edits to the error and log file generation - they should include the …

…specific slidenumber for debugging and failures;
swvanderlaan · Sep 4, 2021 · 8e20e7d · 8e20e7d
1 parent e6d57a2
commit 8e20e7d
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/slideQuantify b/slideQuantify
@@ -224,7 +224,7 @@ else
 		echo ""
 		echoitalic "* slideEMask, which will mask, create a macro, and do NDPISplit when necessary. [ $THIS_SLIDEMASK ]"
 
-# 		JOB_ID_THIS_SLIDEMASK=$(sbatch -J ${THIS_SLIDEMASK} -e ${PROJECTDIR}/errors/slidemask.errors -o ${PROJECTDIR}/logs/slidemask.log ${HOLD_JID_STRING} --mem=${QJOB_MEM_SLIDEMASK} --time=${QJOB_TIME_SLIDEMASK} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable ${SLIDETOOLKITDIR}/slideQuantify_mask.sh ${EMASKTHRESHOLD} )
+		JOB_ID_THIS_SLIDEMASK=$(sbatch -J ${THIS_SLIDEMASK} -e ${PROJECTDIR}/errors/slidemask.${THIS_SLIDEMASK}.errors -o ${PROJECTDIR}/logs/slidemask.${THIS_SLIDEMASK}.log ${HOLD_JID_STRING} --mem=${QJOB_MEM_SLIDEMASK} --time=${QJOB_TIME_SLIDEMASK} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable ${SLIDETOOLKITDIR}/slideQuantify_mask.sh ${EMASKTHRESHOLD} )
 
 		### FOR DEBUG
 		### echocyan "Debug mode - listing slide number and job-id."
@@ -236,29 +236,29 @@ else
 		echo ""
 		echoitalic "* slide2Tiles to create tiles from images. [ $THIS_SLIDE2TILES ]"
 
-# 		JOB_ID_THIS_SLIDE2TILES=$(sbatch -J ${THIS_SLIDE2TILES} -e ${PROJECTDIR}/errors/slide2tiles.errors -o ${PROJECTDIR}/logs/slide2tiles.log --mem=${QJOB_MEM_SLIDE2TILES} --time=${QJOB_TIME_SLIDE2TILES} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --depend=afterany:$JOB_ID_THIS_SLIDEMASK --parsable ${SLIDETOOLKITDIR}/slideQuantify_tiling.sh)
+		JOB_ID_THIS_SLIDE2TILES=$(sbatch -J ${THIS_SLIDE2TILES} -e ${PROJECTDIR}/errors/slide2tiles.${THIS_SLIDE2TILES}.errors -o ${PROJECTDIR}/logs/slide2tiles.${THIS_SLIDE2TILES}.log --mem=${QJOB_MEM_SLIDE2TILES} --time=${QJOB_TIME_SLIDE2TILES} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --depend=afterany:$JOB_ID_THIS_SLIDEMASK --parsable ${SLIDETOOLKITDIR}/slideQuantify_tiling.sh)
 
 
 		### slideNormalize
 		echo ""
 		echoitalic "* slideNormalize for normalization of images. [ $THIS_SLIDENORMALIZE ]"
 
-# 		JOB_ID_THIS_SLIDENORMALIZE=$(sbatch -J ${THIS_SLIDENORMALIZE} -e ${PROJECTDIR}/errors/slidenormalize.errors -o ${PROJECTDIR}/logs/slidenormalize.log  --mem=${QJOB_MEM_SLIDENORM} --time=${QJOB_TIME_SLIDENORM} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --depend=afterany:$JOB_ID_THIS_SLIDE2TILES --parsable ${SLIDETOOLKITDIR}/slideQuantify_normalizing.sh ${EMASKTHRESHOLD} )
+		JOB_ID_THIS_SLIDENORMALIZE=$(sbatch -J ${THIS_SLIDENORMALIZE} -e ${PROJECTDIR}/errors/slidenormalize.${THIS_SLIDENORMALIZE}.errors -o ${PROJECTDIR}/logs/slidenormalize.${THIS_SLIDENORMALIZE}.log  --mem=${QJOB_MEM_SLIDENORM} --time=${QJOB_TIME_SLIDENORM} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --depend=afterany:$JOB_ID_THIS_SLIDE2TILES --parsable ${SLIDETOOLKITDIR}/slideQuantify_normalizing.sh ${EMASKTHRESHOLD} )
 
 
 		### CellProfiler
 		echo ""
 		echoitalic "* CellProfiler to analyze images. [ $THIS_CELLPROFILER ]"
 
-# 		JOB_ID_THIS_CELLPROFILER=$(sbatch -J ${THIS_CELLPROFILER} -e ${PROJECTDIR}/errors/slidecellprofiler.errors -o ${PROJECTDIR}/logs/slidecellprofiler.log --mem=${QJOB_MEM_CP} --time=${QJOB_TIME_CP} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --depend=afterany:$JOB_ID_THIS_SLIDENORMALIZE --parsable ${SLIDETOOLKITDIR}/slideQuantify_cellprofiler.sh ${PIPELINE} )
-		JOB_ID_THIS_CELLPROFILER=$(sbatch -J ${THIS_CELLPROFILER} -e ${PROJECTDIR}/errors/slidecellprofiler.errors -o ${PROJECTDIR}/logs/slidecellprofiler.log --mem=${QJOB_MEM_CP} --time=${QJOB_TIME_CP} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable ${SLIDETOOLKITDIR}/slideQuantify_cellprofiler.sh ${PIPELINE} ${STAIN} ${SLIDE_NUM} )
+		JOB_ID_THIS_CELLPROFILER=$(sbatch -J ${THIS_CELLPROFILER} -e ${PROJECTDIR}/errors/slidecellprofiler.${THIS_CELLPROFILER}.errors -o ${PROJECTDIR}/logs/slidecellprofiler.${THIS_CELLPROFILER}.log --mem=${QJOB_MEM_CP} --time=${QJOB_TIME_CP} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --depend=afterany:$JOB_ID_THIS_SLIDENORMALIZE --parsable ${SLIDETOOLKITDIR}/slideQuantify_cellprofiler.sh ${PIPELINE} ${STAIN} ${SLIDE_NUM} )
+# 		JOB_ID_THIS_CELLPROFILER=$(sbatch -J ${THIS_CELLPROFILER} -e ${PROJECTDIR}/errors/slidecellprofiler.errors -o ${PROJECTDIR}/logs/slidecellprofiler.log --mem=${QJOB_MEM_CP} --time=${QJOB_TIME_CP} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable ${SLIDETOOLKITDIR}/slideQuantify_cellprofiler.sh ${PIPELINE} ${STAIN} ${SLIDE_NUM} )
 
 
 		### Wrap Up
 		echo ""
 		echoitalic "* WrapUp the work we have done, and clean house. [ $THIS_WRAPUP ]"
 
-		JOB_ID_THIS_WRAPUP=$(sbatch -J ${THIS_WRAPUP} -e ${PROJECTDIR}/errors/slidewrapup.errors -o ${PROJECTDIR}/logs/slidewrapup.log --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable --depend=afterany:$JOB_ID_THIS_CELLPROFILER ${SLIDETOOLKITDIR}/slideQuantify_wrapup.sh ${STAIN} ${RANDOM_SAMPLE} )
+		JOB_ID_THIS_WRAPUP=$(sbatch -J ${THIS_WRAPUP} -e ${PROJECTDIR}/errors/slidewrapup.${THIS_WRAPUP}.errors -o ${PROJECTDIR}/logs/slidewrapup.${THIS_WRAPUP}.log --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable --depend=afterany:$JOB_ID_THIS_CELLPROFILER ${SLIDETOOLKITDIR}/slideQuantify_wrapup.sh ${STAIN} ${RANDOM_SAMPLE} )
 
 
 		echo ""