Running METAP SERVER Thu Aug 20 10:20:02 CEST 2015 ID=15082010194611419 /home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin /home/metap2/data + echo 'we are here' we are here + pwd /home/metap2/public_html/users/15082010194611419 + hostname metap + uname -a Linux metap 3.13.0-43-generic #72-Ubuntu SMP Mon Dec 8 19:35:06 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux + echo 'this is the environment' this is the environment + env RATIOS=n OUTLIER=n MISSING=n DATADIR=/home/metap2/data SHELL=/bin/sh JOBID=drug dosing study in liver tissue (2 phenotypes) REFERENCE=n PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/home/metap2/public_html/users/15082010194611419 PRIVAT=0 LANG=en_US.UTF-8 SHLVL=1 HOME=/home/metap2 ID=15082010194611419 DEL_METABS=n FORMAT=csv_kegg LOGNAME=metap2 EMAIL=testUser USERID=testUser DEVELOPT= _=/usr/bin/env + echo 'this is a first R script that works on the input data' this is a first R script that works on the input data + '[' '' = werner ']' + '[' '' = karsten ']' + '[' '' = gabi ']' + '[' '' = elisabeth ']' + process_metaP_data.R RUNNING /home/metap2/exec/process_metaP_data.R Use of uninitialized value $out0 in substitution (s///) at /home/metap2/exec/readAux.pl line 66. Use of uninitialized value $out0 in substitution (s///) at /home/metap2/exec/readAux.pl line 67. Use of uninitialized value in transliteration (tr///) at /home/metap2/exec/readAux.pl line 68. Use of uninitialized value $out0 in concatenation (.) or string at /home/metap2/exec/readAux.pl line 69. Use of uninitialized value $max_length in numeric lt (<) at /home/metap2/exec/readAux.pl line 71. -rw-rw-r-- 1 metap2 metap2 29665 Aug 20 10:21 .R.Rout adding: summary.csv (deflated 49%) adding: colsToMark.x.csv (deflated 65%) adding: phenotypes.csv (deflated 68%) adding: data_all.csv (deflated 51%) adding: processing_log.txt (deflated 51%) adding: options (deflated 36%) adding: colsToMark.csv (deflated 11%) adding: phenotypes_numeric.csv (deflated 57%) adding: rowsToMark.csv (deflated 72%) adding: metabNamesMapping.csv (deflated 69%) adding: out_params.txt (stored 0%) adding: input (deflated 50%) adding: data.csv (deflated 51%) adding: phenotypes.txt (deflated 69%) adding: phenotypes_for_QC.csv (deflated 51%) adding: histograms.pdf (deflated 90%) adding: barplots/X2.aminobutyrate_barplot_DAY.png (deflated 18%) adding: barplots/X3.indoxyl.sulfate_barplot_DOSE_MG_KG.png (deflated 20%) adding: barplots/maltotriose_barplot_DAY.png (deflated 23%) adding: barplots/pipecolate_barplot_DOSE_MG_KG.png (deflated 25%) adding: barplots/creatine_barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/threonine_barplot.map (deflated 79%) adding: barplots/valine_barplot.map (deflated 79%) adding: barplots/X4.guanidinobutanoate_barplot.png (deflated 27%) adding: barplots/ophthalmate._barplot.map (deflated 79%) adding: barplots/serine_barplot.png (deflated 24%) adding: barplots/mannose_barplot.png (deflated 23%) adding: barplots/X5.oxoproline_barplot_DAY.png (deflated 20%) adding: barplots/saccharopine_barplot.png (deflated 22%) adding: barplots/aspartate_barplot.png (deflated 26%) adding: barplots/maltotriose_barplot_DOSE_MG_KG.png (deflated 28%) adding: barplots/glutathione.oxidized..GSSG._barplot.map (deflated 78%) adding: barplots/X5.methylthioadenosine..MTA._barplot.png (deflated 24%) adding: barplots/glutamine_barplot.map (deflated 79%) adding: barplots/betaine.aldehyde_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/X3.phosphoglycerate_barplot_DOSE_MG_KG.png (deflated 20%) adding: barplots/hypotaurine_barplot.png (deflated 22%) adding: barplots/hypotaurine_barplot.map (deflated 79%) adding: barplots/ophthalmate._barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/alanine_barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/glutamate_barplot.map (deflated 79%) adding: barplots/ornithine_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/glutathione.oxidized..GSSG._barplot_DAY.png (deflated 21%) adding: barplots/X5.oxoproline_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/creatine_barplot.png (deflated 21%) adding: barplots/trans.4.hydroxyproline_barplot.png (deflated 25%) adding: barplots/spermidine_barplot.map (deflated 79%) adding: barplots/beta.alanine_barplot_DOSE_MG_KG.png (deflated 18%) adding: barplots/fructose_barplot_DOSE_MG_KG.png (deflated 18%) adding: barplots/methionine_barplot.map (deflated 79%) adding: barplots/creatinine_barplot_DAY.png (deflated 20%) adding: barplots/N.acetylalanine_barplot.map (deflated 78%) adding: barplots/saccharopine_barplot_DAY.png (deflated 20%) adding: barplots/histidine_barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/methionine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/X3.indoxyl.sulfate_barplot.png (deflated 22%) adding: barplots/X3.phosphoglycerate_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/maltose_barplot.png (deflated 24%) adding: barplots/betaine.aldehyde_barplot.png (deflated 23%) adding: barplots/glycine_barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/lactate_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/maltose_barplot_DAY.png (deflated 21%) adding: barplots/phenylalanine_barplot_DOSE_MG_KG.png (deflated 18%) adding: barplots/kynurenine_barplot.png (deflated 29%) adding: barplots/beta.alanine_barplot.png (deflated 21%) adding: barplots/alanine_barplot_DAY.png (deflated 18%) adding: barplots/glutamate_barplot.png (deflated 26%) adding: barplots/pipecolate_barplot_WEIGHT_MG.png (deflated 13%) adding: barplots/N.acetylmannosamine_barplot_DOSE_MG_KG.png (deflated 17%) adding: barplots/glucose_barplot.map (deflated 79%) adding: barplots/leucine_barplot.map (deflated 79%) adding: barplots/glycine_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/N.acetylglucosamine.6.phosphate_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/glycerate_barplot_DAY.png (deflated 21%) adding: barplots/asparagine_barplot.map (deflated 79%) adding: barplots/arginine_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/glucose_barplot_DOSE_MG_KG.png (deflated 22%) adding: barplots/mannose_barplot_DOSE_MG_KG.png (deflated 17%) adding: barplots/X5.oxoproline_barplot.png (deflated 22%) adding: barplots/tryptophan_barplot.png (deflated 27%) adding: barplots/tryptophan_barplot_DAY.png (deflated 21%) adding: barplots/arginine_barplot_DAY.png (deflated 17%) adding: barplots/lactate_barplot.map (deflated 79%) adding: barplots/kynurenine_barplot.map (deflated 79%) adding: barplots/kynurenine_barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/urea_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/glutathione.reduced..GSH._barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/glutathione.reduced..GSH._barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/X5.methylthioadenosine..MTA._barplot_DAY.png (deflated 20%) adding: barplots/phenylalanine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/X4.guanidinobutanoate_barplot.map (deflated 79%) adding: barplots/lactate_barplot.png (deflated 22%) adding: barplots/spermidine_barplot_DAY.png (deflated 23%) adding: barplots/fructose_barplot_DAY.png (deflated 18%) adding: barplots/beta.alanine_barplot_DAY.png (deflated 16%) adding: barplots/citrulline_barplot.map (deflated 79%) adding: barplots/hypotaurine_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/lysine_barplot_DOSE_MG_KG.png (deflated 18%) adding: barplots/glycerate_barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/glutamine_barplot_DAY.png (deflated 20%) adding: barplots/phosphoenolpyruvate..PEP._barplot_DAY.png (deflated 21%) adding: barplots/serine_barplot.map (deflated 79%) adding: barplots/maltose_barplot.map (deflated 80%) adding: barplots/saccharopine_barplot_DOSE_MG_KG.png (deflated 18%) adding: barplots/citrulline_barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/N.acetylglucosamine.6.phosphate_barplot.png (deflated 23%) adding: barplots/NN.dimethylarginine..ADMA._barplot_DAY.png (deflated 17%) adding: barplots/galactose.1.phosphate_barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/sorbitol..glucitol._barplot.map (deflated 79%) adding: barplots/beta.alanine_barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/leucine_barplot_WEIGHT_MG.png (deflated 12%) adding: barplots/threonine_barplot.png (deflated 21%) adding: barplots/serine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/X3.indoxyl.sulfate_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/S.adenosylhomocysteine..SAH._barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/sorbitol..glucitol._barplot_DOSE_MG_KG.png (deflated 27%) adding: barplots/tyrosine_barplot.png (deflated 23%) adding: barplots/ophthalmate._barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/arginine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/N.acetylmethionine_barplot_DOSE_MG_KG.png (deflated 32%) adding: barplots/creatinine_barplot.png (deflated 27%) adding: barplots/aspartate_barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/sorbitol..glucitol._barplot_DAY.png (deflated 24%) adding: barplots/X2.aminobutyrate_barplot.png (deflated 22%) adding: barplots/isoleucine_barplot_DAY.png (deflated 20%) adding: barplots/NN.dimethylarginine..ADMA._barplot.map (deflated 78%) adding: barplots/spermidine_barplot_DOSE_MG_KG.png (deflated 24%) adding: barplots/pipecolate_barplot.map (deflated 79%) adding: barplots/X2.aminoadipate_barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/tryptophan_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/phosphoenolpyruvate..PEP._barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/isoleucine_barplot.map (deflated 79%) adding: barplots/X3.phosphoglycerate_barplot.map (deflated 78%) adding: barplots/beta.alanine_barplot.map (deflated 79%) adding: barplots/N.acetylmethionine_barplot_WEIGHT_MG.png (deflated 13%) adding: barplots/X15.anhydroglucitol..15.AG._barplot_DAY.png (deflated 20%) adding: barplots/urea_barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/glutamine_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/valine_barplot.png (deflated 26%) adding: barplots/maltotriose_barplot_WEIGHT_MG.png (deflated 12%) adding: barplots/S.adenosylhomocysteine..SAH._barplot.png (deflated 21%) adding: barplots/glycerate_barplot.png (deflated 28%) adding: barplots/N.acetylglucosamine_barplot.map (deflated 78%) adding: barplots/ornithine_barplot.png (deflated 24%) adding: barplots/pipecolate_barplot.png (deflated 31%) adding: barplots/tryptophan_barplot.map (deflated 79%) adding: barplots/betaine_barplot_DAY.png (deflated 23%) adding: barplots/maltotriose_barplot.png (deflated 32%) adding: barplots/aspartate_barplot_DAY.png (deflated 18%) adding: barplots/alanine_barplot.map (deflated 79%) adding: barplots/lysine_barplot.map (deflated 79%) adding: barplots/proline_barplot_DAY.png (deflated 17%) adding: barplots/citrulline_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/X2.aminobutyrate_barplot_DOSE_MG_KG.png (deflated 17%) adding: barplots/tyrosine_barplot.map (deflated 79%) adding: barplots/leucine_barplot.png (deflated 27%) adding: barplots/glutamate_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/gamma.aminobutyrate..GABA._barplot.map (deflated 79%) adding: barplots/X5.oxoproline_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/X5.oxoproline_barplot.map (deflated 79%) adding: barplots/valine_barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/methionine_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/proline_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/X3.indoxyl.sulfate_barplot_DAY.png (deflated 18%) adding: barplots/alanine_barplot.png (deflated 24%) adding: barplots/glycerate_barplot.map (deflated 79%) adding: barplots/galactose.1.phosphate_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/sorbitol..glucitol._barplot_WEIGHT_MG.png (deflated 12%) adding: barplots/methionine_barplot_DAY.png (deflated 20%) adding: barplots/urea_barplot_DAY.png (deflated 17%) adding: barplots/N.acetylmethionine_barplot.map (deflated 79%) adding: barplots/X15.anhydroglucitol..15.AG._barplot.png (deflated 27%) adding: barplots/maltose_barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/creatinine_barplot.map (deflated 78%) adding: barplots/glycine_barplot.png (deflated 21%) adding: barplots/NN.dimethylarginine..ADMA._barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/phenylalanine_barplot.map (deflated 79%) adding: barplots/X15.anhydroglucitol..15.AG._barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/tyrosine_barplot_DOSE_MG_KG.png (deflated 20%) adding: barplots/maltose_barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/creatine_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/glycine_barplot_DAY.png (deflated 15%) adding: barplots/histidine_barplot_DAY.png (deflated 18%) adding: barplots/creatine_barplot_DAY.png (deflated 19%) adding: barplots/kynurenine_barplot_DAY.png (deflated 22%) adding: barplots/threonine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/valine_barplot_DOSE_MG_KG.png (deflated 23%) adding: barplots/S.adenosylhomocysteine..SAH._barplot.map (deflated 79%) adding: barplots/asparagine_barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/fructose_barplot.map (deflated 79%) adding: barplots/glutamate_barplot_DOSE_MG_KG.png (deflated 20%) adding: barplots/glycine_barplot.map (deflated 79%) adding: barplots/S.adenosylhomocysteine..SAH._barplot_DAY.png (deflated 16%) adding: barplots/ophthalmate._barplot_DAY.png (deflated 19%) adding: barplots/betaine_barplot.map (deflated 79%) adding: barplots/X15.anhydroglucitol..15.AG._barplot.map (deflated 79%) adding: barplots/trans.4.hydroxyproline_barplot.map (deflated 79%) adding: barplots/N.acetylglucosamine_barplot_DAY.png (deflated 19%) adding: barplots/betaine.aldehyde_barplot.map (deflated 78%) adding: barplots/X5.methylthioadenosine..MTA._barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/tryptophan_barplot_DOSE_MG_KG.png (deflated 23%) adding: barplots/glutathione.oxidized..GSSG._barplot_DOSE_MG_KG.png (deflated 23%) adding: barplots/N.acetylalanine_barplot.png (deflated 25%) adding: barplots/histidine_barplot.map (deflated 79%) adding: barplots/N.acetylmannosamine_barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/phosphoenolpyruvate..PEP._barplot.png (deflated 22%) adding: barplots/threonine_barplot_DOSE_MG_KG.png (deflated 20%) adding: barplots/threonine_barplot_DAY.png (deflated 21%) adding: barplots/X2.aminoadipate_barplot.png (deflated 29%) adding: barplots/alanine_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/betaine.aldehyde_barplot_DAY.png (deflated 18%) adding: barplots/N.acetylglucosamine.6.phosphate_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/phosphoenolpyruvate..PEP._barplot.map (deflated 79%) adding: barplots/proline_barplot.map (deflated 79%) adding: barplots/gamma.aminobutyrate..GABA._barplot_DAY.png (deflated 18%) adding: barplots/arginine_barplot.png (deflated 29%) adding: barplots/creatinine_barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/NN.dimethylarginine..ADMA._barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/lactate_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/glutamate_barplot_DAY.png (deflated 18%) adding: barplots/serine_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/isoleucine_barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/X4.guanidinobutanoate_barplot_DOSE_MG_KG.png (deflated 24%) adding: barplots/proline_barplot.png (deflated 22%) adding: barplots/sorbitol..glucitol._barplot.png (deflated 31%) adding: barplots/X2.aminoadipate_barplot_DOSE_MG_KG.png (deflated 24%) adding: barplots/N.acetylglucosamine_barplot.png (deflated 23%) adding: barplots/tyrosine_barplot_DAY.png (deflated 18%) adding: barplots/X3.indoxyl.sulfate_barplot.map (deflated 79%) adding: barplots/glycerate_barplot_DOSE_MG_KG.png (deflated 23%) adding: barplots/X4.guanidinobutanoate_barplot_WEIGHT_MG.png (deflated 12%) adding: barplots/N.acetylmannosamine_barplot.map (deflated 78%) adding: barplots/spermidine_barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/lysine_barplot.png (deflated 24%) adding: barplots/mannose_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/NN.dimethylarginine..ADMA._barplot.png (deflated 25%) adding: barplots/betaine_barplot_DOSE_MG_KG.png (deflated 25%) adding: barplots/glutathione.reduced..GSH._barplot.map (deflated 79%) adding: barplots/N.acetylglucosamine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/X5.methylthioadenosine..MTA._barplot.map (deflated 78%) adding: barplots/glucose_barplot.png (deflated 23%) adding: barplots/mannose_barplot.map (deflated 79%) adding: barplots/N.acetylglucosamine.6.phosphate_barplot_DAY.png (deflated 19%) adding: barplots/glutathione.reduced..GSH._barplot_DAY.png (deflated 19%) adding: barplots/creatinine_barplot_DOSE_MG_KG.png (deflated 20%) adding: barplots/lactate_barplot_DAY.png (deflated 17%) adding: barplots/gamma.aminobutyrate..GABA._barplot_DOSE_MG_KG.png (deflated 20%) adding: barplots/citrulline_barplot.png (deflated 22%) adding: barplots/N.acetylalanine_barplot_DAY.png (deflated 17%) adding: barplots/glutathione.reduced..GSH._barplot.png (deflated 28%) adding: barplots/glucose_barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/betaine_barplot_WEIGHT_MG.png (deflated 12%) adding: barplots/galactose.1.phosphate_barplot.map (deflated 79%) adding: barplots/tyrosine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/X2.aminobutyrate_barplot.map (deflated 78%) adding: barplots/glutamine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/N.acetylmethionine_barplot_DAY.png (deflated 27%) adding: barplots/hypotaurine_barplot_DAY.png (deflated 19%) adding: barplots/ornithine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/X2.aminoadipate_barplot_DAY.png (deflated 20%) adding: barplots/X2.aminoadipate_barplot.map (deflated 79%) adding: barplots/ophthalmate._barplot.png (deflated 24%) adding: barplots/aspartate_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/lysine_barplot_DAY.png (deflated 18%) adding: barplots/N.acetylalanine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/citrulline_barplot_DAY.png (deflated 18%) adding: barplots/histidine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/glutathione.oxidized..GSSG._barplot_WEIGHT_MG.png (deflated 12%) adding: barplots/urea_barplot.png (deflated 22%) adding: barplots/asparagine_barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/phenylalanine_barplot_DAY.png (deflated 21%) adding: barplots/leucine_barplot_DAY.png (deflated 22%) adding: barplots/saccharopine_barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/valine_barplot_DAY.png (deflated 19%) adding: barplots/saccharopine_barplot.map (deflated 79%) adding: barplots/cysteine_barplot_DOSE_MG_KG.png (deflated 17%) adding: barplots/N.acetylalanine_barplot_DOSE_MG_KG.png (deflated 20%) adding: barplots/N.acetylmannosamine_barplot.png (deflated 21%) adding: barplots/trans.4.hydroxyproline_barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/X2.aminobutyrate_barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/galactose.1.phosphate_barplot_DAY.png (deflated 19%) adding: barplots/histidine_barplot.png (deflated 26%) adding: barplots/fructose_barplot.png (deflated 20%) adding: barplots/X5.methylthioadenosine..MTA._barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/asparagine_barplot.png (deflated 26%) adding: barplots/S.adenosylhomocysteine..SAH._barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/asparagine_barplot_DAY.png (deflated 20%) adding: barplots/betaine.aldehyde_barplot_DOSE_MG_KG.png (deflated 19%) adding: barplots/pipecolate_barplot_DAY.png (deflated 22%) adding: barplots/spermidine_barplot.png (deflated 30%) adding: barplots/cysteine_barplot_WEIGHT_MG.png (deflated 9%) adding: barplots/glutamine_barplot.png (deflated 23%) adding: barplots/lysine_barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/creatine_barplot.map (deflated 78%) adding: barplots/serine_barplot_DAY.png (deflated 18%) adding: barplots/methionine_barplot.png (deflated 23%) adding: barplots/leucine_barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/ribitol..adonitol._barplot.png (stored 0%) adding: barplots/gamma.aminobutyrate..GABA._barplot.png (deflated 23%) adding: barplots/betaine_barplot.png (deflated 32%) adding: barplots/cysteine_barplot.png (deflated 22%) adding: barplots/aspartate_barplot.map (deflated 79%) adding: barplots/X4.guanidinobutanoate_barplot_DAY.png (deflated 21%) adding: barplots/isoleucine_barplot_DOSE_MG_KG.png (deflated 18%) adding: barplots/galactose.1.phosphate_barplot.png (deflated 21%) adding: barplots/N.acetylglucosamine_barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/proline_barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/X15.anhydroglucitol..15.AG._barplot_DOSE_MG_KG.png (deflated 21%) adding: barplots/N.acetylglucosamine.6.phosphate_barplot.map (deflated 78%) adding: barplots/phosphoenolpyruvate..PEP._barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/glucose_barplot_DAY.png (deflated 17%) adding: barplots/N.acetylmethionine_barplot.png (deflated 37%) adding: barplots/kynurenine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/trans.4.hydroxyproline_barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/ornithine_barplot.map (deflated 79%) adding: barplots/phenylalanine_barplot.png (deflated 25%) adding: barplots/cysteine_barplot_DAY.png (deflated 18%) adding: barplots/gamma.aminobutyrate..GABA._barplot_WEIGHT_MG.png (deflated 11%) adding: barplots/ornithine_barplot_DAY.png (deflated 19%) adding: barplots/X3.phosphoglycerate_barplot_DAY.png (deflated 20%) adding: barplots/trans.4.hydroxyproline_barplot_DAY.png (deflated 23%) adding: barplots/cysteine_barplot.map (deflated 79%) adding: barplots/isoleucine_barplot.png (deflated 23%) adding: barplots/fructose_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/arginine_barplot.map (deflated 79%) adding: barplots/urea_barplot.map (deflated 79%) adding: barplots/hypotaurine_barplot_WEIGHT_MG.png (deflated 10%) adding: barplots/maltotriose_barplot.map (deflated 79%) adding: barplots/mannose_barplot_DAY.png (deflated 17%) adding: barplots/glutathione.oxidized..GSSG._barplot.png (deflated 26%) adding: barplots/X3.phosphoglycerate_barplot.png (deflated 25%) adding: barplots/N.acetylmannosamine_barplot_DAY.png (deflated 17%) adding: data_all_beforeCheck.csv (deflated 51%) adding: data_beforeCheck.csv (deflated 51%) adding: phenotypes_nominal.csv (deflated 76%) adding: aux.txt (stored 0%) adding: server_log.txt (deflated 87%) adding: keggMapping.csv (deflated 60%) adding: phenotypes_beforeCheck.csv (deflated 68%) FINISHED with /home/metap2/exec/process_metaP_data.R + echo 'these are the files that are now here:' these are the files that are now here: + ls -ltra total 3744 -rw-r--r-- 1 www-data www-data 66723 Aug 20 10:19 input.tmp -rw-r--r-- 1 www-data www-data 66714 Aug 20 10:19 input -rw-r--r-- 1 www-data www-data 1258 Aug 20 10:19 phenotypes.txt.tmp -rw-r--r-- 1 www-data www-data 1258 Aug 20 10:19 phenotypes.txt -rw-r--r-- 1 www-data www-data 0 Aug 20 10:19 aux.txt -rw-r--r-- 1 www-data www-data 281 Aug 20 10:19 options -rwxr-xr-x 1 www-data www-data 611 Aug 20 10:19 metaPjob.cmd -rw-rw-r-- 1 metap2 metap2 1 Aug 20 10:20 out_params.txt -rw-rw-r-- 1 metap2 metap2 65673 Aug 20 10:20 input_4R -rw-rw-r-- 1 metap2 metap2 4322 Aug 20 10:20 keggMapping.csv -rw-rw-r-- 1 metap2 metap2 6643 Aug 20 10:20 metabNamesMapping.csv -rw-rw-r-- 1 metap2 metap2 67535 Aug 20 10:20 data_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 1210 Aug 20 10:20 phenotypes_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 68075 Aug 20 10:20 data_all_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 2 Aug 20 10:20 cv.ok -rw-rw-r-- 1 metap2 metap2 3903 Aug 20 10:20 colsToMark.x.csv -rw-rw-r-- 1 metap2 metap2 336 Aug 20 10:20 rowsToMark.csv -rw-rw-r-- 1 metap2 metap2 65 Aug 20 10:20 colsToMark.csv -rw-rw-r-- 1 metap2 metap2 67059 Aug 20 10:20 data.csv -rw-rw-r-- 1 metap2 metap2 203 Aug 20 10:20 phenotypes_for_QC.csv -rw-rw-r-- 1 metap2 metap2 825 Aug 20 10:20 phenotypes.csv -rw-rw-r-- 1 metap2 metap2 67681 Aug 20 10:20 data_all.csv -rw-rw-r-- 1 metap2 metap2 626 Aug 20 10:20 phenotypes_nominal.csv -rw-rw-r-- 1 metap2 metap2 533 Aug 20 10:20 phenotypes_numeric.csv -rw-rw-r-- 1 metap2 metap2 20563 Aug 20 10:20 summary.csv -rw-rw-r-- 1 metap2 metap2 1772989 Aug 20 10:20 histograms.pdf drwxrwxrwx 1331 metap2 metap2 135168 Aug 20 10:21 .. drwxrwxrwx 2 www-data www-data 20480 Aug 20 10:21 barplots -rw-rw-r-- 1 metap2 metap2 29665 Aug 20 10:21 .R.Rout -rw-rw-r-- 1 metap2 metap2 1246 Aug 20 10:21 processing_log.txt -rw-rw-r-- 1 metap2 metap2 23459 Aug 20 10:21 server_log.txt -rw-rw-r-- 1 metap2 metap2 1247150 Aug 20 10:21 download.zip drwxrwxrwx 3 www-data www-data 4096 Aug 20 10:21 . + set - Finishing METAP SERVER