binning supports single-end reads

CHANGELOG

@@ -2,13 +2,15 @@ metaWRAP v=0.9 (In development)
  General
  fixed major bug with running metawrap in a custom conda environments
  fixed bug caused by multiple metawrap installations
+ bin/metaWRAP excecutable is not a symlink pointing to bin/metawrap
  Bin_refinement
  fixed bug with plotting refinement iterations
  delete bins that have a size 0 after dereplication
  fixed shebang in summarize_checkm.py
  allowed pplacer to use multiple threads, drastically speeding up the module
  module no longer clears output DIR before starting. safer this way
  Binning
+ nos uspports single-end read inputs
  added metabat1 binning option
  fixed checkm tmp directory handling when using the --run-checkm option
  fixed perl5 library handling when running maxbin2

bin/metaWRAP

@@ -0,0 +1 @@
+metawrap

bin/metawrap

@@ -2,7 +2,7 @@
 #SBATCH
 #SBATCH --job-name=metaWRAP
 #SBATCH --partition=lrgmem
-#SBATCH --time=48:0:0
+#SBATCH --time=72:0:0
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=48
 #SBATCH --cpus-per-task=1
@@ -103,7 +103,7 @@ elif [ "$1" = "-h" ] || [ "$1" = "--help" ]; then
  exit 0
 elif [ "$1" = "-v" ] || [ "$1" = "--version" ]; then
  echo ""
- echo "metaWRAP v=0.8.9"
+ echo "metaWRAP v=0.9"
  echo ""
  exit 0
 else

bin/metawrap-modules/binning.sh

@@ -32,6 +32,7 @@ help_message () {
  echo " --maxbin2 bin contigs with MaxBin2"
  echo " --concoct bin contigs with CONCOCT (warning: this one is slow...)"
  echo " --run-checkm immediately run CheckM on the bin results"
+ echo " --single-end non-paired reads mode (provide *.fastq files)"
  echo "";}
 
 comm () { ${SOFT}/print_comment.py "$1" "-"; }
@@ -74,10 +75,11 @@ source $config_file
 # default params
 threads=1; mem=4; out=false; ASSEMBLY=false
 # long options defaults
-metabat1=false; metabat2=false; maxbin2=false; concoct=false; checkm=false
+metabat1=false; metabat2=false; maxbin2=false; concoct=false
+checkm=false; single_end=false
 
 # load in params
-OPTS=`getopt -o ht:m:o:a: --long help,metabat1,metabat2,maxbin2,concoct,run-checkm -- "$@"`
+OPTS=`getopt -o ht:m:o:a: --long help,metabat1,metabat2,maxbin2,concoct,run-checkm,single-end -- "$@"`
 # make sure the params are entered correctly
 if [ $? -ne 0 ]; then help_message; exit 1; fi
 
@@ -94,12 +96,12 @@ while true; do
  --maxbin2) maxbin2=true; shift 1;;
  --concoct) concoct=true; shift 1;;
  --run-checkm) checkm=true; shift 1;;
+ --single-end) single_end=true; shift 1;;
  --) help_message; exit 1; shift; break ;;
  *) break;;
  esac
 done
 
-
 ########################################################################################################
 ######################## MAKING SURE EVERYTHING IS SET UP ########################
 ########################################################################################################
@@ -113,24 +115,37 @@ fi
 #check if the assembly file exists
 if [ ! -s $ASSEMBLY ]; then error "$ASSEMBLY does not exist. Exiting..."; fi
 
-# check for at least one pair of read fastq files:
-F="no"; R="no"
-for num in "$@"; do
- if [[ $num == *"_1.fastq" ]]; then F="yes"; fi
- if [[ $num == *"_2.fastq" ]]; then R="yes"; fi
-done
-if [ $F = "no" ] || [ $R = "no" ]; then
- comm "Unable to find proper fastq read pair in the format *_1.fastq and *_2.fastq"
- help_message; exit 1
+if [ $single_end = false ]; then
+ # check for at least one pair of read fastq files:
+ F="no"; R="no"
+ for num in "$@"; do
+ if [[ $num == *"_1.fastq" ]]; then F="yes"; fi
+ if [[ $num == *"_2.fastq" ]]; then R="yes"; fi
+ done
+ if [ $F = "no" ] || [ $R = "no" ]; then
+ comm "Unable to find proper fastq read pair in the format *_1.fastq and *_2.fastq"
+ help_message; exit 1
+ fi
+else
+ # check for at least one fastq read
+ F="no"
+ for num in "$@"; do
+ if [[ $num == *".fastq" ]]; then F="yes"; fi
+ done
+ if [ $F = "no" ]; then
+ comm "Unable to find read files in format *.fastq (for single-end reads)"
+ help_message; exit 1
+ fi
 fi
 
-#determine number of fastq read files provided:
-num_of_F_read_files=$(for I in "$@"; do echo $I | grep _1.fastq; done | wc -l)
-num_of_R_read_files=$(for I in "$@"; do echo $I | grep _2.fastq; done | wc -l)
-
-comm "$num_of_F_read_files forward and $num_of_R_read_files reverse read files detected"
-if [ ! $num_of_F_read_files == $num_of_R_read_files ]; then error "Number of F and R reads must be the same!"; fi
+if [ $single_end = false ]; then
+ #determine number of fastq read files provided:
+ num_of_F_read_files=$(for I in "$@"; do echo $I | grep _1.fastq; done | wc -l)
+ num_of_R_read_files=$(for I in "$@"; do echo $I | grep _2.fastq; done | wc -l)
 
+ comm "$num_of_F_read_files forward and $num_of_R_read_files reverse read files detected"
+ if [ ! $num_of_F_read_files == $num_of_R_read_files ]; then error "Number of F and R reads must be the same!"; fi
+fi
 
 # Make sure at least one binning method was chosen
 if [ $metabat2 = false ] && [ $metabat1 = false ] &&[ $maxbin2 = false ] && [ $concoct = false ]; then
@@ -171,35 +186,56 @@ comm "Indexing assembly file"
 bwa index ${out}/work_files/assembly.fa
 if [[ $? -ne 0 ]] ; then error "Something went wrong with indexing the assembly. Exiting."; fi
 
-echo -e "sample\tsample_size\tmean\tstdev" > ${out}/insert_sizes.txt
+if [ $single_end = false ]; then
+ echo -e "sample\tsample_size\tmean\tstdev" > ${out}/insert_sizes.txt
+fi
+
 # If there are several pairs of reads passed, they are processed sepperately
 for num in "$@"; do
- if [[ $num == *"_1.fastq"* ]]; then 
- reads_1=$num
- reads_2=${num%_*}_2.fastq
- if [ ! -s $reads_1 ]; then error "$reads_1 does not exist. Exiting..."; fi
- if [ ! -s $reads_2 ]; then error "$reads_2 does not exist. Exiting..."; fi
-
- tmp=${reads_1##*/}
- sample=${tmp%_*}
-
- if [[ ! -f ${out}/work_files/${sample}.bam ]]; then
- comm "Aligning $reads_1 and $reads_2 back to assembly, sorting the alignment, and gathering statistics on insert lengths"
- echo -n -e "${sample}\t" >> ${out}/insert_sizes.txt
- bwa mem -t $threads ${out}/work_files/assembly.fa $reads_1 $reads_2\
- | tee >( awk '{ if ($9 > 0) { N+=1; S+=$9; S2+=$9*$9 }} END { M=S/N; print ""N"\t "M"\t "sqrt ((S2-M*M*N)/(N-1))}'\
- >> ${out}/insert_sizes.txt ) \
- | samtools view -@ $threads -bS - | samtools sort -T ${out}/work_files/tmp-samtools -@ $threads -O bam \
- -o ${out}/work_files/${sample}.bam -
+ if [ $single_end = false ]; then
+ if [[ $num == *"_1.fastq"* ]]; then 
+ reads_1=$num
+ reads_2=${num%_*}_2.fastq
+ if [ ! -s $reads_1 ]; then error "$reads_1 does not exist. Exiting..."; fi
+ if [ ! -s $reads_2 ]; then error "$reads_2 does not exist. Exiting..."; fi
+
+ tmp=${reads_1##*/}
+ sample=${tmp%_*}
 
- if [[ $? -ne 0 ]]; then error "Something went wrong with aligning/sorting the reads to the assembly!"; fi
- else
- comm "skipping aligning $sample reads to assembly because ${out}/work_files/${sample}.bam already exists."
+ if [[ ! -f ${out}/work_files/${sample}.bam ]]; then
+ comm "Aligning $reads_1 and $reads_2 back to assembly, sorting the alignment, and gathering statistics on insert lengths"
+ echo -n -e "${sample}\t" >> ${out}/insert_sizes.txt
+ bwa mem -t $threads ${out}/work_files/assembly.fa $reads_1 $reads_2\
+ | tee >( awk '{ if ($9 > 0) { N+=1; S+=$9; S2+=$9*$9 }} END { M=S/N; print ""N"\t "M"\t "sqrt ((S2-M*M*N)/(N-1))}'\
+ >> ${out}/insert_sizes.txt ) \
+ | samtools view -@ $threads -bS - | samtools sort -T ${out}/work_files/tmp-samtools -@ $threads -O bam \
+ -o ${out}/work_files/${sample}.bam -
+
+ if [[ $? -ne 0 ]]; then error "Something went wrong with aligning/sorting the reads to the assembly!"; fi
+ else
+ comm "skipping aligning $sample reads to assembly because ${out}/work_files/${sample}.bam already exists."
+ fi
  fi
  fi
-done
-
 
+ if [ $single_end = true ]; then
+ if [[ $num == *".fastq"* ]]; then
+ reads=$num
+ if [ ! -s $reads ]; then error "$reads does not exist. Exiting..."; fi
+ tmp=${reads##*/}
+ sample=${tmp%.*}
+ if [[ ! -f ${out}/work_files/${sample}.bam ]]; then
+ comm "Aligning $reads back to assembly, and sorting the alignment"
+ bwa mem -t $threads ${out}/work_files/assembly.fa $reads \
+ | samtools view -@ $threads -bS - | samtools sort -T ${out}/work_files/tmp-samtools -@ $threads -O bam \
+ -o ${out}/work_files/${sample}.bam -
+ if [[ $? -ne 0 ]]; then error "Something went wrong with aligning/sorting the reads to the assembly!"; fi
+ else
+ comm "skipping aligning $sample reads to assembly because ${out}/work_files/${sample}.bam already exists."
+ fi
+ fi
+ fi 
+done
 
 
 if [ $metabat2 = true ]; then
@@ -225,6 +261,23 @@ fi
 
 
 
+if [ $metabat1 = true ]; then
+ ########################################################################################################
+ ######################## RUNNING METABAT1 ########################
+ ########################################################################################################
+ announcement "RUNNING METABAT1"
+
+ comm "making contig depth file..."
+ jgi_summarize_bam_contig_depths --outputDepth ${out}/work_files/metabat_depth.txt ${out}/work_files/*.bam
+ if [[ $? -ne 0 ]]; then error "Something went wrong with making contig depth file. Exiting."; fi
+
+ comm "Starting binning with metaBAT2..."
+ metabat1 -i ${out}/work_files/assembly.fa -a ${out}/work_files/metabat_depth.txt\
+ -o ${out}/metabat1_bins/bin -m 1500 -t $threads --unbinned --superspecific
+ if [[ $? -ne 0 ]]; then error "Something went wrong with running MetaBAT1. Exiting"; fi
+
+
+
 if [ $metabat1 = true ]; then
  ########################################################################################################
  ######################## RUNNING METABAT1 ########################
@@ -303,23 +356,6 @@ if [ $maxbin2 = true ]; then
  if [[ $? -ne 0 ]]; then error "Something went wrong with running MaxBin2. Exiting."; fi
  if [[ $(ls ${out}/work_files/maxbin2_out/ | grep bin | grep .fasta | wc -l) -lt 1 ]]; then error "MaxBin2 did not pruduce a single bin. Something went wrong. Exiting."; fi
 
- mkdir ${out}/maxbin2_bins
- N=0
- for i in $(ls ${out}/work_files/maxbin2_out/ | grep bin | grep .fasta); do
- cp ${out}/work_files/maxbin2_out/$i ${out}/maxbin2_bins/bin.${N}.fa
- N=$((N + 1))
- done
- comm "MaxBin2 finished successfully, and found $(ls -l ${out}/maxbin2_bins | grep .fa | wc -l) bins!"
-
- if [ $checkm = true ]; then
- run_checkm ${out}/maxbin2_bins
- fi
-fi
-
-
-if [ $concoct = true ]; then
- ########################################################################################################
- ######################## RUNNING CONCOCT ########################
  ########################################################################################################
  announcement "RUNNING CONCOCT"