projects/radseq/novogene/dosamW.sh

   1 #!/bin/bash
   2 #$ -v PERL5LIB,PATH,PYTHONPATH,LD_LIBRARY_PATH
   3 #$ -cwd -r y -l vf=3.2g,p=5
   4 #$ -e /dev/null
   5 #$ -S /bin/bash -t 1-20
   6
   7 MY_HOST=`/bin/hostname`
   8 MY_DATE=`/bin/date`
   9 env
  10 echo "================================================================"
  11 echo JOB_NAME=$JOB_NAME
  12 echo JOB_ID=$JOB_ID
  13 echo SGE_TASK_ID=$SGE_TASK_ID
  14 echo SGE_TASK_FIRST=$SGE_TASK_FIRST
  15 echo SGE_TASK_LAST=$SGE_TASK_LAST
  16 echo NSLOTS=$NSLOTS
  17 echo QUEUE=$QUEUE
  18 echo SGE_CWD_PATH=$SGE_CWD_PATH
  19 echo PATH=$PATH
  20 echo SGE_STDIN_PATH=$SGE_STDIN_PATH
  21 echo SGE_STDOUT_PATH=$SGE_STDOUT_PATH
  22 echo SGE_STDERR_PATH=$SGE_STDERR_PATH
  23 echo SGE_O_HOST=$SGE_O_HOST
  24 echo SGE_O_PATH=$SGE_O_PATH
  25 echo "================================================================"
  26
  27 echo "Running job JOB_NAME=$JOB_NAME task SGE_TASK_ID=$SGE_TASK_ID on $MY_HOST at $MY_DATE"
  28 echo "Running job JOB_NAME=$JOB_NAME task SGE_TASK_ID=$SGE_TASK_ID on $MY_HOST at $MY_DATE" >out/p/$MAIN.samlog
  29
  30 SEEDFILE=ng/fqmW.lst
  31 SEED=$(/bin/sed -n -e "${SGE_TASK_ID} p" $SEEDFILE)
  32 PATH=$(/bin/sed -n -e "${SGE_TASK_ID} p" $SEEDFILE|/bin/awk -F"\t" '{print $1}')
  33 MAIN=$(/bin/sed -n -e "${SGE_TASK_ID} p" $SEEDFILE|/bin/awk -F"\t" '{print $2}')
  34 /usr/local/bin/bwa aln -l 17 -q 10 -t 6 cat62 $PATH/$MAIN.1.fq.gz >out/p/$MAIN.1.sai 2>>out/p/$MAIN.samlog
  35 /bin/date >> out/p/$MAIN.samlog
  36 /usr/local/bin/bwa aln -l 17 -q 10 -t 6 cat62 $PATH/$MAIN.2.fq.gz >out/p/$MAIN.2.sai 2>>out/p/$MAIN.samlog
  37 /bin/date >> out/p/$MAIN.samlog
  38 /usr/local/bin/bwa sampe -a 800 cat62 out/p/$MAIN.1.sai out/p/$MAIN.2.sai $PATH/$MAIN.1.fq.gz $PATH/$MAIN.2.fq.gz 2>>out/p/$MAIN.samlog | /bin/gzip -9c >out/p/$MAIN.rawsam.gz
  39 /bin/date >> out/p/$MAIN.samlog
  40 /usr/bin/perl ng/pickR1orR2XTUreads.pl out/p/$MAIN.rawsam.gz out/p/$MAIN.sam.gz
  41 /bin/date >> out/p/$MAIN.samlog
  42 /usr/local/bin/samtools view -bS out/p/$MAIN.sam.gz >out/p/$MAIN.bam 2>>out/p/$MAIN.samlog
  43 /usr/local/bin/samtools sort -m 3200000000 out/p/$MAIN.bam out/p/$MAIN.sort
  44 #/usr/local/bin/samtools rmdup out/p/$MAIN.sort.bam out/p/$MAIN.rmdup.bam
  45 /bin/date >> out/p/$MAIN.samlog
  46