#!/bin/bash
# Grid Engine Options
#$ -l c7
#$ -N VE_sequential
#$ -l h_vmem=4G,h_rt=72:00:00
#$ -j y
#$ -pe mp 21
WORKDIR=/SCRATCH/cricasre/Metagen
FILTERDIR=/SCRATCH/cricasre/Metagen/trimming
SQUEEZEDIR=/home/cricasre/SqueezeMeta

########################
### SQUEEZE ANALYSIS ###
########################

# Sample file for Squeeze

DT=$(date "+%Y/%m/%d %H:%M:%S")
echo "$DT:Creating samples files for SqueezeMeta"

mkdir -p $WORKDIR
cd $WORKDIR

if [ ! -f samples_clean.txt ]
 then
  cd $FILTERDIR
  ls *fastq.gz|sed "s/_filter_R1.fastq.gz//g"|sed "s/_filter_R2.fastq.gz//g" >ID
  ls *fastq.gz > fastq
  ls *fastq.gz|sed 's/.*R2.fastq.gz/pair2/g'|sed 's/.*R1.fastq.gz/pair1/g' >pair
  paste ID fastq pair > $WORKDIR/samples_clean.txt
  rm ID fastq pair
 fi

#Execution SqueezeMeta
cd $WORKDIR

DT=$(date "+%Y/%m/%d %H:%M:%S")
echo "$DT:Staring SqueezeMeta"
pwd

#Seqmerge analysis
SQUEEZEDIR/scripts/SqueezeMeta.pl -p filter_merge17754 -m seqmerge -s samples_clean.txt -f $FILTERDIR -t 21 -b 14