Commit 7e5bb5e2 authored by Swati Parekh's avatar Swati Parekh
Browse files

final commit after slurm debugging

parent 0cf89e92

listPrefix.sh

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mergeBAM.sh

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splitfq.sh

100644 → 100755
+2 −1
Original line number Diff line number Diff line
@@ -32,6 +32,7 @@ function splitfqgz() { 
	project=$6



  n=`expr $nreads / $nthreads`

  n=`expr $n + 1`

  nl=`expr $n \* 4`

  pref=`basename $fqfile .gz`

  d=`dirname $fqfile`

zUMIs-config_shiny.R

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zUMIs-master.sh

+22 −20
Original line number Diff line number Diff line
@@ -144,33 +144,35 @@ then 


    if [[ $f =~ \.gz$ ]]; then

      echo "splitfq"

      for i in $fqfiles;do sbatch --cpus-per-task=1 --job-name=splitfq --mem=10M --wrap="bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfqgz $project $f" > $outdir/$project.splitfq.slurmjobid.txt;done

      for i in $fqfiles;do sbatch --cpus-per-task=1 --job-name=splitfq --mem=10M --wrap="bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfqgz $project $f" >> $outdir/$project.slurmjobid.txt;done

    else

      for i in $fqfiles;do sbatch --cpus-per-task=1 --job-name=splitfq --mem=10M --wrap="bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfq $project $f" > $outdir/$project.splitfq.slurmjobid.txt;done

      for i in $fqfiles;do sbatch --cpus-per-task=1 --job-name=splitfq --mem=10M --wrap="bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfq $project $f" >> $outdir/$project.slurmjobid.txt;done

    fi



    j=`cat $outdir/$project.splitfq.slurmjobid.txt | cut -f4 -d' '`

    j=`cat $outdir/$project.slurmjobid.txt | cut -f4 -d' ' | tr '\n' ':' | sed 's/.$//'`

	echo $j

    sbatch --cpus-per-task=1 --job-name=listPrefix --dependency=afterok:$j --mem=1M --wrap="bash $zumisdir/listPrefix.sh $zumisdir $tmpMerge $f $project $yaml $samtoolsexc $Rexc $pigzexc" >> $outdir/$project.slurmjobid.txt

	echo "listPrefix"

    j=`cat $outdir/$project.slurmjobid.txt | cut -f4 -d' ' | tr '\n' ':' | sed 's/.$//'`

	echo $j

  #  for x in `cat $tmpMerge/$project.listPrefix.txt`;do sbatch --cpus-per-task=$num_threads --dependency=afterok:$j --mem=10M --wrap="bash $zumisdir/fqfilter_v2.pl $yaml $samtoolsexc $Rexc $pigzexc $zumisdir $x" > $outdir/$project.slurmjobid.txt;done



    sbatch --cpus-per-task=1 --job-name=listPrefix --dependency=afterok:'$j' --mem=1M --wrap="bash $zumisdir/listPrefix.sh $zumisdir $tmpMerge $f $project $yaml $samtoolsexc $Rexc $pigzexc" > $outdir/$project.listPrefix.slurmjobid.txt

  #  j=`cat $outdir/$project.slurmjobid.txt | cut -f4 -d' ' | tr '\n' ':' | sed 's/.$//'`



    j=`cat $outdir/$project.listPrefix.slurmjobid.txt | cut -f4 -d' '`

    sbatch --cpus-per-task=1 --job-name=mergeBAM --dependency=afterok:$j --mem=1M --wrap="bash $zumisdir/mergeBAM.sh $zumisdir $tmpMerge $num_threads $project $outdir $yaml" >> $outdir/$project.slurmjobid.txt



  #  for x in `cat $tmpMerge/$project.listPrefix.txt`;do sbatch --cpus-per-task=$num_threads --dependency=afterok:'$j' --mem=10M --wrap="bash $zumisdir/fqfilter_v2.pl $yaml $samtoolsexc $Rexc $pigzexc $zumisdir $x" > $outdir/$project.fqfilter_v2.slurmjobid.txt;done



  #  j=`cat $outdir/$project.fqfilter_v2.slurmjobid.txt | cut -f4 -d' '`



    sbatch --cpus-per-task=1 --job-name=splitfq=mergeBAM --dependency=afterok:'$j' --mem=1M --wrap="bash $zumisdir/mergeBAM.sh $zumisdir $tmpMerge $num_threads $project $outdir $yaml" > $outdir/$project.mergeBAM.slurmjobid.txt



    j=`cat $outdir/$project.mergeBAM.slurmjobid.txt | cut -f4 -d' '`

    j=`cat $outdir/$project.slurmjobid.txt | cut -f4 -d' ' | tr '\n' ':' | sed 's/.$//'`



  else



    if [[ $f =~ \.gz$ ]]; then

      for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfqgz $project $f;done

      for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfqgz $project $f & done

      wait

      pref=`basename $f .gz`

      l=`ls $tmpMerge$pref* | sed "s|$tmpMerge$pref||" | sed 's/.gz//'`

    else

      for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfq $project $f;done

      for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfq $project $f & done

      wait

      pref=`basename $f`

      l=`ls $tmpMerge$pref* | sed "s|$tmpMerge$pref||"`

    fi
@@ -188,8 +190,8 @@ then 
  echo "Starting Mapping..."

  if [[ "$isslurm" == "yes" ]]; then

    memory=`du -sh $genomedir | cut -f1` #STAR genome index size

    j=`cat $outdir/$project.mergeBAM.slurmjobid.txt | cut -f4 -d' '`

    sbatch --dependency=afterok:'$j' --job-name=mapping --mem=$memory --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-mapping.R $yaml" > $outdir/$project.mapping.slurmjobid.txt

    j=`cat $outdir/$project.slurmjobid.txt | cut -f4 -d' ' | tr '\n' ':' | sed 's/.$//'`

    sbatch --dependency=afterok:$j --job-name=mapping --mem=$memory --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-mapping.R $yaml" >> $outdir/$project.slurmjobid.txt

  else

    $Rexc $zumisdir/zUMIs-mapping.R $yaml

  fi
@@ -208,8 +210,8 @@ then 
    else

      mem_limit=`expr $mem_limit \* 1000`

    fi

    j=`cat $outdir/$project.mapping.slurmjobid.txt | cut -f4 -d' '`

    sbatch --dependency=afterok:'$j' --mem=$mem_limit --job-name=dge --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-dge2.R $yamlnew" > $outdir/$project.dge.slurmjobid.txt

    j=`cat $outdir/$project.slurmjobid.txt | cut -f4 -d' ' | tr '\n' ':' | sed 's/.$//'`

    sbatch --dependency=afterok:$j --mem=$mem_limit --job-name=dge --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-dge2.R $yamlnew" >> $outdir/$project.slurmjobid.txt

   else

     $Rexc $zumisdir/zUMIs-dge2.R $yamlnew

   fi
@@ -225,8 +227,8 @@ then 
  if [[ "$isstats" == "yes" ]]; then

    echo "Starting descriptive statistics..."

    if [[ "$isslurm" == "yes" ]]; then

      j=`cat $outdir/$project.dge.slurmjobid.txt | cut -f4 -d' '`

      sbatch --dependency=afterok:'$j' --mem=5000 --job-name=stats --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-stats2.R $yamlnew" > $outdir/$project.stats.slurmjobid.txt

      j=`cat $outdir/$project.slurmjobid.txt | cut -f4 -d' ' | tr '\n' ':' | sed 's/.$//'`

      sbatch --dependency=afterok:$j --mem=5000 --job-name=stats --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-stats2.R $yamlnew" >> $outdir/$project.slurmjobid.txt

    else

      $Rexc $zumisdir/zUMIs-stats2.R $yamlnew

    fi

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