diff --git a/compute5/NGS_Automated/copyProjectDataToPrm.sh b/compute5/NGS_Automated/copyProjectDataToPrm.sh
index 7372878e..8878c993 100755
--- a/compute5/NGS_Automated/copyProjectDataToPrm.sh
+++ b/compute5/NGS_Automated/copyProjectDataToPrm.sh
@@ -35,7 +35,7 @@ echo "Logfiles will be written to $LOGDIR"
 for line in ${ARR[@]}
 do
         projectName=${line}
-        LOGGER=${LOGDIR}/${projectName}.copyProjectDataToPrm.logger
+        LOGGER=${LOGDIR}/${projectName}/${projectName}.copyProjectDataToPrm.logger
 
         FINISHED="no"
 
@@ -49,7 +49,7 @@ do
 	makeProjectDataDir=$(ssh ${groupname}-dm@calculon.hpc.rug.nl "sh ${PROJECTSDIRPRM}/checkProjectData.sh ${PROJECTSDIRPRM} ${projectName}")	
 	
 	copyProjectDataDiagnosticsClusterToPrm="${PROJECTSDIR}/${projectName}/* ${groupname}-dm@calculon.hpc.rug.nl:${PROJECTSDIRPRM}/${projectName}"
-	if [[ -f $LOGDIR/${projectName}/${projectName}.pipeline.finished && ! -f $LOGDIR/${projectName}/${projectName}.projectDataCopiedToPrm ]]
+	if [[ -d $LOGDIR/${projectName}/ && ! -f $LOGDIR/${projectName}/${projectName}.projectDataCopiedToPrm ]]
 	then
 		countFilesProjectDataDirTmp=$(ls -R ${PROJECTSDIR}/${projectName}/*/results/ | wc -l)
 		module load hashdeep/4.4-foss-2015b
@@ -76,19 +76,16 @@ do
                                 then
                                         echo "md5sum check failed, the copying will start again" >> ${LOGGER}
                                         rsync -r -av --exclude rawdata/ ${copyProjectDataDiagnosticsClusterToPrm} >> $LOGGER 2>&1
-					echo "copy failed" >> $LOGDIR/${projectName}.copyProjectDataToPrm.failed
+					echo "copy failed" >> $LOGDIR/${projectName}/${projectName}.copyProjectDataToPrm.failed
                                 elif [[ "${COPIEDTOPRM}" == *"PASS"* ]]
                                 then
-                                        touch $LOGDIR/${projectName}.projectDataCopiedToPrm
+                                        touch $LOGDIR/${projectName}/${projectName}.projectDataCopiedToPrm
 					echo "finished copying project data to calculon" >> ${LOGGER}
 					printf "De project data voor project ${projectName} is gekopieerd naar ${PROJECTSDIRPRM}" | mail -s "project data for project ${projectName} is copied to permanent storage" ${ONTVANGER}
 
-					mv $LOGDIR/${projectName}.projectDataCopiedToPrm $LOGDIR/${projectName}/
-					mv $LOGDIR/${projectName}.copyProjectDataToPrm.logger $LOGDIR/${projectName}/
-
-				  	if [ -f $LOGDIR/${projectName}.copyProjectDataToPrm.failed ] 
+				  	if [ -f $LOGDIR/${projectName}/${projectName}.copyProjectDataToPrm.failed ] 
                                         then
-						rm $LOGDIR/${projectName}.copyProjectDataToPrm.failed
+						rm $LOGDIR/${projectName}/${projectName}.copyProjectDataToPrm.failed
 					fi
                                 fi
                         else
@@ -98,9 +95,9 @@ do
                 fi
         fi
 
-	if [ -f $LOGDIR/${projectName}.copyProjectDataToPrm.failed ]
+	if [ -f $LOGDIR/${projectName}/${projectName}.copyProjectDataToPrm.failed ]
 	then
-		COUNT=$(cat $LOGDIR/${projectName}.copyProjectDataToPrm.failed | wc -l)
+		COUNT=$(cat $LOGDIR/${projectName}/${projectName}.copyProjectDataToPrm.failed | wc -l)
 		if [ $COUNT == 10  ]
 		then
 			HOSTNA=$(hostname)
diff --git a/compute5/NGS_Automated/copyRawDataToDiagnosticsCluster.sh b/compute5/NGS_Automated/copyRawDataToDiagnosticsCluster.sh
index 744d8637..0cf90cc1 100755
--- a/compute5/NGS_Automated/copyRawDataToDiagnosticsCluster.sh
+++ b/compute5/NGS_Automated/copyRawDataToDiagnosticsCluster.sh
@@ -29,19 +29,18 @@ for line in ${gattacaSamplesheets[@]}
 do
 	csvFile=$(basename $line)
 	filePrefix="${csvFile%.*}"
-	LOGGER=${LOGDIR}/${filePrefix}.copyToDiagnosticsCluster.logger
+	LOGGER=${LOGDIR}/${filePrefix}/${filePrefix}.copyToDiagnosticsCluster.logger
 
-	if [ -d ${LOGDIR}/${filePrefix}/ ]
+	if [ ! -d ${LOGDIR}/${filePrefix}/ ]
 	then
-		echo "everything is finished of ${filePrefix}"
-		continue
+		mkdir ${LOGDIR}/${filePrefix}/
 	fi
  
 	function finish {
-		if [ -f ${LOGDIR}/${filePrefix}.copyToDiagnosticsCluster.locked ]
+		if [ -f ${LOGDIR}/${filePrefix}/${filePrefix}.copyToDiagnosticsCluster.locked ]
         	then
 	        	echo "TRAPPED"
-        		rm ${LOGDIR}/${filePrefix}.copyToDiagnosticsCluster.locked
+        		rm ${LOGDIR}/${filePrefix}/${filePrefix}.copyToDiagnosticsCluster.locked
 		fi
 	}
 	trap finish HUP INT QUIT TERM EXIT ERR
@@ -62,24 +61,24 @@ do
 		continue;
 	fi
 
-	if [ -f $LOGDIR/${filePrefix}.dataCopiedToDiagnosticsCluster ]
+	if [ -f $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToDiagnosticsCluster ]
 	then
 		continue;
 	fi
 
-	if [ -f ${LOGDIR}/${filePrefix}.copyToDiagnosticsCluster.locked ]
+	if [ -f ${LOGDIR}/${filePrefix}/${filePrefix}.copyToDiagnosticsCluster.locked ]
 	then
 		exit 0
 	fi
-	touch ${LOGDIR}/${filePrefix}.copyToDiagnosticsCluster.locked
+	touch ${LOGDIR}/${filePrefix}/${filePrefix}.copyToDiagnosticsCluster.locked
 
 	## Check if samplesheet is copied
 	copyRawGatToDiagnosticsCluster="umcg-ateambot@${gattacaAddress}:${GATTACA}/runs/run_${run}_${sequencer}/results/${filePrefix}* ${RAWDATADIR}/$filePrefix"
 
-	if [[ ! -f ${SAMPLESHEETSDIR}/$csvFile || ! -f $LOGDIR/${filePrefix}.SampleSheetCopied ]]
+	if [[ ! -f ${SAMPLESHEETSDIR}/$csvFile || ! -f $LOGDIR/${filePrefix}/${filePrefix}.SampleSheetCopied ]]
         then
                 scp umcg-ateambot@${gattacaAddress}:${GATTACA}/Samplesheets/${csvFile} ${SAMPLESHEETSDIR}
-                touch $LOGDIR/${filePrefix}.SampleSheetCopied
+                touch $LOGDIR/${filePrefix}/${filePrefix}.SampleSheetCopied
         fi
 	## Check if data is already copied to DiagnosticsCluster
 
@@ -91,7 +90,7 @@ do
 	fi
 
 
-	if [[ -d ${RAWDATADIR}/$filePrefix  && ! -f $LOGDIR/${filePrefix}.dataCopiedToDiagnosticsCluster ]]
+	if [[ -d ${RAWDATADIR}/$filePrefix  && ! -f $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToDiagnosticsCluster ]]
 	then
 		##Compare how many files are on both the servers in the directory
 		countFilesRawDataDirTmp=$(ls ${RAWDATADIR}/${filePrefix}/${filePrefix}* | wc -l)
@@ -110,7 +109,7 @@ do
 				then
 					echo "data copied to DiagnosticsCluster" >> $LOGGER
 					printf ".. done \n" >> $LOGGER
-					touch $LOGDIR/${filePrefix}.dataCopiedToDiagnosticsCluster
+					touch $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToDiagnosticsCluster
 					touch ${filePrefix}.md5sums.checked
 				else
 					echo "md5sum check failed, the copying will start again" >> $LOGGER
@@ -124,7 +123,7 @@ do
 			echo "data copied to DiagnosticsCluster" >> $LOGGER
 		fi
 	fi
-rm ${LOGDIR}/${filePrefix}.copyToDiagnosticsCluster.locked
+rm ${LOGDIR}/${filePrefix}/${filePrefix}.copyToDiagnosticsCluster.locked
 done
 
 trap - EXIT
diff --git a/compute5/NGS_Automated/copyRawDataToPrm.sh b/compute5/NGS_Automated/copyRawDataToPrm.sh
index 5abc3596..e5183c1a 100755
--- a/compute5/NGS_Automated/copyRawDataToPrm.sh
+++ b/compute5/NGS_Automated/copyRawDataToPrm.sh
@@ -35,7 +35,7 @@ for line in ${ARR[@]}
 do
         csvFile=$(basename $line)
         filePrefix="${csvFile%.*}"
-        LOGGER=${LOGDIR}/${filePrefix}.copyToPrm.logger
+        LOGGER=${LOGDIR}/${filePrefix}/${filePrefix}.copyToPrm.logger
 
         FINISHED="no"
         OLDIFS=$IFS
@@ -45,11 +45,6 @@ do
         run=$3
         IFS=$OLDIFS
 
-	if [ -d ${LOGDIR}/${filePrefix}/ ]
-        then
-                continue
-        fi
-
         if [ -f ${LOGDIR}/copyDataToPrm.sh.locked ]
         then
 		echo "copyToPrm is locked"
@@ -61,12 +56,6 @@ do
 	##get header to decide later which column is project
         HEADER=$(head -1 ${line})
 
-        if [ -d ${LOGDIR}/${filePrefix}/ ]
-        then
-            	echo "(startPipeline) everything is finished of ${filePrefix}"
-                continue
-        fi
-
 	##Remove header, only want to keep samples
         sed '1d' $line > ${LOGDIR}/TMP/${filePrefix}.utmp
         OLDIFS=$IFS
@@ -96,7 +85,7 @@ do
 	copyRawDiagnosticsClusterToPrm="${RAWDATADIR}/${filePrefix}/* ${groupname}-dm@calculon.hpc.rug.nl:${RAWDATADIRPRM}/${filePrefix}"
 	makeRawDataDir=$(ssh ${groupname}-dm@calculon.hpc.rug.nl "sh ${RAWDATADIRPRM}/../checkRawData.sh ${RAWDATADIRPRM} ${filePrefix}")
 
-	if [[ -f $LOGDIR/${filePrefix}.dataCopiedToDiagnosticsCluster && ! -f $LOGDIR/${filePrefix}.dataCopiedToPrm ]]
+	if [[ -f $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToDiagnosticsCluster && ! -f $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToPrm ]]
 	then
 		countFilesRawDataDirTmp=$(ls ${RAWDATADIR}/${filePrefix}/${filePrefix}* | wc -l)
 		if [ "${makeRawDataDir}" == "f" ]
@@ -115,22 +104,20 @@ do
                                 then
                                         echo "md5sum check failed, the copying will start again" >> ${LOGGER}
                                         rsync -r -av ${copyRawDiagnosticsClusterToPrm} >> $LOGGER 2>&1
-					echo "copy failed" >> $LOGDIR/${filePrefix}.failed
+					echo "copy failed" >> $LOGDIR/${filePrefix}/${filePrefix}.failed
                                 elif [[ "${COPIEDTOPRM}" == *"PASS"* ]]
                                 then
 					scp ${SAMPLESHEETSDIR}/${csvFile} ${groupname}-dm@calculon.hpc.rug.nl:${RAWDATADIRPRM}/${filePrefix}/
 					scp ${SAMPLESHEETSDIR}/${csvFile} ${groupname}-dm@calculon.hpc.rug.nl:${SAMPLESHEETSPRMDIR}
 					echo "finished copying data to calculon" >> ${LOGGER}
-
-					mkdir $LOGDIR/${filePrefix}/
-					echo "Moving ${filePrefix} logfiles to $LOGDIR/${filePrefix}/ and removing tmp finished files" >> $LOGGER
 					
-					rm $LOGDIR/${filePrefix}.SampleSheetCopied
-					rm $LOGDIR/${filePrefix}.dataCopiedToDiagnosticsCluster
-					mv $LOGDIR/${filePrefix}.copyToDiagnosticsCluster.logger $LOGDIR/${filePrefix}/
-					mv $LOGDIR/${filePrefix}.copyToPrm.logger $LOGDIR/${filePrefix}/
-					mv ${LOGDIR}/TMP/${filePrefix}.unique.projects $LOGDIR/${filePrefix}/projects.txt
+					#rm $LOGDIR/${filePrefix}.SampleSheetCopied
+					#rm $LOGDIR/${filePrefix}.dataCopiedToDiagnosticsCluster
+					#mv $LOGDIR/${filePrefix}.copyToDiagnosticsCluster.logger $LOGDIR/${filePrefix}/
+					#mv $LOGDIR/${filePrefix}.copyToPrm.logger $LOGDIR/${filePrefix}/
+					#mv ${LOGDIR}/TMP/${filePrefix}.unique.projects $LOGDIR/${filePrefix}/projects.txt
 					echo "finished with rawdata" >> ${LOGDIR}/${filePrefix}/${filePrefix}.copyToPrm.logger
+
 					if ls ${RAWDATADIR}/${filePrefix}/${filePrefix}*.log 1> /dev/null 2>&1
 					then
 						logFileStatistics=$(cat ${RAWDATADIR}/${filePrefix}/${filePrefix}*.log)
@@ -140,9 +127,9 @@ do
 						fi
 						echo -e "De data voor project ${filePrefix} is gekopieerd naar ${RAWDATADIRPRM}" | mail -s "${filePrefix} copied to permanent storage" ${ONTVANGER}
 					fi
-				  	if [ -f $LOGDIR/${filePrefix}.failed ] 
+				  	if [ -f $LOGDIR/${filePrefix}/${filePrefix}.failed ] 
                                         then
-						rm $LOGDIR/${filePrefix}.failed
+						rm $LOGDIR/${filePrefix}/${filePrefix}.failed
 					fi
                                 fi
                         else
@@ -153,9 +140,9 @@ do
                 fi
         fi
 
-	if [ -f $LOGDIR/${filePrefix}.failed ]
+	if [ -f $LOGDIR/${filePrefix}/${filePrefix}.failed ]
 	then
-		COUNT=$(cat $LOGDIR/${filePrefix}.failed | wc -l)
+		COUNT=$(cat $LOGDIR/${filePrefix}/${filePrefix}.failed | wc -l)
 		if [ $COUNT == 10  ]
 		then
 			HOSTNA=$(hostname)
diff --git a/compute5/NGS_Automated/pipelineFinished.sh b/compute5/NGS_Automated/pipelineFinished.sh
index dc04802a..abd8ff38 100644
--- a/compute5/NGS_Automated/pipelineFinished.sh
+++ b/compute5/NGS_Automated/pipelineFinished.sh
@@ -22,47 +22,28 @@ for i in ${ALLFINISHED[@]}
 do
 	filename=$(basename $i)
 	projectName="${filename%%.*}"
-	if [ ! -d ${LOGDIR}/${projectName}/ ]
-	then
-		mkdir -p ${LOGDIR}/${projectName}/
-		for i in $(ls ${PROJECTSDIR}/${projectName}/*/rawdata/ngs/*); do if [ -L $i ];then readlink $i > ${LOGDIR}/${projectName}.rawdatalink ; fi;done
+	for i in $(ls ${PROJECTSDIR}/${projectName}/*/rawdata/ngs/*); do if [ -L $i ];then readlink $i > ${LOGDIR}/${projectName}/${projectName}.rawdatalink ; fi;done
 
-		while read line ; do dirname $line > ${LOGDIR}/${projectName}.rawdatalinkDirName; done<${LOGDIR}/${projectName}.rawdatalink
+	while read line ; do dirname $line > ${LOGDIR}/${projectName}/${projectName}.rawdatalinkDirName; done<${LOGDIR}/${projectName}/${projectName}.rawdatalink
 
-		rawDataName=$(while read line ; do basename $line ; done<${LOGDIR}/${projectName}.rawdatalinkDirName)
-
-		if [ -f ${LOGDIR}/${rawDataName}.pipeline.logger ]
-		then
-			mv ${LOGDIR}/${rawDataName}.pipeline.logger ${LOGDIR}/${rawDataName}/
-		fi
-		if [ -f ${LOGDIR}/${rawDataName}.scriptsGenerated ]
-		then
-			mv ${LOGDIR}/${rawDataName}.scriptsGenerated ${LOGDIR}/${rawDataName}/
-		fi
+		rawDataName=$(while read line ; do basename $line ; done<${LOGDIR}/${projectName}/${projectName}.rawdatalinkDirName)
 
 		echo "moving ${projectName} files to ${LOGDIR}/${projectName}/ and removing tmp finished files"
-		if [[ -f ${LOGDIR}/${projectName}.pipeline.logger  && -f ${LOGDIR}/${projectName}.pipeline.started && -f ${LOGDIR}/${projectName}.rawdatalink && -f ${LOGDIR}/${projectName}.rawdatalinkDirName ]]
+		if [[ -f ${LOGDIR}/${projectName}/${projectName}.pipeline.logger  && -f ${LOGDIR}/${projectName}/${projectName}.pipeline.started && -f ${LOGDIR}/${projectName}/${projectName}.rawdatalink && -f ${LOGDIR}/${projectName}/${projectName}.rawdatalinkDirName ]]
 		then 
-			mv ${LOGDIR}/${projectName}.pipeline.logger ${LOGDIR}/${projectName}/
-			rm ${LOGDIR}/${projectName}.pipeline.started
-			rm ${LOGDIR}/${projectName}.rawdatalink
-			rm ${LOGDIR}/${projectName}.rawdatalinkDirName
 			touch ${LOGDIR}/${projectName}/${rawDataName}
+			mv ${LOGDIR}/${projectName}.pipeline.finished ${LOGDIR}/${projectName}/
+
+		else
+			echo "there is/are missing some files:${projectName}.pipeline.logger or  ${projectName}.pipeline.started or ${projectName}/${projectName}.rawdatalink or ${projectName}.rawdatalinkDirName"
+			echo "there is/are missing some files:${projectName}.pipeline.logger or  ${projectName}.pipeline.started or ${projectName}/${projectName}.rawdatalink or ${projectName}.rawdatalinkDirName" >> ${LOGDIR}/${projectName}/${projectName}.pipeline.logger
 		fi
-		if [ -f ${LOGDIR}/${projectName}.pipeline.failed ]
-		then
-			mv ${LOGDIR}/${projectName}.pipeline.failed ${LOGDIR}/${projectName}/
-		fi
-	fi
 	if [ ! -f ${LOGDIR}/${projectName}/${projectName}.pipeline.finished.mailed ]
 	then
 		printf "The results can be found: ${PROJECTSDIR}/${projectName} \n\nCheers from the GCC :)"| mail -s "NGS_DNA pipeline is finished for project ${projectName} on `date +%d/%m/%Y` `date +%H:%M`" ${ONTVANGER}
 		touch ${LOGDIR}/${projectName}/${projectName}.pipeline.finished.mailed
-		rm ${LOGDIR}/${projectName}.pipeline.finished
 
 	fi
 
-
-
 done
 
diff --git a/compute5/NGS_Automated/startPipeline.sh b/compute5/NGS_Automated/startPipeline.sh
index 98c4ffd0..2aa96872 100755
--- a/compute5/NGS_Automated/startPipeline.sh
+++ b/compute5/NGS_Automated/startPipeline.sh
@@ -32,12 +32,6 @@ do
 	##get header to decide later which column is project
 	HEADER=$(head -1 ${i})
 
-	if [ -d ${LOGDIR}/${filePrefix}/ ]
-        then
-                echo "(startPipeline) everything is finished of ${filePrefix}"
-                continue
-        fi
-
 	##Remove header, only want to keep samples
 	sed '1d' $i > ${LOGDIR}/TMP/${filePrefix}.tmp
 	OLDIFS=$IFS
@@ -77,7 +71,7 @@ do
 	miSeqRun="no"
 	while read line
         do
-        	if [[ "${line}" == *"CARDIO"* || "${line}" == *"DER_v1"* || "${line}" == *"DYS_v3"* || "${line}" == *"EPI_v3"* || "${line}" == *"LEVER_v1"* || "${line}" == *"NEURO_v1"* || "${line}" == *"ONCO_v1"* || "${line}" == *"PCS_v1"* ]]
+        	if [[ "${line}" == *"CARDIO_v"* || "${line}" == *"DER_v"* || "${line}" == *"DYS_v"* || "${line}" == *"EPI_v"* || "${line}" == *"LEVER_v"* || "${line}" == *"NEURO_v"* || "${line}" == *"ONCO_v"* || "${line}" == *"PCS_v"* ]]
 		then
 			miSeqRun="yes"
 			break
@@ -90,13 +84,13 @@ do
         sequencer=$2
         run=$3
 	IFS=$OLDIFS
-        LOGGER=${LOGDIR}/${filePrefix}.pipeline.logger
+        LOGGER=${LOGDIR}/${filePrefix}/${filePrefix}.pipeline.logger
 
 	####
 	### Decide if the scripts should be created (per Samplesheet)
 	##
 	#
-	if [[ -f $LOGDIR/${filePrefix}.dataCopiedToDiagnosticsCluster && ! -f $LOGDIR/${filePrefix}.scriptsGenerated ]]
+	if [[ -f $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToDiagnosticsCluster  && ! -f $LOGDIR/${filePrefix}/${filePrefix}.scriptsGenerated ]]
         then
                	### Step 4: Does the pipeline need to run?
                	if [ "${pipeline}" == "RNA-Lexogen-reverse" ]
@@ -149,7 +143,7 @@ do
 			cd scripts
 
 			sh submit.sh
-			touch $LOGDIR/${filePrefix}.scriptsGenerated
+			touch $LOGDIR/${filePrefix}/${filePrefix}.scriptsGenerated
 		fi
 	fi
 
@@ -157,20 +151,25 @@ do
 	### If generatedscripts is already done, step in this part to submit the jobs (per project)
 	##
 	#
-	if [ -f $LOGDIR/${filePrefix}.scriptsGenerated ] 
+	if [ -f $LOGDIR/${filePrefix}/${filePrefix}.scriptsGenerated ] 
 	then
 		for PROJECT in ${PROJECTARRAY[@]}
 		do
+			if [ ! -d ${LOGDIR}/${PROJECT} ]
+			then
+				mkdir ${LOGDIR}/${PROJECT}
+			fi
+ 
 			WHOAMI=$(whoami)
 			HOSTN=$(hostname)
-		        LOGGER=${LOGDIR}/${PROJECT}.pipeline.logger
-			if [ ! -f ${LOGDIR}/${PROJECT}.pipeline.started ]
+		        LOGGER=${LOGDIR}/${PROJECT}/${PROJECT}.pipeline.logger
+			if [ ! -f ${LOGDIR}/${PROJECT}/${PROJECT}.pipeline.started ]
 			then
 				cd ${PROJECTSDIR}/${PROJECT}/run01/jobs/
 				sh submit.sh
 
-				touch ${LOGDIR}/${PROJECT}.pipeline.started
-				echo "${LOGDIR}/${PROJECT} started" >> $LOGGER
+				touch ${LOGDIR}/${PROJECT}/${PROJECT}.pipeline.started
+				echo "${PROJECT} started" >> $LOGGER
 
 				printf "Pipeline: ${pipeline}\nStarttime:`date +%d/%m/%Y` `date +%H:%M`\nProject: $PROJECT\nStarted by: $WHOAMI\nHost: ${HOSTN}\n\nProgress can be followed via the command squeue -u $WHOAMI on $HOSTN.\nYou will receive an email when the pipeline is finished!\n\nCheers from the GCC :)" | mail -s "NGS_DNA pipeline is started for project $PROJECT on `date +%d/%m/%Y` `date +%H:%M`" ${ONTVANGER}
 				sleep 40