Merge pull request #63 from UMCUGenetics/Release/2.2.2

Release/2.2.2
UMCUGenetics · Nov 2, 2021 · 5ad46a5 · 5ad46a5
2 parents 4181138 + 228fabe
commit 5ad46a5
Show file tree

Hide file tree

Showing 8 changed files with 344 additions and 31 deletions.
diff --git a/pipeline/run.sh b/pipeline/run.sh
@@ -168,7 +168,7 @@ done
 job_ids=\${job_ids::-1}
 echo \${job_ids}
 
-sbatch --job-name=1-queueStart_${name} --time=${queue_1_time} --mem=${queue_1_mem} --dependency=afterany:\${job_ids}:+10 --output=${outdir}/logs/queue/1-queueStart.o --error=${outdir}/logs/queue/1-queueStart.e ${global_sbatch_parameters} ${outdir}/jobs/queue/1-queueStart.sh
+sbatch --job-name=1-queueStart_${name} --time=${queue_1_time} --mem=${queue_1_mem} --dependency=afterok:\${job_ids}:+5 --output=${outdir}/logs/queue/1-queueStart.o --error=${outdir}/logs/queue/1-queueStart.e ${global_sbatch_parameters} ${outdir}/jobs/queue/1-queueStart.sh
 EOF
 
 # 1-queueStart.sh
@@ -193,7 +193,8 @@ for mzML in ${outdir}/1-data/*.mzML ; do
 
   ${rscript} ${scripts}/2-DIMS.R \$mzML ${outdir} ${trim} ${dims_thresh} ${resol} ${scripts}
   " > ${outdir}/jobs/2-DIMS/\${input}.sh
-  cur_id=\$(sbatch --job-name=2-dims_\${input}_${name} --time=${job_2_time} --mem=${job_2_mem} --dependency=afterok:\${break_id}:+10 --output=${outdir}/logs/2-DIMS/\${input}.o --error=${outdir}/logs/2-DIMS/\${input}.e ${global_sbatch_parameters} ${outdir}/jobs/2-DIMS/\${input}.sh)
+
+  cur_id=\$(sbatch --job-name=2-dims_\${input}_${name} --time=${job_2_time} --mem=${job_2_mem} --dependency=afterok:\${break_id}:+5 --output=${outdir}/logs/2-DIMS/\${input}.o --error=${outdir}/logs/2-DIMS/\${input}.e ${global_sbatch_parameters} ${outdir}/jobs/2-DIMS/\${input}.sh)
   job_ids+="\${cur_id}:"
 done
 job_ids=\${job_ids::-1} # remove last :
@@ -203,11 +204,12 @@ echo "#!/bin/sh
 
 /hpc/local/CentOS7/common/lang/R/3.2.2/bin/Rscript ${scripts}/3-averageTechReplicates.R ${indir} ${outdir} ${nrepl} ${thresh2remove} ${dims_thresh} ${scripts}
 " > ${outdir}/jobs/3-averageTechReplicates/average.sh
-avg_id=\$(sbatch --job-name=3-average_\${input}_${name} --time=${job_3_time} --mem=${job_3_mem} --dependency=afterok:\${job_ids}:+10 --output=${outdir}/logs/3-averageTechReplicates/average.o --error=${outdir}/logs/3-averageTechReplicates/average.e ${global_sbatch_parameters} ${outdir}/jobs/3-averageTechReplicates/average.sh)
+
+avg_id=\$(sbatch --job-name=3-average_\${input}_${name} --time=${job_3_time} --mem=${job_3_mem} --dependency=afterok:\${job_ids}:+5 --output=${outdir}/logs/3-averageTechReplicates/average.o --error=${outdir}/logs/3-averageTechReplicates/average.e ${global_sbatch_parameters} ${outdir}/jobs/3-averageTechReplicates/average.sh)
 
 # start next queue
-sbatch --job-name=2-queuePeakFinding_positive_${name} --time=${queue_2_time} --mem=${queue_2_mem} --dependency=afterok:\${avg_id}:+10 --output=${outdir}/logs/queue/2-queuePeakFinding_positive.o --error=${outdir}/logs/queue/2-queuePeakFinding_positive.e ${global_sbatch_parameters} ${outdir}/jobs/queue/2-queuePeakFinding_positive.sh
-sbatch --job-name=2-queuePeakFinding_negative_${name} --time=${queue_2_time} --mem=${queue_2_mem} --dependency=afterok:\${avg_id}:+10 --output=${outdir}/logs/queue/2-queuePeakFinding_negative.o --error=${outdir}/logs/queue/2-queuePeakFinding_negative.e ${global_sbatch_parameters} ${outdir}/jobs/queue/2-queuePeakFinding_negative.sh
+sbatch --job-name=2-queuePeakFinding_positive_${name} --time=${queue_2_time} --mem=${queue_2_mem} --dependency=afterok:\${avg_id}:+5 --output=${outdir}/logs/queue/2-queuePeakFinding_positive.o --error=${outdir}/logs/queue/2-queuePeakFinding_positive.e ${global_sbatch_parameters} ${outdir}/jobs/queue/2-queuePeakFinding_positive.sh
+sbatch --job-name=2-queuePeakFinding_negative_${name} --time=${queue_2_time} --mem=${queue_2_mem} --dependency=afterok:\${avg_id}:+5 --output=${outdir}/logs/queue/2-queuePeakFinding_negative.o --error=${outdir}/logs/queue/2-queuePeakFinding_negative.e ${global_sbatch_parameters} ${outdir}/jobs/queue/2-queuePeakFinding_negative.sh
 EOF
 
 # 14-cleanup.sh
@@ -300,7 +302,7 @@ echo "#!/bin/sh
 
 /hpc/local/CentOS7/common/lang/R/3.2.2/bin/Rscript ${scripts}/5-collectSamples.R ${outdir} ${scanmode}
 " > ${outdir}/jobs/5-collectSamples/${scanmode}.sh
-col_id=\$(sbatch --job-name=5-collectSamples_${scanmode}_${name} --time=${job_5_time} --mem=${job_5_mem} --dependency=afterany:\${job_ids}:+10 --output=${outdir}/logs/5-collectSamples/${scanmode}.o --error=${outdir}/logs/5-collectSamples/${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/5-collectSamples/${scanmode}.sh)
+col_id=\$(sbatch --job-name=5-collectSamples_${scanmode}_${name} --time=${job_5_time} --mem=${job_5_mem} --dependency=afterok:\${job_ids}:+5 --output=${outdir}/logs/5-collectSamples/${scanmode}.o --error=${outdir}/logs/5-collectSamples/${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/5-collectSamples/${scanmode}.sh)
 
 # hmdb_part.R
 echo "#!/bin/sh
@@ -319,7 +321,7 @@ hmdb_id_2=\$(sbatch --job-name=hmdb_part_adductSums_${scanmode}_${name} --time=$
 echo "${hmdb_id_2}" > ${outdir}/logs/hmdb_2
 
 # start next queue
-sbatch --job-name=3-queuePeakGrouping_${scanmode}_${name} --time=${queue_3_time} --mem=${queue_3_mem} --dependency=afterany:\${col_id}:\${hmdb_id_1}:\${hmdb_id_2}:+10 --output=${outdir}/logs/queue/3-queuePeakGrouping_${scanmode}.o --error=${outdir}/logs/queue/3-queuePeakGrouping_${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/queue/3-queuePeakGrouping_${scanmode}.sh
+sbatch --job-name=3-queuePeakGrouping_${scanmode}_${name} --time=${queue_3_time} --mem=${queue_3_mem} --dependency=afterok:\${col_id}:\${hmdb_id_1}:\${hmdb_id_2}:+5 --output=${outdir}/logs/queue/3-queuePeakGrouping_${scanmode}.o --error=${outdir}/logs/queue/3-queuePeakGrouping_${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/queue/3-queuePeakGrouping_${scanmode}.sh
 EOF
 
   # 3-queuePeakGrouping.sh
@@ -344,10 +346,10 @@ echo "#!/bin/sh
 
 /hpc/local/CentOS7/common/lang/R/3.2.2/bin/Rscript ${scripts}/7-collectSamplesGroupedHMDB.R ${outdir} ${scanmode} ${ppm}
 " > ${outdir}/jobs/7-collectSamplesGroupedHMDB/${scanmode}.sh
-col_id=\$(sbatch --job-name=7-collectSamplesGroupedHMDB_${scanmode}_${name} --time=${job_7_time} --mem=${job_7_mem} --dependency=afterany:\${job_ids}:+10 --output=${outdir}/logs/7-collectSamplesGroupedHMDB/${scanmode}.o --error=${outdir}/logs/7-collectSamplesGroupedHMDB/${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/7-collectSamplesGroupedHMDB/${scanmode}.sh)
+col_id=\$(sbatch --job-name=7-collectSamplesGroupedHMDB_${scanmode}_${name} --time=${job_7_time} --mem=${job_7_mem} --dependency=afterok:\${job_ids}:+5 --output=${outdir}/logs/7-collectSamplesGroupedHMDB/${scanmode}.o --error=${outdir}/logs/7-collectSamplesGroupedHMDB/${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/7-collectSamplesGroupedHMDB/${scanmode}.sh)
 
 # start next queue
-sbatch --job-name=4-queuePeakGroupingRest_${scanmode}_${name} --time=${queue_4_time} --mem=${queue_4_mem} --dependency=afterany:\${col_id}:+10 --output=${outdir}/logs/queue/4-queuePeakGroupingRest_${scanmode}.o --error=${outdir}/logs/queue/4-queuePeakGroupingRest_${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/queue/4-queuePeakGroupingRest_${scanmode}.sh
+sbatch --job-name=4-queuePeakGroupingRest_${scanmode}_${name} --time=${queue_4_time} --mem=${queue_4_mem} --dependency=afterok:\${col_id}:+5 --output=${outdir}/logs/queue/4-queuePeakGroupingRest_${scanmode}.o --error=${outdir}/logs/queue/4-queuePeakGroupingRest_${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/queue/4-queuePeakGroupingRest_${scanmode}.sh
 EOF
 
   # 4-queuePeakGroupingRest.sh
@@ -369,7 +371,7 @@ done
 job_ids=\${job_ids::-1}
 
 # start next queue
-sbatch --job-name=5-queueFillMissing_${scanmode}_${name} --time=${queue_5_time} --mem=${queue_5_mem} --dependency=afterany:\${job_ids}:+10 --output=${outdir}/logs/queue/5-queueFillMissing_${scanmode}.o --error=${outdir}/logs/queue/5-queueFillMissing_${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/queue/5-queueFillMissing_${scanmode}.sh
+sbatch --job-name=5-queueFillMissing_${scanmode}_${name} --time=${queue_5_time} --mem=${queue_5_mem} --dependency=afterok:\${job_ids}:+5 --output=${outdir}/logs/queue/5-queueFillMissing_${scanmode}.o --error=${outdir}/logs/queue/5-queueFillMissing_${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/queue/5-queueFillMissing_${scanmode}.sh
 EOF
 
   # 5-queueFillMissing.sh
@@ -388,6 +390,7 @@ for file in ${outdir}/8-grouping_rest/${scanmode}_* ; do
   cur_id=\$(sbatch --job-name=9-runFillMissing_1_\${input}_${scanmode}_${name} --time=${job_9a_time} --mem=${job_9a_mem} --output=${outdir}/logs/9-runFillMissing/rest_${scanmode}_\${input}.o --error=${outdir}/logs/9-runFillMissing/rest_${scanmode}_\${input}.e ${global_sbatch_parameters} ${outdir}/jobs/9-runFillMissing/rest_${scanmode}_\${input}.sh)
   job_ids+="\${cur_id}:"
 done
+wait
 
 for file in ${outdir}/6-grouping_hmdb/*_${scanmode}.RData ; do
   input=\$(basename \$file .RData)
@@ -397,20 +400,21 @@ for file in ${outdir}/6-grouping_hmdb/*_${scanmode}.RData ; do
 
   /hpc/local/CentOS7/common/lang/R/3.2.2/bin/Rscript ${scripts}/9-runFillMissing.R \$file ${outdir} ${scanmode} ${thresh} ${resol} ${scripts}
   " > ${outdir}/jobs/9-runFillMissing/hmdb_${scanmode}_\${input}.sh
-  cut_id=\$(sbatch --job-name=9-runFillMissing_2_\${input}_${scanmode}_${name} --time=${job_9b_time} --mem=${job_9b_mem} --output=${outdir}/logs/9-runFillMissing/hmdb_${scanmode}_\${input}.o --error=${outdir}/logs/9-runFillMissing/hmdb_${scanmode}_\${input}.e ${global_sbatch_parameters} ${outdir}/jobs/9-runFillMissing/hmdb_${scanmode}_\${input}.sh)
+  cur_id=\$(sbatch --job-name=9-runFillMissing_2_\${input}_${scanmode}_${name} --time=${job_9b_time} --mem=${job_9b_mem} --output=${outdir}/logs/9-runFillMissing/hmdb_${scanmode}_\${input}.o --error=${outdir}/logs/9-runFillMissing/hmdb_${scanmode}_\${input}.e ${global_sbatch_parameters} ${outdir}/jobs/9-runFillMissing/hmdb_${scanmode}_\${input}.sh)
   job_ids+="\${cur_id}:"
 done
+wait
 job_ids=\${job_ids::-1}
 
 # 10-collectSamplesFilled
 echo "#!/bin/sh
 
 /hpc/local/CentOS7/common/lang/R/3.2.2/bin/Rscript ${scripts}/10-collectSamplesFilled.R ${outdir} ${scanmode} ${normalization} ${scripts} ${z_score}  ${ppm}
 " > ${outdir}/jobs/10-collectSamplesFilled/${scanmode}.sh
-col_id=\$(sbatch --job-name=10-collectSamplesFilled_${scanmode}_${name} --time=${job_10_time} --mem=${job_10_mem} --dependency=afterany:\${job_ids}:+10 --output=${outdir}/logs/10-collectSamplesFilled/${scanmode}.o --error=${outdir}/logs/10-collectSamplesFilled/${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/10-collectSamplesFilled/${scanmode}.sh)
+col_id=\$(sbatch --job-name=10-collectSamplesFilled_${scanmode}_${name} --time=${job_10_time} --mem=${job_10_mem} --dependency=afterok:\${job_ids}:+5 --output=${outdir}/logs/10-collectSamplesFilled/${scanmode}.o --error=${outdir}/logs/10-collectSamplesFilled/${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/10-collectSamplesFilled/${scanmode}.sh)
 
 # start next queue
-sbatch --job-name=6-queueSumAdducts_${scanmode}_${name} --time=${queue_6_time} --mem=${queue_6_mem} --dependency=afterany:\${col_id}:+10 --output=${outdir}/logs/queue/6-queueSumAdducts_${scanmode}.o --error=${outdir}/logs/queue/6-queueSumAdducts_${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/queue/6-queueSumAdducts_${scanmode}.sh
+sbatch --job-name=6-queueSumAdducts_${scanmode}_${name} --time=${queue_6_time} --mem=${queue_6_mem} --dependency=afterok:\${col_id}:+5 --output=${outdir}/logs/queue/6-queueSumAdducts_${scanmode}.o --error=${outdir}/logs/queue/6-queueSumAdducts_${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/queue/6-queueSumAdducts_${scanmode}.sh
 EOF
 
   # 6-queueSumAdducts.sh
@@ -436,7 +440,7 @@ echo "#!/bin/sh
 
 /hpc/local/CentOS7/common/lang/R/3.2.2/bin/Rscript ${scripts}/12-collectSamplesAdded.R ${outdir} ${scanmode} ${scripts}
 " > ${outdir}/jobs/12-collectSamplesAdded/${scanmode}.sh
-col_id=\$(sbatch --job-name=12-collectSamplesAdded_${scanmode}_${name} --time=${job_12_time} --mem=${job_12_mem} --dependency=afterany:\${job_ids}:+10 --output=${outdir}/logs/12-collectSamplesAdded/${scanmode}.o --error=${outdir}/logs/12-collectSamplesAdded/${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/12-collectSamplesAdded/${scanmode}.sh)
+col_id=\$(sbatch --job-name=12-collectSamplesAdded_${scanmode}_${name} --time=${job_12_time} --mem=${job_12_mem} --dependency=afterok:\${job_ids}:+5 --output=${outdir}/logs/12-collectSamplesAdded/${scanmode}.o --error=${outdir}/logs/12-collectSamplesAdded/${scanmode}.e ${global_sbatch_parameters} ${outdir}/jobs/12-collectSamplesAdded/${scanmode}.sh)
 
 if [ -f "${outdir}/logs/done" ]; then   # if one of the scanmodes has already finished
   echo other scanmode already finished queueing - queue next step
@@ -448,8 +452,8 @@ if [ -f "${outdir}/logs/done" ]; then   # if one of the scanmodes has already fi
 
   ${rscript} ${scripts}/13-excelExport.R ${outdir} ${name} ${matrix} ${db2} ${z_score}
   " > ${outdir}/jobs/13-excelExport.sh
-  exp_id=\$(sbatch --job-name=13-excelExport_${name} --time=${job_13_time} --mem=${job_13_mem} --dependency=afterany:\${col_ids}:+10 --output=${outdir}/logs/13-excelExport/exp.o --error=${outdir}/logs/13-excelExport/exp.e ${global_sbatch_parameters} ${outdir}/jobs/13-excelExport.sh)
-  sbatch --job-name=14-cleanup_${name} --time=${job_14_time} --mem=${job_14_mem} --dependency=afterany:\${exp_id}:+10 --output=${outdir}/logs/14-cleanup.o --error=${outdir}/logs/14-cleanup.e ${global_sbatch_parameters} ${outdir}/jobs/14-cleanup.sh
+  exp_id=\$(sbatch --job-name=13-excelExport_${name} --time=${job_13_time} --mem=${job_13_mem} --dependency=afterok:\${col_ids}:+5 --output=${outdir}/logs/13-excelExport/exp.o --error=${outdir}/logs/13-excelExport/exp.e ${global_sbatch_parameters} ${outdir}/jobs/13-excelExport.sh)
+  sbatch --job-name=14-cleanup_${name} --time=${job_14_time} --mem=${job_14_mem} --dependency=afterok:\${exp_id}:+5 --output=${outdir}/logs/14-cleanup.o --error=${outdir}/logs/14-cleanup.e ${global_sbatch_parameters} ${outdir}/jobs/14-cleanup.sh
 else
   echo other scanmode not queued yet, not yet queueing next step
   echo \${col_id} > ${outdir}/logs/done

diff --git a/pipeline/scripts/10-collectSamplesFilled.R b/pipeline/scripts/10-collectSamplesFilled.R
@@ -24,10 +24,10 @@ ppm <- as.numeric(cmd_args[6])
 #z_score <- 0
 
 object.files = list.files(paste(outdir, "9-samplePeaksFilled", sep="/"), full.names=TRUE, pattern=scanmode)
-
 outlist.tot=NULL
 for (i in 1:length(object.files)) {
   load(object.files[i])
+  print(print(object.files[i]))
   outlist.tot = rbind(outlist.tot, final.outlist.idpat3)
 }
 

diff --git a/pipeline/tools/settings.config-csf b/pipeline/tools/settings.config-csf
@@ -0,0 +1,65 @@
+# manual 
+thresh_pos=2000
+thresh_neg=2000
+dims_thresh=100
+trim=0.1
+nrepl=3
+normalization=disabled
+thresh2remove=1000000000
+resol=140000
+[email protected]
+matrix=CSF
+proteowizard=/hpc/dbg_mz/tools/proteowizard_3.0.19252-aa45583de
+db=/hpc/dbg_mz/tools/db/HMDB_add_iso_corrNaCl_withIS_withC5OH.RData
+db2=/hpc/dbg_mz/tools/db/HMDB_with_info_relevance_IS_C5OH.RData
+z_score=1
+job_0_time=00:15:00
+job_0_mem=2G
+job_1_time=00:15:00
+job_1_mem=2G
+job_2_time=00:15:00
+job_2_mem=4G
+job_3_time=02:30:00
+job_3_mem=5G
+job_4_time=02:00:00
+job_4_mem=8G
+job_5_time=03:00:00
+job_5_mem=8G
+job_6_time=04:30:00
+job_6_mem=4G
+job_7_time=02:00:00
+job_7_mem=8G
+job_8_time=02:00:00
+job_8_mem=8G
+job_9a_time=01:30:00
+job_9a_mem=4G
+job_9b_time=01:30:00
+job_9b_mem=4G
+job_10_time=02:00:00
+job_10_mem=8G
+job_11_time=03:30:00
+job_11_mem=8G
+job_12_time=01:30:00
+job_12_mem=8G
+job_13_time=02:00:00
+job_13_mem=8G
+job_14_time=00:15:00
+job_14_mem=500M
+queue_0_time=00:15:00
+queue_0_mem=1G
+queue_1_time=00:15:00
+queue_1_mem=1G
+queue_2_time=00:15:00
+queue_2_mem=500M
+queue_3_time=00:15:00
+queue_3_mem=500M
+queue_4_time=00:15:00
+queue_4_mem=500M
+queue_5_time=00:15:00
+queue_5_mem=500M
+queue_6_time=00:15:00
+queue_6_mem=500M
+job_hmdb1_time=04:00:00
+job_hmdb1_mem=8G
+job_hmdb2_time=04:00:00
+job_hmdb2_mem=8G
diff --git a/pipeline/tools/settings.config-dbs b/pipeline/tools/settings.config-dbs
@@ -0,0 +1,64 @@
+# manual
+thresh_pos=2000
+thresh_neg=2000
+dims_thresh=100
+trim=0.1
+nrepl=3
+normalization=disabled
+thresh2remove=500000000
+resol=140000
+[email protected]
+matrix=DBS
+z_score=1
+db=/hpc/dbg_mz/tools/db/HMDB_add_iso_corrNaCl_withIS_withC5OH.RData
+db2=/hpc/dbg_mz/tools/db/HMDB_with_info_relevance_IS_C5OH.RData
+job_0_time=00:15:00
+job_0_mem=2G
+job_1_time=00:15:00
+job_1_mem=2G
+job_2_time=00:15:00
+job_2_mem=4G
+job_3_time=02:30:00
+job_3_mem=5G
+job_4_time=02:00:00
+job_4_mem=8G
+job_5_time=03:00:00
+job_5_mem=8G
+job_6_time=04:30:00
+job_6_mem=4G
+job_7_time=02:00:00
+job_7_mem=8G
+job_8_time=02:00:00
+job_8_mem=8G
+job_9a_time=01:30:00
+job_9a_mem=4G
+job_9b_time=01:30:00
+job_9b_mem=4G
+job_10_time=02:00:00
+job_10_mem=8G
+job_11_time=03:30:00
+job_11_mem=8G
+job_12_time=01:30:00
+job_12_mem=8G
+job_13_time=02:00:00
+job_13_mem=8G
+job_14_time=00:15:00
+job_14_mem=500M
+queue_0_time=00:15:00
+queue_0_mem=1G
+queue_1_time=00:15:00
+queue_1_mem=1G
+queue_2_time=00:15:00
+queue_2_mem=500M
+queue_3_time=00:15:00
+queue_3_mem=500M
+queue_4_time=00:15:00
+queue_4_mem=500M
+queue_5_time=00:15:00
+queue_5_mem=500M
+queue_6_time=00:15:00
+queue_6_mem=500M
+job_hmdb1_time=04:00:00
+job_hmdb1_mem=8G
+job_hmdb2_time=04:00:00
+job_hmdb2_mem=8G
diff --git a/pipeline/tools/settings.config-example b/pipeline/tools/settings.config-example
diff --git a/pipeline/tools/settings.config-plasma b/pipeline/tools/settings.config-plasma
@@ -0,0 +1,64 @@
+# manual
+thresh_pos=2000
+thresh_neg=2000
+dims_thresh=100
+trim=0.1
+nrepl=3
+normalization=disabled
+thresh2remove=1000000000
+resol=140000
+[email protected]
+matrix=Plasma
+z_score=1
+db=/hpc/dbg_mz/tools/db/HMDB_add_iso_corrNaCl_withIS_withC5OH.RData
+db2=/hpc/dbg_mz/tools/db/HMDB_with_info_relevance_IS_C5OH.RData
+job_0_time=00:15:00
+job_0_mem=2G
+job_1_time=00:15:00
+job_1_mem=2G
+job_2_time=00:15:00
+job_2_mem=4G
+job_3_time=02:30:00
+job_3_mem=5G
+job_4_time=02:00:00
+job_4_mem=8G
+job_5_time=03:00:00
+job_5_mem=8G
+job_6_time=04:30:00
+job_6_mem=4G
+job_7_time=02:00:00
+job_7_mem=8G
+job_8_time=02:00:00
+job_8_mem=8G
+job_9a_time=01:30:00
+job_9a_mem=4G
+job_9b_time=01:30:00
+job_9b_mem=4G
+job_10_time=02:00:00
+job_10_mem=8G
+job_11_time=03:30:00
+job_11_mem=8G
+job_12_time=01:30:00
+job_12_mem=8G
+job_13_time=02:00:00
+job_13_mem=8G
+job_14_time=00:15:00
+job_14_mem=500M
+queue_0_time=00:15:00
+queue_0_mem=1G
+queue_1_time=00:15:00
+queue_1_mem=1G
+queue_2_time=00:15:00
+queue_2_mem=500M
+queue_3_time=00:15:00
+queue_3_mem=500M
+queue_4_time=00:15:00
+queue_4_mem=500M
+queue_5_time=00:15:00
+queue_5_mem=500M
+queue_6_time=00:15:00
+queue_6_mem=500M
+job_hmdb1_time=04:00:00
+job_hmdb1_mem=8G
+job_hmdb2_time=04:00:00
+job_hmdb2_mem=8G