Did you provide the read group information to bowtie2? If so, show the parameters you used.

Here is the script I am using to run Bowtie2....Where would I add the read group information?

#!/bin/bash
#shell
#$ -S /bin/bash
#$ -pe smp_2 10

##### export OMPI_MCA_orte_rsh_agent="rsh:ssh"
##### export LD_LIBRARY_PATH=/usr/global/openmpi-1.5.3-w-psm/lib:$LD_LIBRARY_PATH
#####
#
#    variables that need to be set/changed by user
#
#####

######
#
#   unpaired reads:  script is set up to handle up to 5 (use UNPAIRED_READ_1...UNPAIRED_READ_5) to specify basenames 
#
######

export UNPAIRED_READ_1="GEO_Rep2_FAIRE_P1B9_S2_R2_001_Trimmomatic"            ## JOB_NAME WILL be based on read_1
          ## BASENAME for read_2 (no filetype extension)
          ## BASENAME for first file containing unpaired reads

export REFERENCE_GENOME="mm9.RM"    ## genome against which alignments are to be made

#
#   Build unpaired read list from basenames specified above
#   also move various files to $TMPDIR and uncompress if applicable 
#

export UNPAIRED_READS=${TMPDIR}/${UNPAIRED_READ_1}.fastq          ### UNPAIRED_READ_1
gzip ${SGE_O_WORKDIR}/${UNPAIRED_READ_1}.fastq
cp ${SGE_O_WORKDIR}/${UNPAIRED_READ_1}.fastq.gz ${TMPDIR}
gunzip ${TMPDIR}/${UNPAIRED_READ_1}.fastq.gz

if env | grep -q ^UNPAIRED_READ_2=
then
  export UNPAIRED_READS=${UNPAIRED_READS},${TMPDIR}/${UNPAIRED_READ_2}.fastq    ### UNPAIRED_READ_2
  gzip ${SGE_O_WORKDIR}/${UNPAIRED_READ_2}.fastq
  cp ${SGE_O_WORKDIR}/${UNPAIRED_READ_2}.fastq.gz ${TMPDIR}
  gunzip ${TMPDIR}/${UNPAIRED_READ_2}.fastq.gz
fi

if env | grep -q ^UNPAIRED_READ_3=
then
  export UNPAIRED_READS=${UNPAIRED_READS},${TMPDIR}/${UNPAIRED_READ_3}.fastq    ### UNPAIRED_READ_3
  gzip ${SGE_O_WORKDIR}/${UNPAIRED_READ_3}.fastq
  cp ${SGE_O_WORKDIR}/${UNPAIRED_READ_3}.fastq.gz ${TMPDIR}
  gunzip ${TMPDIR}/${UNPAIRED_READ_3}.fastq.gz
fi

if env | grep -q ^UNPAIRED_READ_4=
then
  export UNPAIRED_READS=${UNPAIRED_READS},${TMPDIR}/${UNPAIRED_READ_4}.fastq   ### UNPAIRED_READ_4
  gzip ${SGE_O_WORKDIR}/${UNPAIRED_READ_4}.fastq
  cp ${SGE_O_WORKDIR}/${UNPAIRED_READ_4}.fastq.gz ${TMPDIR}
  gunzip ${TMPDIR}/${UNPAIRED_READ_4}.fastq.gz
fi

if env | grep -q ^UNPAIRED_READ_5=
then
  export UNPAIRED_READS=${UNPAIRED_READS},${TMPDIR}/${UNPAIRED_READ_5}.fastq    ### UNPAIRED_READ_5
  gzip ${SGE_O_WORKDIR}/${UNPAIRED_READ_5}.fastq
  cp ${SGE_O_WORKDIR}/${UNPAIRED_READ_5}.fastq.gz ${TMPDIR}
  gunzip ${TMPDIR}/${UNPAIRED_READ_5}.fastq.gz
fi
printenv UNPAIRED_READS

### ls -l $TMPDIR
##### export UNPAIRED_READS=${TMPDIR}/${UNPAIRED_READ_1}.fastq,${TMPDIR}/${UNPAIRED_READ_2}.fastq,${TMPDIR}/${UNPAIRED_READ_3}.fastq

#
#   Set up our executable path so that we have mpirun and friends as well as mpiblast and associates in
#      our executable path
#

export BOWTIE2_PATH=/usr/global/bowtie2-2.1.0/bin   ## PATH to bowtie2 suite
export TWOBIT_PATH=/home/jscarsda/bin/x86_64
export PATH=$BOWTIE2_PATH:$PATH

#
#   environment variable BOWTIE2_INDEXES specifies directory where reference genomes reside if not in current directory
#

export BOWTIE2_INDEXES=/home/jlandry/reference_genomes_mm9_masked

#
#    compress the data to be aligned to enable more efficient copying of data to $TMPDIR, which is a unique directory on
#    the /tmp filesystem on the node on which this job is running.  This directory is created by the queueing system for
#    our job.
#

#### gzip ${SGE_O_WORKDIR}/${UNPAIRED_READ_1}.fastq
#### gzip ${SGE_O_WORKDIR}/${UNPAIRED_READ_2}.fastq
#### gzip ${SGE_O_WORKDIR}/${UNPAIRED_READ_3}.fastq

#
#  copy files containing reads to be aligned to ${TMPDIR} since local I/O is much faster than nfs I/O
#
#

#
#   run bowtie2 to perform alignments
#

time bowtie2-align -p $NSLOTS -N 1 -x $REFERENCE_GENOME -U $UNPAIRED_READS \
                                                        -S ${TMPDIR}/${UNPAIRED_READ_1}.${JOB_ID}.sam --no-unal

#
#    gzip output sam file
#

gzip ${TMPDIR}/${UNPAIRED_READ_1}.${JOB_ID}.sam

#
#   copy compressed sam file back to home directory
#

cp ${TMPDIR}/${UNPAIRED_READ_1}.${JOB_ID}.sam.gz ${SGE_O_WORKDIR}