasks"
echo " untouched files for trimming must be *.F.fq.gz and *.R.fq.gz"
echo " files trimmed for assembly (mkREF) must be *r1.fq.gz *r2.fq.gz"
echo " files trimmed for mapping (mkBAM) must be *R1.fq.gz *R2.fq.gz"
if [ "$FUNKTION" == "trimFQ" ]; then
F="F"
Fwild="*.F.fq.gz"
Fsed=".F.fq.gz"
R="R"
Rwild="*.R.fq.gz"
Rsed=".R.fq.gz"
echo "";echo " extensions selected: $Fwild $Rwild"
elif [ "$FUNKTION" == "trimFQref" ]; then
F="F"
Fwild="*.F.fq.gz"
Fsed=".F.fq.gz"
R="R"
Rwild="*.R.fq.gz"
Rsed=".R.fq.gz"
echo "";echo " extensions selected: $Fwild $Rwild"
elif [ "$FUNKTION" == "trimFQmap" ]; then
F="F"
Fwild="*.F.fq.gz"
Fsed=".F.fq.gz"
R="R"
Rwild="*.R.fq.gz"
Rsed=".R.fq.gz"
echo "";echo " extensions selected: $Fwild $Rwild"
elif [ "$FUNKTION" == "mkREF" ]; then
F="r1"
Fwild="*.r1.fq.gz"
Fsed=".r1.fq.gz"
R="r2"
Rwild="*.r2.fq.gz"
Rsed=".r2.fq.gz"
echo "";echo " extensions selected: $Fwild $Rwild"
elif [ "$FUNKTION" == "mkBAM" ]; then
F="R1"
Fwild="*.R1.fq.gz"
Fsed=".R1.fq.gz"
R="R2"
Rwild="*.R2.fq.gz"
Rsed=".R2.fq.gz"
echo "";echo " extensions selected: $Fwild $Rwild"
elif [ "$FUNKTION" == "fltrBAM" ]; then
F="R1"
#Fwild="*-RAW.bam"
#Fsed=".${CUTOFFS}-RAW.bam"
Fwild="*.R1.fq.gz"
Fsed=".R1.fq.gz"
R="R2"
Rwild="*.R2.fq.gz"
Rsed=".R2.fq.gz"
echo "";echo " extensions selected: $Fwild $Rwild"
elif [ "$FUNKTION" == "mkVCF" ]; then
F="R1"
Fwild="*.R1.fq.gz"
Fsed=".R1.fq.gz"
# Fwild="*-RG.bam"
# Fsed=".${CUTOFFS}-RG.bam"
R="R2"
Rwild="*.R2.fq.gz"
Rsed=".R2.fq.gz"
echo "";echo " extensions selected: $Fwild $Rwild"
else
echo "";echo " Couldn't decide which file extensions were selected"
F="r1"
Fwild="*.r1.fq.gz"
Fsed=".r1.fq.gz"
R="r2"
Rwild="*.r2.fq.gz"
Rsed=".r2.fq.gz"
echo "";echo " extensions selected: $Fwild $Rwild"
fi
if [ "$FUNKTION" == "fltrBAM" ]; then
NumInd=$(ls *.${CUTOFFS}-RAW.bam | wc -l)
#Create list of sample names
if [ ! -s "namelist.$CUTOFF.$CUTOFF2" ];then
ls *.${CUTOFFS}-RAW.bam > namelist.$CUTOFFS
sed -i'' -e "s/*.${CUTOFFS}-RAW.bam//g" namelist.$CUTOFFS
elif [ "$(grep -c '^' namelist.$CUTOFFS)" != "$NumInd" ]; then
echo "";echo " The existing namelist file does not match the present sample set and is being recreated. "
ls *.${CUTOFFS}-RAW.bam > namelist.$CUTOFFS
sed -i'' -e "s/*.${CUTOFFS}-RAW.bam//g" namelist.$CUTOFFS
else
echo "";echo " The namelist file already exists and was not recreated. "
echo " If you experience errors, you should delete the namelist file."
fi
elif [ "$FUNKTION" == "mkVCF" ]; then
NumInd=$(ls *.${CUTOFFS}-RG.bam | wc -l)
#Create list of sample names
if [ ! -s "namelist.$CUTOFF.$CUTOFF2" ];then
ls *.${CUTOFFS}-RG.bam > namelist.$CUTOFFS
sed -i'' -e "s/*.${CUTOFFS}-RG.bam//g" namelist.$CUTOFFS
elif [ "$(grep -c '^' namelist.$CUTOFFS)" != "$NumInd" ]; then
echo "";echo " The existing namelist file does not match the present sample set and is being recreated. "
ls *.${CUTOFFS}-RG.bam > namelist.$CUTOFFS
sed -i'' -e "s/*.${CUTOFFS}-RG.bam//g" namelist.$CUTOFFS
else
echo "";echo " The namelist file already exists and was not recreated. "
echo " If you experience errors, you should delete the namelist file."
fi
else
NumInd=$(ls $Fwild | wc -l)
NumInd=$(($NumInd - 0))
#Create list of sample names
if [ ! -s "namelist.$CUTOFF.$CUTOFF2" ];then
ls $Fwild > namelist.$CUTOFFS
sed -i'' -e "s/$Fsed//g" namelist.$CUTOFFS
elif [ "$(grep -c '^' namelist.$CUTOFFS)" != "$NumInd" ]; then
echo "";echo " The existing namelist file does not match the present sample set and is being recreated. "
ls $Fwild > namelist.$CUTOFFS
sed -i'' -e "s/*.${CUTOFFS}-RAW.bam//g" namelist.$CUTOFFS
else
echo "";echo " The namelist file already exists and was not recreated. "
echo " If you experience errors, you should delete the namelist file."
fi
fi
#Create an array of sample names
#NUMNAMES=$(mawk '/_/' namelist.$CUTOFFS | wc -l)
NUMNAMES=$(grep -c '^' namelist.$CUTOFFS)
if [ "$NUMNAMES" == "$NumInd" ]; then
NAMES=( `cat "namelist.$CUTOFFS" `)
echo " ";echo " The samples being processed are:"
cat namelist.$CUTOFFS | parallel --no-notice "echo ' '{}"
echo ""
else
echo ""; echo " "`date` " ERROR: NUMNAMES=$NUMNAMES NUMIND=$NumInd"
echo " Individuals do not follow the dDocent naming convention."
echo " Please rename individuals to: Locality_Individual.F.fq.gz"
echo " For example: LocA_001.F.fq.gz"
exit 1
fi
#Sets a start time variable
STARTTIME=$(date)
##Section of logic statements that dictates the order and function of processing the pipeline
if [ "$FixStacks" == "yes" ]; then
FIXSTACKS
fi
if [ "$FUNKTION" == "trimFQ" ]; then
echo " ";echo " "`date` "Trimming reads "
TrimReadsRef #$NUMProc $R $CONFIG #& 2> ./mkREF/trimref.log
TrimReads #$NUMProc $R $CONFIG #& 2> ./mkBAM/trim.log
fi
if [ "$FUNKTION" == "trimFQref" ]; then
echo " ";echo " "`date` "Trimming reads "
TrimReadsRef #$NUMProc $R $CONFIG #& 2> ./mkREF/trimref.log
fi
if [ "$FUNKTION" == "trimFQmap" ]; then
echo " ";echo " "`date` "Trimming reads "
TrimReads #$NUMProc $R $CONFIG #& 2> ./mkBAM/trim.log
fi
if [ "$FUNKTION" == "mkREF" ]; then
Assemble #$NUMProc $CONFIG $Rsed $NumInd $Fwild $Rwild $awk NAMES
fi
if [ "$FUNKTION" == "mkBAM" ]; then
MAP2REF #$CUTOFF.$CUTOFF2 $NUMProc $CONFIG $ATYPE $Rsed NAMES
fi
if [ "$FUNKTION" == "fltrBAM" ]; then
FILTERBAM #$CUTOFFS $NUMProc $CONFIG $ATYPE
fi
if [ "$FUNKTION" == "mkVCF" ]; then
GENOTYPE #$CUTOFFS $NUMProc $CONFIG
fi
##Checking for possible errors
# if [ "$MAP" != "no" ]; then
if [ "$FUNKTION" == "mkBAM" ]; then
ERROR1=$(mawk '/developer/' bwa* | wc -l 2>/dev/null)
fi
#CEB this was causing an error, there's no bam.log created
# ERROR2=$(mawk '/error/' *.bam.log | wc -l 2>/dev/null)
#ERRORS=$(($ERROR1 + $ERROR2))
#Move various log files to own directory
if [ ! -d "logfiles" ]; then
mkdir logfiles
fi
mv *.log log ./logfiles 2> /dev/null
#Sending a completion email
#CEB this was causing error: mawk: cannot open ./logfiles/Final.log (No such file or directory)
#if [ $ERRORS -gt 0 ]; then
# echo -e "dDocent has finished with errors in" `pwd` "\n\ndDocent started" $STARTTIME "\n\ndDocent finished" `date` "\n\nPlease check log files\n\n" `mawk '/After filtering, kept .* out of a possible/' ./logfiles/Final.log` "\n\ndDocent 2.24 \nThe 'd' is silent, hillbilly." | mailx -s "dDocent has finished with ERRORS!" $MAIL
#else
# echo -e "dDocent has finished with an analysis in" `pwd` "\n\ndDocent started" $STARTTIME "\n\ndDocent finished" `date` "\n\n" `mawk '/After filtering, kept .* out of a possible/' ./logfiles/Final.log` "\n\ndDocent 2.24 \nIt is pronounced Dee-Docent, professor." | mailx -s "dDocent has finished" $MAIL
#fi
#Creates (or appends to) a dDocent run file recording variables
#RMH added ALL variables
echo "Variables used in dDocent Run at" $STARTTIME >> dDocent.runs
echo "Number of Processors" >> dDocent.runs
echo $NUMProc >> dDocent.runs
echo "Maximum Memory" >> dDocent.runs
echo $MAXMemory >> dDocent.runs
echo "Trimming" >> dDocent.runs
echo $TRIM >> dDocent.runs
echo "TRIM_LENGTH_ASSEMBLY" >> dDocent.runs
echo $TRIM_LENGTH_ASSEMBLY >> dDocent.runs
echo "SEED_ASSEMBLY" >> dDocent.runs
echo $SEED_ASSEMBLY >> dDocent.runs
echo "PALIMDROME_ASSEMBLY" >> dDocent.runs
echo $PALIMDROME_ASSEMBLY >> dDocent.runs
echo "SIMPLE_ASSEMBLY" >> dDocent.runs
echo $SIMPLE_ASSEMBLY >> dDocent.runs
echo "windowSize_ASSEMBLY" >> dDocent.runs
echo $windowSize_ASSEMBLY >> dDocent.runs
echo "windowQuality_ASSEMBLY" >> dDocent.runs
echo $windowQuality_ASSEMBLY >> dDocent.runs
echo "TRAILING_ASSEMBLY" >> dDocent.runs
echo $TRAILING_ASSEMBLY >> dDocent.runs
echo "TRIM_LENGTH_MAPPING" >> dDocent.runs
echo $TRIM_LENGTH_MAPPING >> dDocent.runs
echo "LEADING_MAPPING" >> dDocent.runs
echo $LEADING_MAPPING >> dDocent.runs
echo "TRAILING_MAPPING" >> dDocent.runs
echo $TRAILING_MAPPING >> dDocent.runs
echo "HEADCROP" >> dDocent.runs
echo $HEADCROP >> dDocent.runs
echo "FixStacks" >> dDocent.runs
echo $FixStacks >> dDocent.runs
# echo "Assembly?" >> dDocent.runs
# echo $ASSEMBLY >> dDocent.runs
echo "Type_of_Assembly" >> dDocent.runs
echo $ATYPE >> dDocent.runs
echo "Clustering_Similarity%" >> dDocent.runs
echo $simC >> dDocent.runs
echo "HPC" >> dDocent.runs
echo $HPC >> dDocent.runs
echo "MANCUTOFF" >> dDocent.runs
echo $MANCUTOFF >> dDocent.runs
echo "CUTOFF" >> dDocent.runs
echo $CUTOFF >> dDocent.runs
echo "CUTOFF2" >> dDocent.runs
echo $CUTOFF2 >> dDocent.runs
# echo "Mapping_Reads?" >> dDocent.runs
# echo $MAP >> dDocent.runs
echo "Mapping_Match_Value" >> dDocent.runs
echo $optA >> dDocent.runs
echo "Mapping_MisMatch_Value" >> dDocent.runs
echo $optB >> dDocent.runs
echo "Mapping_GapOpen_Penalty" >> dDocent.runs
echo $optO >> dDocent.runs
echo "MAPPING_MIN_ALIGNMENT_SCORE" >> dDocent.runs
echo $MAPPING_MIN_ALIGNMENT_SCORE >> dDocent.runs
echo "MAPPING_CLIPPING_PENALTY" >> dDocent.runs
echo $MAPPING_CLIPPING_PENALTY >> dDocent.runs
echo "MAPPING_MIN_QUALITY" >> dDocent.runs
echo $MAPPING_MIN_QUALITY >> dDocent.runs
echo "SAMTOOLS_VIEW_F" >> dDocent.runs
echo $SAMTOOLS_VIEW_F >> dDocent.runs
# echo "Calling_SNPs?" >> dDocent.runs
# echo $SNP >> dDocent.runs
echo "POOLS" >> dDocent.runs
echo $POOLS >> dDocent.runs
echo "POOL_PLOIDY_FILE" >> dDocent.runs
echo $POOL_PLOIDY_FILE >> dDocent.runs
echo "PLOIDY" >> dDocent.runs
echo $PLOIDY >> dDocent.runs
echo "BEST_N_ALLELES" >> dDocent.runs
echo $BEST_N_ALLELES >> dDocent.runs
echo "MIN_MAPPING_QUAL" >> dDocent.runs
echo $MIN_MAPPING_QUAL >> dDocent.runs
echo "MIN_BASE_QUAL" >> dDocent.runs
echo $MIN_BASE_QUAL >> dDocent.runs
echo "HAPLOTYPE_LENGTH" >> dDocent.runs
echo $HAPLOTYPE_LENGTH >> dDocent.runs
echo "MIN_REPEAT_ENTROPY" >> dDocent.runs
echo $MIN_REPEAT_ENTROPY >> dDocent.runs
echo "MIN_COVERAGE" >> dDocent.runs
echo $MIN_COVERAGE >> dDocent.runs
echo "MIN_ALT_FRACTION" >> dDocent.runs
echo $MIN_ALT_FRACTION >> dDocent.runs
echo "FREEBAYES_C" >> dDocent.runs
echo $FREEBAYES_C >> dDocent.runs
echo "FREEBAYES_G" >> dDocent.runs
echo $FREEBAYES_G >> dDocent.runs
echo "FREEBAYES_z" >> dDocent.runs
echo $FREEBAYES_z >> dDocent.runs
echo "Email" >> dDocent.runs
echo $MAIL >> dDocent.runs
}
###############################################################################################
##Function definitions
###############################################################################################
##############################################################################################
#Function for correcting stacks file errors (antiquated?)
###############################################################################################
FIXSTACKS () {
echo "";echo " "`date` " Fixing Stacks anomalies"
#STACKS adds a strange _1 or _2 character to the end of processed reads, this looks for checks for errant characters and replaces them.
#This functionality is now parallelized and will run if only SE sequences are used.
STACKS=$(cat namelist.$CUTOFFS| parallel -j $NUMProc --no-notice "zcat {}$Fsed | head -1" | mawk '!/\/1/' | wc -l)
FB1=$(( $NUMProc / 2 ))
if [ $STACKS -gt 0 ]; then
echo " Removing the _1 character and replacing with /1 in the name of every sequence"
cat namelist.$CUTOFFS | parallel -j $FB1 --no-notice "zcat {}.$F.fq.gz | sed -e 's:_1$:/1:g' > {}.$F.fq"
rm $Fwild
cat namelist.$CUTOFFS | parallel -j $FB1 --no-notice "gzip {}.$F.fq"
fi
if [ -f "${NAMES[@]:(-1)}"$Rsed ]; then
STACKS=$(cat namelist.$CUTOFFS| parallel -j $NUMProc --no-notice "zcat {}$Rsed | head -1" | mawk '!/\/2/' | wc -l)
if [ $STACKS -gt 0 ]; then
echo " Removing the _2 character and replacing with /2 in the name of every sequence"
cat namelist.$CUTOFFS | parallel -j $FB1 --no-notice "zcat {}.$R.fq.gz | sed -e 's:_2$:/2:g' > {}.$R.fq"
rm $Rwild
cat namelist.$CUTOFFS | parallel -j $FB1 --no-notice "gzip {}.$R.fq"
fi
fi
}
##############################################################################################
#Function for trimming reads using trimmomatic
###############################################################################################
TrimReadsRef () {
# NUMProc=$1
# R=$2
# CONFIG=$3
echo " "
echo `date` "Trimming reads for reference genome"
TRIMMOMATIC=$(find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null | head -1)
ADAPTERS=$(find ${PATH//:/ } -maxdepth 2 -name TruSeq3-PE-2.fa 2> /dev/null | head -1)
# TRIM_LENGTH_ASSEMBLY=$(grep 'trimmomatic MINLEN (integer, mkREF only)' $CONFIG | awk '{print $1;}')
# SEED_ASSEMBLY=$(grep 'trimmomatic ILLUMINACLIP:<seed mismatches> (integer)' $CONFIG | awk '{print $1;}')
# PALIMDROME_ASSEMBLY=$(grep 'trimmomatic ILLUMINACLIP:<palindrome clip thresh> (integer)' $CONFIG | awk '{print $1;}')
# SIMPLE_ASSEMBLY=$(grep 'trimmomatic ILLUMINACLIP:<simple clip thresh> (integer)' $CONFIG | awk '{print $1;}')
# windowSize_ASSEMBLY=$(grep 'trimmomatic SLIDINGWINDOW:<windowSize> (integer)' $CONFIG | awk '{print $1;}')
# windowQuality_ASSEMBLY=$(grep 'trimmomatic SLIDINGWINDOW:<windowQuality> (integer)' $CONFIG | awk '{print $1;}')
# TRAILING_ASSEMBLY=$(grep 'trimmomatic TRAILING:<quality> (integer, mkREF only)' $CONFIG | awk '{print $1;}')
# HEADCROP=$(grep 'HEADCROP:<length> (integer, only Read1 for ezRAD)' $CONFIG | awk '{print $1;}')
echo "TRIMMOMATIC= $TRIMMOMATIC"
echo "ADAPTERS= $ADAPTERS"
echo "NUMProc= $NUMProc"
echo "SEED_ASSEMBLY= $SEED_ASSEMBLY"
echo "PALIMDROME_ASSEMBLY= $PALIMDROME_ASSEMBLY"
echo "SIMPLE_ASSEMBLY= $SIMPLE_ASSEMBLY"
echo "TRAILING_ASSEMBLY= $TRAILING_ASSEMBLY"
echo "windowSize_ASSEMBLY= $windowSize_ASSEMBLY"
echo "windowQuality_ASSEMBLY= $windowQuality_ASSEMBLY"
echo "TRIM_LENGTH_ASSEMBLY= $TRIM_LENGTH_ASSEMBLY"
echo "F= $F"
echo "R= $R"
if [ ! -d "mkREF" ]; then mkdir mkREF &>/dev/null; fi
if [ ! -d "./mkREF/unpaired" ]; then mkdir ./mkREF/unpaired &>/dev/null; fi
if [ ! -d "./mkREF/logs" ]; then mkdir ./mkREF/logs &>/dev/null; fi
if [ -f "${NAMES[1]}".$R.fq.gz ]; then
THREADS=1 #CEB I tried different numbers here and 1 seems to be best
Proc=$(($NUMProc/$THREADS))
echo "${NAMES[@]}" | sed 's/ /\n/g' | parallel --no-notice -j $Proc "java -jar $TRIMMOMATIC PE -threads $THREADS -phred33 {}.F.fq.gz {}.R.fq.gz ./mkREF/{}.r1.fq.gz ./mkREF/unpaired/{}.unpairedF.fq.gz ./mkREF/{}.r2.fq.gz ./mkREF/unpaired/{}.unpairedR.fq.gz ILLUMINACLIP:$ADAPTERS:$SEED_ASSEMBLY:$PALIMDROME_ASSEMBLY:$SIMPLE_ASSEMBLY HEADCROP:$HEADCROP TRAILING:$TRAILING_ASSEMBLY SLIDINGWINDOW:$windowSize_ASSEMBLY:$windowQuality_ASSEMBLY CROP:$TRIM_LENGTH_ASSEMBLY MINLEN:$TRIM_LENGTH_ASSEMBLY &> ./mkREF/logs/{}.trim.log"
else
echo "${NAMES[@]}" | sed 's/ /\n/g' | parallel --no-notice -j $NUMProc "java -jar $TRIMMOMATIC SE -threads 1 -phred33 {}.F.fq.gz ./mkREF/{}.r1.fq.gz ILLUMINACLIP:$ADAPTERS:$SEED_ASSEMBLY:$PALIMDROME_ASSEMBLY:$SIMPLE_ASSEMBLY HEADCROP:$HEADCROP TRAILING:$TRAILING_ASSEMBLY SLIDINGWINDOW:$windowSize_ASSEMBLY:$windowQuality_ASSEMBLY CROP:$TRIM_LENGTH_ASSEMBLY MINLEN:$TRIM_LENGTH_ASSEMBLY &> ./mkREF/logs/{}.trim.log"
fi
if [[ $HEADCROP != 0 ]]; then
echo "${NAMES[@]}" | sed 's/ /\n/g' | parallel --no-notice -j $NUMProc "java -jar $TRIMMOMATIC SE -threads 1 -phred33 ./mkREF/{}.r1.fq.gz ./mkREF/{}.r1.fq.gz.ezRAD HEADCROP:$HEADCROP &> ./mkREF/logs/{}.trim.log"
mkdir ./mkREF/unheadcropped
ls ./mkREF/*r1.fq.gz | parallel --no-notice "mv {} ./mkREF/unheadcropped"
rename .fq.gz.ezRAD .fq.gz ./mkREF/*.fq.gz.ezRAD
fi
#RMH housekeeping
# rm *_r1.fq.gz
}
##############################################################################################
#Function for trimming reads using trimmomatic
###############################################################################################
TrimReads () {
# NUMProc=$1
# R=$2
echo " "
echo; echo `date` "Trimming reads for mapping"
TRIMMOMATIC=$(find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null | head -1)
ADAPTERS=$(find ${PATH//:/ } -maxdepth 2 -name TruSeq3-PE-2.fa 2> /dev/null | head -1)
# TRIM_LENGTH_ASSEMBLY=$(grep 'trimmomatic MINLEN (integer, mkREF only)' $CONFIG | awk '{print $1;}')
# SEED_ASSEMBLY=$(grep 'trimmomatic ILLUMINACLIP:<seed mismatches> (integer)' $CONFIG | awk '{print $1;}')
# PALIMDROME_ASSEMBLY=$(grep 'trimmomatic ILLUMINACLIP:<palindrome clip thresh> (integer)' $CONFIG | awk '{print $1;}')
# SIMPLE_ASSEMBLY=$(grep 'trimmomatic ILLUMINACLIP:<simple clip thresh> (integer)' $CONFIG | awk '{print $1;}')
# windowSize_ASSEMBLY=$(grep 'trimmomatic SLIDINGWINDOW:<windowSize> (integer)' $CONFIG | awk '{print $1;}')
# windowQuality_ASSEMBLY=$(grep 'trimmomatic SLIDINGWINDOW:<windowQuality> (integer)' $CONFIG | awk '{print $1;}')
# TRAILING_ASSEMBLY=$(grep 'trimmomatic TRAILING:<quality> (integer, mkREF only)' $CONFIG | awk '{print $1;}')
# TRIM_LENGTH_MAPPING=$(grep 'trimmomatic MINLEN (integer, mkBAM only)' $CONFIG | awk '{print $1;}')
# LEADING_MAPPING=$(grep 'trimmomatic LEADING:<quality> (integer, mkBAM only)' $CONFIG | awk '{print $1;}')
# TRAILING_MAPPING=$(grep 'trimmomatic TRAILING:<quality> (integer, mkBAM only)' $CONFIG | awk '{print $1;}')
# HEADCROP=$(grep 'HEADCROP:<length> (integer, only Read1 for ezRAD)' $CONFIG | awk '{print $1;}')
if [ ! -d "mkBAM" ]; then mkdir mkBAM &>/dev/null; fi
if [ ! -d "./mkBAM/unpaired" ]; then mkdir ./mkBAM/unpaired &>/dev/null; fi
if [ ! -d "./mkBAM/logs" ]; then mkdir ./mkBAM/logs &>/dev/null; fi
if [ -f "${NAMES[1]}".$R.fq.gz ]; then
THREADS=1 #CEB I tried different numbers here and 1 seems to be best
Proc=$(($NUMProc/$THREADS))
echo "${NAMES[@]}" | sed 's/ /\n/g' | parallel --no-notice -j $Proc "java -jar $TRIMMOMATIC PE -threads $THREADS -phred33 {}.F.fq.gz {}.R.fq.gz ./mkBAM/{}.R1.fq.gz ./mkBAM/unpaired/{}.unpairedF.fq.gz ./mkBAM/{}.R2.fq.gz ./mkBAM/unpaired/{}.unpairedR.fq.gz ILLUMINACLIP:$ADAPTERS:$SEED_ASSEMBLY:$PALIMDROME_ASSEMBLY:$SIMPLE_ASSEMBLY HEADCROP:$HEADCROP LEADING:$LEADING_MAPPING TRAILING:$TRAILING_MAPPING SLIDINGWINDOW:$windowSize_ASSEMBLY:$windowQuality_ASSEMBLY MINLEN:$TRIM_LENGTH_MAPPING &> ./mkBAM/logs/{}.trim.log"
else
echo "${NAMES[@]}" | sed 's/ /\n/g' | parallel --no-notice -j $NUMProc "java -jar $TRIMMOMATIC SE -threads 1 -phred33 {}.F.fq.gz ./mkBAM/{}.R1.fq.gz ILLUMINACLIP:$ADAPTERS:$SEED_ASSEMBLY:$PALIMDROME_ASSEMBLY:$SIMPLE_ASSEMBLY HEADCROP:$HEADCROP LEADING:$LEADING_MAPPING TRAILING:$TRAILING_MAPPING SLIDINGWINDOW:$windowSize_ASSEMBLY:$windowQuality_ASSEMBLY MINLEN:$TRIM_LENGTH_MAPPING &> ./mkBAM/logs/{}.trim.log"
fi
if [[ $HEADCROP != 0 ]]; then
echo "${NAMES[@]}" | sed 's/ /\n/g' | parallel --no-notice -j $NUMProc "java -jar $TRIMMOMATIC SE -threads 1 -phred33 ./mkREF/{}.r1.fq.gz ./mkREF/{}.r1.fq.gz.ezRAD HEADCROP:$HEADCROP &> ./mkREF/logs/{}.trim.log"
mkdir ./mkREF/unheadcropped
ls ./mkREF/*r1.fq.gz | parallel --no-notice "mv {} ./mkREF/unheadcropped"
rename .fq.gz.ezRAD .fq.gz ./mkREF/*.fq.gz.ezRAD
fi
}
###############################################################################################
#Main function for assembly
###############################################################################################
Assemble(){
#Assemble $NUMProc $CONFIG $Rsed $NumInd $Fwild $Rwild $awk NAMES
# $NUMProc $CONFIG $Rsed $NumInd $Fwild $Rwild $awk NAMES
# NUMProc=$1
# CONFIG=$2
# Rsed=$3
# NumInd=$4
# Fwild=$5
# Rwild=$6
# awk=$7
# names=$8[@]
# NAMES=("${!names}")
# ATYPE=$(grep 'Type of reads for assembly (PE, SE, OL, RPE)' $CONFIG | awk '{print $1;}')
# simC=$(grep 'cdhit Clustering_Similarity_Pct (0-1)' $CONFIG | awk '{print $1;}')
# HPC=$(grep 'Get graphs for cutoffs, then stop? (yes or no)' $CONFIG | awk '{print $1;}')
# MANCUTOFF=$(grep 'Manually set cutoffs? (yes or no)' $CONFIG | awk '{print $1;}')
# if [ "$MANCUTOFF" = "no" ]; then
# CUTOFF=$(grep 'Cutoff1 (integer)' $CONFIG | awk '{print $1;}')
# CUTOFF2=$(grep 'Cutoff2 (integer)' $CONFIG | awk '{print $1;}')
# #echo ""; echo `date` " CUTOFF=" $CUTOFF
# #echo ""; echo `date` " CUTOFF2=" $CUTOFF2
# else
# echo ""; echo `date` " ERROR: This is the HPC version of dDocent. Manual cutoffs are not possible. Please change config file settings."
# echo " Aborting dDocentHPC"
# exit
# fi
# CUTOFFS=$CUTOFF.$CUTOFF2
AWK1='BEGIN{P=1}{if(P==1||P==2){gsub(/^[@]/,">");print}; if(P==4)P=0; P++}'
AWK2='!/>/'
AWK3='!/NNN/'
PERLT='while (<>) {chomp; $z{$_}++;} while(($k,$v) = each(%z)) {print "$v\t$k\n";}'
SED1='s/^[ ]*//'
SED2='s/ / /g'
FRL=$(zcat ${NAMES[0]}.r1.fq.gz | mawk '{ print length() | "sort -rn" }' | head -1)
if [ ! -s "namelistfr.$CUTOFFS" ];then
ls $Fwild > namelistfr.$CUTOFFS
ls $Rwild >> namelistfr.$CUTOFFS
sed -i'' -e "s/\.fq\.gz//g" namelistfr.$CUTOFFS
else
echo "";echo " The namelistfr file already exists and was not recreated."
echo " If you experience errors, you should delete the namelistfr file."
fi
#$$$$$$$$$$$CEB$$$$$$$$$$$$$$$$
#this block of code will either align or concatenate r1 & r2 seqs and create a file of unique sequences
echo " "; echo `date` " Reference Genome Assembly Step 1, Select Cutoffs"
if [ ${NAMES[@]:(-1)}.r1.fq.gz -nt ${NAMES[@]:(-1)}.uniq.seqs ];then
echo " ";echo `date` " the *.fq.gz files are newer than the *uniq.seqs files or the *.uniq.seq files do not exist"