Bugzzz

prstoolkit.sh

@@ -314,9 +314,9 @@ else
 # 		
 # 		cat ${SUBPROJECTDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.keep.txt | awk '{ print $2 }' > ${SUBPROJECTDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.keeptofilter.txt
 # 		
-# 		for CHR in $(seq 1 22) X; do 
+		for CHR in $(seq 1 22) X; do 
 		### FOR DEBUGGING
-		for CHR in 22; do
+		### for CHR in 22; do
 
 			echo ""
 			echo "* processing chromosome ${CHR} and extracting relevant variants."
@@ -325,7 +325,7 @@ else
 
 			echo ""
 			echo "* converting to PLINK-binary format."
-			echo "${QCTOOL} -g ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.gen -s ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.sample -threshhold ${THRESHOLD} ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR} -ofiletype binary_ped" > ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.convert.sh
+			echo "${QCTOOL} -g ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.gen -s ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.sample -threshhold ${THRESHOLD} -og ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR} -ofiletype binary_ped" > ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.convert.sh
 			qsub -S /bin/bash -N PRS.CONVERT.${VALIDATIONNAME}.chr${CHR} -hold_jid PRS.FILTER.${VALIDATIONNAME}.chr${CHR} -o ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.convert.log -e ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.convert.errors -l h_vmem=${QMEMCONVERT} -l h_rt=${QRUNTIMECONVERT} -wd ${PARSEDDIR} ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.convert.sh
 
 			echo ""
@@ -351,7 +351,7 @@ else
 
 			echo ""
 			echo "* processing chromosome ${CHR} and converting to PLINK-binary format."
-			echo "${QCTOOL} -g ${VALIDATIONDATA}/${VALIDATIONFILE}${CHR}.gen.gz -s ${VALIDATIONDATA}/${VALIDATIONFILE}${CHR}.sample -threshhold ${THRESHOLD} ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR} -ofiletype binary_ped" > ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.convert.sh
+			echo "${QCTOOL} -g ${VALIDATIONDATA}/${VALIDATIONFILE}${CHR}.gen.gz -s ${VALIDATIONDATA}/${VALIDATIONFILE}${CHR}.sample -threshhold ${THRESHOLD} -og ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR} -ofiletype binary_ped" > ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.convert.sh
 			qsub -S /bin/bash -N PRS.CONVERT.${VALIDATIONNAME}.chr${CHR} -o ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.convert.log -e ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.convert.errors -l h_vmem=${QMEMCONVERT} -l h_rt=${QRUNTIMECONVERT} -wd ${PARSEDDIR} ${PARSEDDIR}/${VALIDATIONNAME}.${POPULATION}.${REFERENCE}.chr${CHR}.convert.sh
 
 		done