bug fix on job dependency issue

    # aligning read2, and merging the two. Keep track of merge names for final 

    # merge. When merge jobs successfully finish, can launch final merge job.  

    if [ -n "$threads" ] && [ -z "$skipsplit" ]

    then

        waitstring_alnwrp="#PBS -W depend=afterok:${jID_splitmv}"

    fi

    echo "waitstring_alnwrp is ${waitstring_alnwrp}"

    timestamp=$(date +"%s" | cut -c 4-10)

    qsub <<ALIGNWRAP

    #PBS -S /bin/bash

    #PBS -o ${logdir}/${timestamp}_alnwrap_${groupname}.log

    #PBS -j oe

    #PBS -N AlnWrp${groupname}

    #PBS -W depend=afterok:${jID_splitmv}

    $waitstring_alnwrp

    ${EMAIL}

    #PBS -m a

    for i in ${read1}