projects/radseq/novogene/dot.sh

   1 #!/bin/bash
   2 #$ -v PERL5LIB,PATH,PYTHONPATH,LD_LIBRARY_PATH
   3 #$ -cwd -r y -l vf=0.9g,p=1
   4 #$ -S /bin/bash -t 1-2
   5
   6
   7 MY_HOST=`/bin/hostname`
   8 MY_DATE=`/bin/date`
   9 echo "================================================================"
  10 echo JOB_NAME=$JOB_NAME
  11 echo JOB_ID=$JOB_ID
  12 echo SGE_TASK_ID=$SGE_TASK_ID
  13 echo SGE_TASK_FIRST=$SGE_TASK_FIRST
  14 echo SGE_TASK_LAST=$SGE_TASK_LAST
  15 echo NSLOTS=$NSLOTS
  16 echo QUEUE=$QUEUE
  17 echo SGE_CWD_PATH=$SGE_CWD_PATH
  18 echo PATH=$PATH
  19 echo SGE_STDIN_PATH=$SGE_STDIN_PATH
  20 echo SGE_STDOUT_PATH=$SGE_STDOUT_PATH
  21 echo SGE_STDERR_PATH=$SGE_STDERR_PATH
  22 echo SGE_O_HOST=$SGE_O_HOST
  23 echo SGE_O_PATH=$SGE_O_PATH
  24 echo "================================================================"
  25
  26 echo "Running job JOB_NAME=$JOB_NAME task SGE_TASK_ID=$SGE_TASK_ID on $MY_HOST at $MY_DATE"
  27 echo "Running job JOB_NAME=$JOB_NAME task SGE_TASK_ID=$SGE_TASK_ID on $MY_HOST at $MY_DATE" >out/$MAIN.sailog
  28
  29 SEEDFILE=ng/t.lst
  30 SEED=$(/bin/sed -n -e "${SGE_TASK_ID} p" $SEEDFILE)
  31 PATH=$(/bin/sed -n -e "${SGE_TASK_ID} p" $SEEDFILE|/bin/awk -F"\t" '{print $1}')
  32 MAIN=$(/bin/sed -n -e "${SGE_TASK_ID} p" $SEEDFILE|/bin/awk -F"\t" '{print $2}')
  33 /usr/local/bin/bwa aln -l 17 -q 10 -t 6 cat62 $PATH/$MAIN.1.fq.gz >out/$MAIN.1.sai 2>>out/$MAIN.sailog
  34 /bin/date >> out/$MAIN.sailog
  35 /usr/local/bin/bwa aln -l 17 -q 10 -t 6 cat62 $PATH/$MAIN.2.fq.gz >out/$MAIN.2.sai 2>>out/$MAIN.sailog
  36 /bin/date >> out/$MAIN.sailog
  37 /usr/local/bin/bwa sampe -a 800 cat62 out/$MAIN.1.sai out/$MAIN.2.sai $PATH/$MAIN.1.fq.gz $PATH/$MAIN.2.fq.gz 2>>out/$MAIN.sailog | /bin/gzip -9c >out/$MAIN.rawsam.gz
  38 /bin/date >> out/$MAIN.sailog
  39 /usr/bin/perl ng/pickR1orR2XTUreads.pl out/$MAIN.rawsam.gz out/$MAIN.sam.gz
  40 /bin/date >> out/$MAIN.sailog
  41 /usr/local/bin/samtools view -bS out/$MAIN.sam.gz >out/$MAIN.bam 2>>out/$MAIN.sailog
  42 /usr/local/bin/samtools sort -m 3200000000 out/$MAIN.bam out/$MAIN.sort
  43 /usr/local/bin/samtools rmdup out/$MAIN.sort.bam out/$MAIN.rmdup.bam
  44 /bin/date >> out/$MAIN.sailog
  45