Change queue on SGE

launch_expansionhunter.sh

@@ -14,7 +14,7 @@
 ## last revision date : 20191102
 ## Known bugs : None
 
-INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
+INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
 DATE="$(date +"%F_%H-%M-%S")"
 OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunter/$DATE"
 OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
@@ -27,5 +27,5 @@ then
     INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_expansionhunter.sh"
 else 
     mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh
+    qsub -pe smp 1 -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh
 fi

launch_gangstr.sh

@@ -11,10 +11,10 @@
 
 ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
 ## Creation Date : 20191104
-## last revision date : 20191104
+## last revision date : 20191117
 ## Known bugs : None
 
-INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
+INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
 DATE="$(date +"%F_%H-%M-%S")"
 OUTPUTDIR="/work/gad/shared/analyse/STR/GangSTR/$DATE"
 OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
@@ -27,5 +27,5 @@ then
     INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_gangstr.sh"
 else 
     mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_gangstr.sh
+    qsub -pe smp 1 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_gangstr.sh
 fi

launch_hipstr.sh

@@ -14,7 +14,7 @@
 ## last revision date : 20191104
 ## Known bugs : None
 
-INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
+INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
 DATE="$(date +"%F_%H-%M-%S")"
 OUTPUTDIR="/work/gad/shared/analyse/STR/HipSTR/$DATE"
 OUTPUTPREFIX="$OUTPUTDIR/$(basename -s .bam "$INPUTFILE")_$DATE"
@@ -28,5 +28,5 @@ then
     INPUTFILE="$INPUTFILE" OUTPUTFILE="$OUTPUTFILE" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_hipstr.sh"
 else 
     mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_hipstr.sh
+    qsub -pe smp 2 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTFILE="$OUTPUTFILE",LOGFILE="$LOGFILE" wrapper_hipstr.sh
 fi

launch_lobstr.sh

@@ -14,7 +14,7 @@
 ## last revision date : 20191104
 ## Known bugs : None
 
-INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
+INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
 DATE="$(date +"%F_%H-%M-%S")"
 OUTPUTDIR="/work/gad/shared/analyse/STR/LobSTR/$DATE"
 OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
@@ -27,5 +27,5 @@ then
     INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_lobstr.sh"
 else 
     mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_lobstr.sh
+    qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_lobstr.sh
 fi

launch_tredparse.sh

@@ -14,7 +14,7 @@
 ## last revision date : 20191103
 ## Known bugs : None
 
-INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
+INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
 DATE="$(date +"%F_%H-%M-%S")"
 OUTPUTDIR="/work/gad/shared/analyse/STR/Tredparse/$DATE"
 LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log"
@@ -26,5 +26,5 @@ then
     INPUTFILE="$INPUTFILE" OUTPUTDIR="$OUTPUTDIR" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_tredparse.sh"
 else 
     mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 1 -q transfer -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$LOGFILE" wrapper_tredparse.sh
+    qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$LOGFILE" wrapper_tredparse.sh
 fi

wrapper_hipstr.sh

@@ -50,9 +50,10 @@ echo "command : FIXME"
 /work/gad/shared/bin/hipstr/HipSTR-2019-11-04/HipSTR \
     --bams "$INPUTFILE" \
     --fasta /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
-    --regions /work/gad/shared/bin/hipstr/STRregions/hg19.hipstr_reference.bed \
     --str-vcf "$OUTPUTFILE"
 
+#    --regions /work/gad/shared/bin/hipstr/STRregions/hg19.hipstr_reference.bed
+
 hipstr_exitcode=$?
 
 echo "hipstr exit code : $hipstr_exitcode"