Running METAP SERVER
Thu Jun 16 16:39:01 CEST 2016
ID=16061616383514696
/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/16061616383514696
+ hostname
metap
+ uname -a
Linux metap 3.13.0-79-generic #123-Ubuntu SMP Fri Feb 19 14:27:58 UTC 2016 x86_64 x86_64 x86_64 GNU/...
+ echo 'this is the environment'
this is the environment
+ env
RATIOS=n
OUTLIER=n
MISSING=n
DATADIR=/home/metap2/data
SHELL=/bin/sh
JOBID=P2_female
REFERENCE=n
PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PWD=/home/metap2/public_html/users/16061616383514696
PRIVAT=0
LANG=en_US.UTF-8
SHLVL=1
HOME=/home/metap2
ID=16061616383514696
DEL_METABS=n
FORMAT=absoluteIDQ
LOGNAME=metap2
EMAIL=unknown
USERID=unknown
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...
Use of uninitialized value $max_length in numeric lt (<) at /home/metap2/exec/readAux.pl line 71.
-rw-rw-r-- 1 metap2 metap2 2131663 Jun 16 16:43 .R.Rout
  adding: batchBoxplot.pdf (deflated 90%)
  adding: sample_description.csv (deflated 66%)
  adding: summary.csv (deflated 56%)
  adding: colsToMark.x.csv (deflated 83%)
  adding: phenotypes.csv (deflated 77%)
  adding: data_all.csv (deflated 66%)
  adding: cv_average.csv (deflated 53%)
  adding: processing_log.txt (deflated 72%)
  adding: options (deflated 39%)
  adding: colsToMark.csv (deflated 30%)
  adding: phenotypes_numeric.csv (deflated 77%)
  adding: cv.pdf (deflated 85%)
  adding: hypothesisTests_complete_data.pdf (deflated 88%)
  adding: bonferroni.csv (deflated 20%)
  adding: rowsToMark.csv (deflated 72%)
  adding: metabNamesMapping.csv (deflated 79%)
  adding: out_params.txt (stored 0%)
  adding: input (deflated 73%)
  adding: data.csv (deflated 66%)
  adding: pValuesForAllMetabolites__AGE.csv (deflated 61%)
  adding: phenotypes.txt (deflated 82%)
  adding: pValuesForAllMetabolites__Batch.key.csv (deflated 76%)
  adding: phenotypes_for_QC.csv (deflated 86%)
  adding: histograms.pdf (deflated 88%)
  adding: PBS_cv.csv (deflated 62%)
  adding: barplots/1014434671_sbarplot.map (deflated 83%)
  adding: barplots/PC.aa.C42.4_barplot_Genotype.png (deflated 17%)
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  adding: barplots/C16_barplot_AGE.png (deflated 17%)
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  adding: barplots/1014434666_sbarplot.map (deflated 83%)
  adding: barplots/PC.aa.C40.1_barplot_Genotype.png (deflated 16%)
  adding: barplots/PC.ae.C40.4_barplot.png (deflated 35%)
  adding: barplots/PC.aa.C40.4_barplot.png (deflated 31%)
  adding: barplots/C6..C4.1.DC._barplot_Radiation.png (deflated 16%)
  adding: barplots/PC.aa.C34.2_barplot_Genotype.png (deflated 24%)
  adding: barplots/PC.ae.C42.5_barplot.png (deflated 21%)
  adding: barplots/1014434749_4keggColoring.csv (deflated 89%)
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  adding: barplots/PC.aa.C34.2_barplot_Radiation.png (deflated 23%)
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  adding: barplots/C2_barplot_AGE.png (deflated 20%)
  adding: barplots/SM.C18.0_barplot_Genotype.png (deflated 22%)
  adding: barplots/C7.DC_barplot_Radiation.png (deflated 17%)
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  adding: barplots/PC.ae.C34.2_barplot_Radiation.png (deflated 24%)
  adding: barplots/PC.aa.C42.5_barplot_AGE.png (deflated 14%)
  adding: barplots/1014435079_sbarplot.map (deflated 83%)
  adding: barplots/Total.AC.OH...Total.AC_barplot.png (deflated 23%)
  adding: barplots/PC.ae.C40.6_barplot.png (deflated 25%)
  adding: barplots/1014435302_4keggColoring.csv (deflated 89%)
  adding: barplots/His_barplot_Radiation.png (deflated 22%)
  adding: barplots/PC.aa.C32.3_barplot_Genotype.png (deflated 16%)
  adding: barplots/1014434860_sbarplot.map (deflated 83%)
  adding: barplots/C16_barplot_Radiation.png (deflated 17%)
  adding: barplots/C7.DC_barplot_AGE.png (deflated 19%)
  adding: barplots/Orn_barplot_Radiation.png (deflated 22%)
  adding: barplots/Carnosine_barplot_AGE.png (deflated 18%)
  adding: barplots/C16.1.OH_barplot.map (deflated 82%)
  adding: barplots/1014435336_4keggColoring.csv (deflated 89%)
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  adding: barplots/1014434720_4keggColoring.csv (deflated 90%)
  adding: barplots/lysoPC.a.C20.4_barplot_Radiation.png (deflated 20%)
  adding: barplots/PC.aa.C34.4_barplot.png (deflated 23%)
  adding: barplots/Glu_barplot_Radiation.png (deflated 22%)
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  adding: barplots/1014434753_sbarplot.png (deflated 33%)
  adding: barplots/1014434893_4keggColoring.csv (deflated 90%)
  adding: barplots/SM.C22.3_barplot_Radiation.png (deflated 17%)
  adding: barplots/Total.SM_barplot_AGE.png (deflated 22%)
  adding: barplots/PC.ae.C36.0_barplot_Radiation.png (deflated 15%)
  adding: barplots/total.DMA_barplot_AGE.png (deflated 33%)
  adding: barplots/C3.DC..C4.OH._barplot_Radiation.png (deflated 16%)
  adding: barplots/PC.ae.C42.5_barplot.map (deflated 83%)
  adding: barplots/PC.ae.C36.1_barplot_AGE.png (deflated 22%)
  adding: barplots/SM.C24.1_barplot_Radiation.png (deflated 21%)
  adding: barplots/1014434715_sbarplot.png (deflated 33%)
  adding: barplots/Met.SO_barplot_Genotype.png (deflated 25%)
  adding: barplots/Kynurenine_barplot_Genotype.png (deflated 21%)
  adding: barplots/1014435011_sbarplot.png (deflated 32%)
  adding: barplots/Trp_barplot_AGE.png (deflated 22%)
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  adding: barplots/PC.ae.C36.1_barplot_Genotype.png (deflated 28%)
  adding: barplots/SM.C18.1_barplot_Genotype.png (deflated 23%)
  adding: barplots/PC.ae.C44.4_barplot_Genotype.png (deflated 19%)
  adding: barplots/Kynurenine_barplot_Radiation.png (deflated 17%)
  adding: barplots/1014435109_sbarplot.map (deflated 83%)
  adding: barplots/lysoPC.a.C26.1_barplot_Radiation.png (deflated 15%)
  adding: barplots/C12.DC_barplot.map (deflated 82%)
  adding: barplots/PC.aa.C42.4_barplot.map (deflated 82%)
  adding: barplots/1014434957_sbarplot.map (deflated 83%)
  adding: barplots/PC.ae.C36.4_barplot.png (deflated 23%)
  adding: barplots/1014435461_4keggColoring.csv (deflated 89%)
  adding: barplots/1014434817_sbarplot.map (deflated 83%)
  adding: barplots/1014435253_sbarplot.png (deflated 33%)
  adding: barplots/1014434841_4keggColoring.csv (deflated 90%)
  adding: barplots/PC.ae.C44.6_barplot_Radiation.png (deflated 17%)
  adding: barplots/C14.1.OH_barplot.map (deflated 82%)
  adding: barplots/PC.ae.C42.0_barplot_AGE.png (deflated 17%)
  adding: barplots/1014435360_sbarplot.png (deflated 35%)
  adding: barplots/C5.1_barplot_AGE.png (deflated 18%)
  adding: barplots/SM..OH..C14.1_barplot.map (deflated 84%)
  adding: barplots/C6..C4.1.DC._barplot_Genotype.png (deflated 20%)
  adding: barplots/C3_barplot_AGE.png (deflated 23%)
  adding: barplots/Leu_barplot_AGE.png (deflated 22%)
  adding: barplots/PC.ae.C38.5_barplot.map (deflated 84%)
  adding: barplots/C0_barplot_AGE.png (deflated 20%)
  adding: barplots/PC.ae.C44.3_barplot_Radiation.png (deflated 19%)
  adding: barplots/C6..C4.1.DC._barplot_AGE.png (deflated 18%)
  adding: barplots/1014435031_sbarplot.png (deflated 32%)
  adding: barplots/PC.ae.C38.1_barplot_AGE.png (deflated 17%)
  adding: barplots/c4.OH.Pro_barplot_Radiation.png (deflated 16%)
  adding: barplots/PC.ae.C36.2_barplot.png (deflated 27%)
  adding: barplots/PC.aa.C38.1_barplot.png (deflated 23%)
  adding: barplots/Ala_barplot.map (deflated 84%)
  adding: barplots/1014435215_sbarplot.map (deflated 83%)
  adding: barplots/PC.ae.C42.4_barplot.png (deflated 22%)
  adding: barplots/SM.C26.0_barplot_Radiation.png (deflated 16%)
  adding: barplots/Orn...Arg_barplot_AGE.png (deflated 18%)
  adding: barplots/PC.ae.C40.1_barplot.png (deflated 36%)
  adding: barplots/Total.SM_barplot_Genotype.png (deflated 26%)
  adding: barplots/PC.aa.C36.2_barplot_AGE.png (deflated 22%)
  adding: barplots/C16.2.OH_barplot_Genotype.png (deflated 21%)
  adding: barplots/lysoPC.a.C26.0_barplot.map (deflated 82%)
  adding: barplots/Trp_barplot.map (deflated 84%)
  adding: barplots/PC.ae.C38.2_barplot.png (deflated 31%)
  adding: barplots/PC.ae.C42.4_barplot_Genotype.png (deflated 20%)
  adding: barplots/C14.2.OH_barplot_AGE.png (deflated 15%)
  adding: barplots/1014434855_sbarplot.png (deflated 32%)
  adding: barplots/SM.C24.1_barplot_AGE.png (deflated 22%)
  adding: barplots/C12.DC_barplot.png (deflated 22%)
  adding: barplots/SM.C26.1_barplot_AGE.png (deflated 12%)
  adding: barplots/C6.1_barplot_Radiation.png (deflated 22%)
  adding: barplots/1014435201_sbarplot.map (deflated 83%)
  adding: barplots/1014434802_4keggColoring.csv (deflated 89%)
  adding: barplots/1014434715_4keggColoring.csv (deflated 89%)
  adding: barplots/PC.ae.C38.2_barplot_Radiation.png (deflated 21%)
  adding: barplots/PC.aa.C38.5_barplot_Genotype.png (deflated 22%)
  adding: barplots/CPT.I.ratio_barplot_AGE.png (deflated 16%)
  adding: barplots/1014435419_sbarplot.png (deflated 34%)
  adding: barplots/DOPA_barplot_Genotype.png (deflated 25%)
  adding: barplots/C4_barplot.png (deflated 30%)
  adding: barplots/Total.lysoPC...Total.PC_barplot_Radiation.png (deflated 16%)
  adding: barplots/C18.1.OH_barplot.map (deflated 82%)
  adding: barplots/C5.M.DC_barplot.png (deflated 22%)
  adding: barplots/Total.SM.non.OH_barplot_Radiation.png (deflated 25%)
  adding: barplots/C12_barplot_Genotype.png (deflated 15%)
  adding: barplots/C18.1.OH_barplot_Radiation.png (deflated 17%)
  adding: barplots/Val_barplot.map (deflated 84%)
  adding: barplots/lysoPC.a.C20.4_barplot.map (deflated 84%)
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  adding: barplots/1014434981_4keggColoring.csv (deflated 89%)
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  adding: barplots/DOPA_barplot.map (deflated 84%)
  adding: barplots/1014434893_sbarplot.png (deflated 32%)
  adding: barplots/1014435389_4keggColoring.csv (deflated 89%)
  adding: barplots/Thr_barplot_Radiation.png (deflated 22%)
  adding: barplots/PC.ae.C36.5_barplot_Radiation.png (deflated 22%)
  adding: barplots/1014434860_4keggColoring.csv (deflated 89%)
  adding: barplots/Lys_barplot_AGE.png (deflated 22%)
  adding: barplots/Lys_barplot.map (deflated 84%)
  adding: barplots/C16.OH_barplot.map (deflated 82%)
  adding: barplots/PC.aa.C40.1_barplot_Radiation.png (deflated 14%)
  adding: barplots/His_barplot_Genotype.png (deflated 25%)
  adding: barplots/Total.lysoPC...Total.PC_barplot_AGE.png (deflated 16%)
  adding: barplots/PC.aa.C24.0_barplot_AGE.png (deflated 15%)
  adding: barplots/C10.2_barplot_Genotype.png (deflated 16%)
  adding: barplots/Spermine_barplot.png (deflated 22%)
  adding: barplots/Asn_barplot.map (deflated 84%)
  adding: barplots/lysoPC.a.C28.0_barplot_Radiation.png (deflated 17%)
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  adding: barplots/DOPA_barplot.png (deflated 30%)
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  adding: barplots/PC.ae.C42.4_barplot_AGE.png (deflated 17%)
  adding: barplots/1014435007_sbarplot.map (deflated 83%)
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  adding: barplots/PC.ae.C42.4_barplot.map (deflated 82%)
  adding: barplots/PC.aa.C38.0_barplot_AGE.png (deflated 22%)
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  adding: barplots/1014434961_4keggColoring.csv (deflated 90%)
  adding: barplots/PC.aa.C40.4_barplot.map (deflated 84%)
  adding: barplots/PC.ae.C30.0_barplot_Radiation.png (deflated 15%)
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  adding: barplots/Ile_barplot_AGE.png (deflated 22%)
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  adding: barplots/PC.aa.C32.3_barplot_Radiation.png (deflated 15%)
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  adding: barplots/Asn_barplot_Genotype.png (deflated 25%)
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  adding: barplots/Ile_barplot_Radiation.png (deflated 22%)
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  adding: barplots/C3.OH_barplot.map (deflated 82%)
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  adding: barplots/Total.SM.OH...Total.SM.non.OH_barplot_Radiation.png (deflated 16%)
  adding: barplots/1014434690_4keggColoring.csv (deflated 89%)
  adding: barplots/PC.aa.C36.0_barplot_Radiation.png (deflated 24%)
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  adding: barplots/C8_barplot_Genotype.png (deflated 15%)
  adding: barplots/Ala_barplot_Radiation.png (deflated 22%)
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  adding: barplots/11000002_sbarplot.png (deflated 34%)
  adding: barplots/Total.SM.OH_barplot.png (deflated 29%)
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  adding: barplots/C10.1_barplot.png (deflated 30%)
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  adding: barplots/lysoPC.a.C20.3_barplot.map (deflated 84%)
  adding: barplots/MUFA..PC....SFA..PC._barplot.map (deflated 84%)
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  adding: barplots/Gly_barplot.map (deflated 84%)
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  adding: barplots/C3_barplot.map (deflated 83%)
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  adding: barplots/PC.ae.C32.1_barplot.map (deflated 82%)
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  adding: barplots/CPT.I.ratio_barplot_Genotype.png (deflated 15%)
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  adding: barplots/SM.C26.1_barplot_Genotype.png (deflated 13%)
  adding: barplots/1014435031_4keggColoring.csv (deflated 89%)
  adding: barplots/PC.aa.C32.0_barplot.png (deflated 28%)
  adding: barplots/PC.aa.C42.5_barplot_Genotype.png (deflated 15%)
  adding: barplots/PC.ae.C40.4_barplot_AGE.png (deflated 22%)
  adding: barplots/1014435045_sbarplot.map (deflated 83%)
  adding: barplots/1014434753_4keggColoring.csv (deflated 89%)
  adding: barplots/PC.ae.C42.2_barplot_Genotype.png (deflated 18%)
  adding: barplots/C16.1_barplot_AGE.png (deflated 16%)
  adding: barplots/1014434768_sbarplot.map (deflated 83%)
  adding: barplots/C12_barplot_AGE.png (deflated 14%)
  adding: barplots/C3.OH_barplot_Radiation.png (deflated 17%)
  adding: barplots/SM.C22.3_barplot_AGE.png (deflated 18%)
  adding: barplots/PC.aa.C42.6_barplot.png (deflated 20%)
  adding: barplots/1014435128_4keggColoring.csv (deflated 89%)
  adding: barplots/C3.OH_barplot.png (deflated 22%)
  adding: barplots/CPT.I.ratio_barplot.png (deflated 19%)
  adding: barplots/PC.aa.C38.6_barplot_AGE.png (deflated 19%)
  adding: barplots/PC.aa.C40.3_barplot.map (deflated 82%)
  adding: barplots/PC.ae.C32.2_barplot.png (deflated 19%)
  adding: barplots/C16.1_barplot.png (deflated 21%)
  adding: barplots/C8_barplot_Radiation.png (deflated 15%)
  adding: barplots/SM.C18.1_barplot_AGE.png (deflated 19%)
  adding: barplots/lysoPC.a.C18.1_barplot.map (deflated 84%)
  adding: barplots/C16_barplot.map (deflated 82%)
  adding: barplots/1014434942_sbarplot.png (deflated 33%)
  adding: barplots/PC.ae.C40.3_barplot.png (deflated 22%)
  adding: barplots/Tyr...Phe_barplot.png (deflated 24%)
  adding: barplots/1014434919_sbarplot.png (deflated 33%)
  adding: barplots/1014434817_4keggColoring.csv (deflated 89%)
  adding: barplots/PC.aa.C36.5_barplot.png (deflated 35%)
  adding: barplots/1014435374_4keggColoring.csv (deflated 90%)
  adding: barplots/Lys_barplot_Radiation.png (deflated 22%)
  adding: barplots/1014435442_sbarplot.map (deflated 83%)
  adding: barplots/PC.aa.C32.0_barplot.map (deflated 84%)
  adding: barplots/PC.ae.C36.5_barplot_Genotype.png (deflated 26%)
  adding: barplots/PC.ae.C34.3_barplot_AGE.png (deflated 16%)
  adding: barplots/Ser_barplot.map (deflated 84%)
  adding: barplots/SM.C26.0_barplot_AGE.png (deflated 15%)
  adding: barplots/C14_barplot.map (deflated 82%)
  adding: barplots/1014435007_4keggColoring.csv (deflated 89%)
  adding: barplots/PEA_barplot_Radiation.png (deflated 17%)
  adding: barplots/C2...C0_barplot_AGE.png (deflated 16%)
  adding: barplots/PC.aa.C24.0_barplot_Radiation.png (deflated 16%)
  adding: barplots/11000002_4keggColoring.csv (deflated 89%)
  adding: barplots/PC.aa.C42.1_barplot.png (deflated 22%)
  adding: barplots/C5.DC..C6.OH._barplot_Radiation.png (deflated 16%)
  adding: barplots/C5.1_barplot_Genotype.png (deflated 21%)
  adding: barplots/C10_barplot.map (deflated 82%)
  adding: barplots/1014434961_sbarplot.map (deflated 83%)
  adding: barplots/1014434715_sbarplot.map (deflated 83%)
  adding: barplots/PC.ae.C38.5_barplot_Radiation.png (deflated 20%)
  adding: barplots/PC.ae.C32.1_barplot_Genotype.png (deflated 14%)
  adding: barplots/PC.ae.C42.1_barplot_AGE.png (deflated 18%)
  adding: barplots/PC.ae.C30.0_barplot_Genotype.png (deflated 16%)
  adding: barplots/1014435201_sbarplot.png (deflated 34%)
  adding: barplots/SM..OH..C22.2_barplot.png (deflated 35%)
  adding: barplots/PC.ae.C32.2_barplot_Genotype.png (deflated 17%)
  adding: barplots/PC.aa.C42.0_barplot_Genotype.png (deflated 18%)
  adding: barplots/Total.SM_barplot_Radiation.png (deflated 22%)
  adding: barplots/MUFA..PC....SFA..PC._barplot_AGE.png (deflated 23%)
  adding: barplots/Spermidine_barplot_Radiation.png (deflated 26%)
  adding: barplots/lysoPC.a.C17.0_barplot_AGE.png (deflated 23%)
  adding: barplots/PC.ae.C34.3_barplot_Radiation.png (deflated 16%)
  adding: barplots/1014435249_sbarplot.map (deflated 83%)
  adding: barplots/Tyr_barplot_AGE.png (deflated 22%)
  adding: barplots/lysoPC.a.C18.0_barplot_Radiation.png (deflated 22%)
  adding: barplots/C16.2_barplot.map (deflated 82%)
  adding: barplots/Asp_barplot.png (deflated 30%)
  adding: barplots/1014434957_sbarplot.png (deflated 32%)
  adding: barplots/C3_barplot_Radiation.png (deflated 24%)
  adding: barplots/1014434919_4keggColoring.csv (deflated 89%)
  adding: barplots/PC.ae.C32.2_barplot_Radiation.png (deflated 15%)
  adding: barplots/PC.aa.C36.0_barplot_Genotype.png (deflated 26%)
  adding: barplots/lysoPC.a.C26.1_barplot.map (deflated 82%)
  adding: data_all_beforeCheck.csv (deflated 77%)
  adding: pValuesForAllMetabolites__Genotype.csv (deflated 64%)
  adding: lowerOutliers.csv (deflated 66%)
  adding: data_beforeCheck.csv (deflated 77%)
  adding: pValuesForAllMetabolites__Radiation.csv (deflated 61%)
  adding: Ref_Plasma-Hum_PK3_cv.csv (deflated 66%)
  adding: phenotypes_nominal.csv (deflated 77%)
  adding: aux.txt (stored 0%)
  adding: server_log.txt (deflated 90%)
  adding: metabolitesForDropping.csv (deflated 62%)
  adding: keggMapping.csv (deflated 84%)
  adding: phenotypes_beforeCheck.csv (deflated 84%)
  adding: refBatchBoxplot.pdf (deflated 94%)
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 12100
-rw-r--r--    1 www-data www-data  390103 Jun 16 16:38 input.tmp
-rw-r--r--    1 www-data www-data    2089 Jun 16 16:38 phenotypes.txt.tmp
-rw-r--r--    1 www-data www-data  390103 Jun 16 16:38 input
-rw-r--r--    1 www-data www-data    2089 Jun 16 16:38 phenotypes.txt
-rw-r--r--    1 www-data www-data       0 Jun 16 16:38 aux.txt
-rw-r--r--    1 www-data www-data     243 Jun 16 16:38 options
-rwxr-xr-x    1 www-data www-data     609 Jun 16 16:38 metaPjob.cmd
drwxrwxrwx 1909 metap2   metap2    212992 Jun 16 16:39 ..
-rw-rw-r--    1 metap2   metap2         1 Jun 16 16:39 out_params.txt
-rw-rw-r--    1 metap2   metap2    389539 Jun 16 16:39 input_4R
-rw-rw-r--    1 metap2   metap2      8271 Jun 16 16:39 keggMapping.csv
-rw-rw-r--    1 metap2   metap2     12372 Jun 16 16:39 metabNamesMapping.csv
-rw-rw-r--    1 metap2   metap2    178934 Jun 16 16:39 data_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2    183725 Jun 16 16:39 data_all_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2      6625 Jun 16 16:39 phenotypes_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2      6472 Jun 16 16:39 PBS_cv.csv
-rw-rw-r--    1 metap2   metap2      5523 Jun 16 16:39 Ref_Plasma-Hum_PK3_cv.csv
-rw-rw-r--    1 metap2   metap2     69936 Jun 16 16:39 cv.pdf
-rw-rw-r--    1 metap2   metap2         2 Jun 16 16:39 cv.ok
-rw-rw-r--    1 metap2   metap2       968 Jun 16 16:39 metabolitesForDropping.csv
-rw-rw-r--    1 metap2   metap2      3140 Jun 16 16:39 cv_average.csv
-rw-rw-r--    1 metap2   metap2    797687 Jun 16 16:39 refBatchBoxplot.pdf
-rw-rw-r--    1 metap2   metap2      3158 Jun 16 16:39 pValuesForAllMetabolites__Batch.key.csv
-rw-rw-r--    1 metap2   metap2    375325 Jun 16 16:39 batchBoxplot.pdf
-rw-rw-r--    1 metap2   metap2      7070 Jun 16 16:39 lowerOutliers.csv
-rw-rw-r--    1 metap2   metap2      8839 Jun 16 16:39 colsToMark.x.csv
-rw-rw-r--    1 metap2   metap2        98 Jun 16 16:39 colsToMark.csv
-rw-rw-r--    1 metap2   metap2       591 Jun 16 16:39 rowsToMark.csv
-rw-rw-r--    1 metap2   metap2    105366 Jun 16 16:39 data.csv
-rw-rw-r--    1 metap2   metap2      1202 Jun 16 16:39 sample_description.csv
-rw-rw-r--    1 metap2   metap2      4298 Jun 16 16:39 phenotypes_for_QC.csv
-rw-rw-r--    1 metap2   metap2      2159 Jun 16 16:39 phenotypes.csv
-rw-rw-r--    1 metap2   metap2    107558 Jun 16 16:39 data_all.csv
-rw-rw-r--    1 metap2   metap2      2159 Jun 16 16:39 phenotypes_nominal.csv
-rw-rw-r--    1 metap2   metap2      1746 Jun 16 16:39 phenotypes_numeric.csv
-rw-rw-r--    1 metap2   metap2     19977 Jun 16 16:39 summary.csv
-rw-rw-r--    1 metap2   metap2   1617601 Jun 16 16:39 histograms.pdf
drwxrwxrwx    2 www-data www-data   65536 Jun 16 16:43 barplots
-rw-rw-r--    1 metap2   metap2      4713 Jun 16 16:43 pValuesForAllMetabolites__AGE.csv
-rw-rw-r--    1 metap2   metap2      4657 Jun 16 16:43 pValuesForAllMetabolites__Radiation.csv
-rw-rw-r--    1 metap2   metap2       115 Jun 16 16:43 bonferroni.csv
-rw-rw-r--    1 metap2   metap2      4578 Jun 16 16:43 pValuesForAllMetabolites__Genotype.csv
-rw-rw-r--    1 metap2   metap2   1354007 Jun 16 16:43 hypothesisTests_complete_data.pdf
-rw-rw-r--    1 metap2   metap2   2131663 Jun 16 16:43 .R.Rout
-rw-rw-r--    1 metap2   metap2      5614 Jun 16 16:43 processing_log.txt
-rw-rw-r--    1 metap2   metap2     80462 Jun 16 16:43 server_log.txt
-rw-rw-r--    1 metap2   metap2   3696582 Jun 16 16:43 download.zip
drwxrwxrwx    3 www-data www-data    4096 Jun 16 16:43 .
+ set -
Finishing METAP SERVER


-----

OPTION:FORMAT:data format: ' absoluteIDQ '
OPTION:MISSING:treat LOD/out of quant. data as missing: ' n '
OPTION:OUTLIER:drop outliers : ' n '
OPTION:REFERENCE:drop reference samples : ' n '
OPTION:DEL_METABS:drop metabolites with cv > 0.25 : ' n '
OPTION:RATIOS:calculate metabolite ratios : ' n '
AUX:Barplots of each metabolite class have equal y axis: TRUE 
Fileformat MetIQ - original - win-lin
Read MetIQ dataset with 449 columns and 94 rows
AbsoluteIDQ data format
EXTRACT:No validity information available
Keeping data annotated as non-valid
EXTRACT: 94  samples and  430  metabolites extracted
AbsoluteIDQ data format
EXTRACT:No validity information available
Keeping data annotated as non-valid
PHENOTYPES_UPLOAD:Found  77  matched lines with  3  phenotypes specified

PHENOTYPES_UPLOAD:Found  AGE Radiation Genotype as non-data quality phenotypes

REPLICATES:Added sample description for info on replicates for data quality checks
BATCHES:Added Plate.bar.code as a phenotypes for data quality checks
Wrote machted dataset to data_all_beforeCheck.csv
NA_COLS:For following metabolites all values are missing: C0.Status C10.Status C10.1.Status C10.2.Status C12.Status C12.DC.Status C12.1.Status C14.Status C14.1.Status C14.1.OH.Status C14.2.Status C14.2.OH.Status C16.Status C16.OH.Status C16.1.Status C16.1.OH.Status C16.2.Status C16.2.OH.Status C18.Status C18.1.Status C18.1.OH.Status C18.2.Status C2.Status C3.Status C5.OH..C3.DC.M..Status C3.OH.Status C3.1.Status C4.Status C3.DC..C4.OH..Status C4.1.Status C5.Status C5.DC..C6.OH..Status C5.M.DC.Status C5.1.Status C5.1.DC.Status C6..C4.1.DC..Status C6.1.Status C7.DC.Status C8.Status C9.Status Ala.Status Arg.Status Asn.Status Asp.Status Cit.Status Gln.Status Glu.Status Gly.Status His.Status Ile.Status Leu.Status Lys.Status Met.Status Orn.Status Phe.Status Pro.Status Ser.Status Thr.Status Trp.Status Tyr.Status Val.Status Ac.Orn.Status ADMA.Status alpha.AAA.Status c4.OH.Pro.Status Carnosine.Status Creatinine.Status DOPA.Status Dopamine.Status Histamine.Status Kynurenine.Status Met.SO.Status Nitro.Tyr.Status PEA.Status Putrescine.Status SDMA.Status Serotonin.Status Spermidine.Status Spermine.Status t4.OH.Pro.Status Taurine.Status total.DMA.Status lysoPC.a.C14.0.Status lysoPC.a.C16.0.Status lysoPC.a.C16.1.Status lysoPC.a.C17.0.Status lysoPC.a.C18.0.Status lysoPC.a.C18.1.Status lysoPC.a.C18.2.Status lysoPC.a.C20.3.Status lysoPC.a.C20.4.Status lysoPC.a.C24.0.Status lysoPC.a.C26.0.Status lysoPC.a.C26.1.Status lysoPC.a.C28.0.Status lysoPC.a.C28.1.Status PC.aa.C24.0.Status PC.aa.C26.0.Status PC.aa.C28.1.Status PC.aa.C30.0.Status PC.aa.C30.2.Status PC.aa.C32.0.Status PC.aa.C32.1.Status PC.aa.C32.2.Status PC.aa.C32.3.Status PC.aa.C34.1.Status PC.aa.C34.2.Status PC.aa.C34.3.Status PC.aa.C34.4.Status PC.aa.C36.0.Status PC.aa.C36.1.Status PC.aa.C36.2.Status PC.aa.C36.3.Status PC.aa.C36.4.Status PC.aa.C36.5.Status PC.aa.C36.6.Status PC.aa.C38.0.Status PC.aa.C38.1.Status PC.aa.C38.3.Status PC.aa.C38.4.Status PC.aa.C38.5.Status PC.aa.C38.6.Status PC.aa.C40.1.Status PC.aa.C40.2.Status PC.aa.C40.3.Status PC.aa.C40.4.Status PC.aa.C40.5.Status PC.aa.C40.6.Status PC.aa.C42.0.Status PC.aa.C42.1.Status PC.aa.C42.2.Status PC.aa.C42.4.Status PC.aa.C42.5.Status PC.aa.C42.6.Status PC.ae.C30.0.Status PC.ae.C30.1.Status PC.ae.C30.2.Status PC.ae.C32.1.Status PC.ae.C32.2.Status PC.ae.C34.0.Status PC.ae.C34.1.Status PC.ae.C34.2.Status PC.ae.C34.3.Status PC.ae.C36.0.Status PC.ae.C36.1.Status PC.ae.C36.2.Status PC.ae.C36.3.Status PC.ae.C36.4.Status PC.ae.C36.5.Status PC.ae.C38.0.Status PC.ae.C38.1.Status PC.ae.C38.2.Status PC.ae.C38.3.Status PC.ae.C38.4.Status PC.ae.C38.5.Status PC.ae.C38.6.Status PC.ae.C40.1.Status PC.ae.C40.2.Status PC.ae.C40.3.Status PC.ae.C40.4.Status PC.ae.C40.5.Status PC.ae.C40.6.Status PC.ae.C42.0.Status PC.ae.C42.1.Status PC.ae.C42.2.Status PC.ae.C42.3.Status PC.ae.C42.4.Status PC.ae.C42.5.Status PC.ae.C44.3.Status PC.ae.C44.4.Status PC.ae.C44.5.Status PC.ae.C44.6.Status SM..OH..C14.1.Status SM..OH..C16.1.Status SM..OH..C22.1.Status SM..OH..C22.2.Status SM..OH..C24.1.Status SM.C16.0.Status SM.C16.1.Status SM.C18.0.Status SM.C18.1.Status SM.C20.2.Status SM.C22.3.Status SM.C24.0.Status SM.C24.1.Status SM.C26.0.Status SM.C26.1.Status H1.Status X.C2.C3....C0.Status AAA.Status C2...C0.Status CPT.I.ratio.Status MUFA..PC..Status MUFA..PC....SFA..PC..Status Orn...Arg.Status PUFA..PC..Status PUFA..PC....MUFA..PC..Status PUFA..PC....SFA..PC..Status SFA..PC..Status Total..PC.SM..Status Total.AC...C0.Status Total.AC.DC...Total.AC.Status Total.AC.OH...Total.AC.Status Total.lysoPC.Status Total.lysoPC...Total.PC.Status Total.PC.Status Total.PC.aa.Status Total.PC.ae.Status Total.SM.Status Total.SM...Total..SM.PC..Status Total.SM...Total.PC.Status Total.SM.non.OH.Status Total.SM.OH.Status Total.SM.OH...Total.SM.non.OH.Status Tyr...Phe.Status AAA PUFA..PC. PUFA..PC....MUFA..PC. SFA..PC. Total..PC.SM. Total.lysoPC Total.PC Total.PC.aa Total.PC.ae . Has been deleted
NA_ROWS:For following samples all values are missing: NA NA NA . Has been deleted 
DEL_METAB:Found  99 metabolites with cv above  0.25 
Boxplots generated
Wrote extreme outliers into  lowerOutliers.csv 
No extreme outliers identified
 85  samples and  206  metabolites in checked data set
Wrote machted dataset to data_all.csv
Phenotype  AGE  is nominal
Phenotype  Radiation  is numeric
Phenotype  Radiation  added to nominal phenotypes also
Phenotype  Genotype  is nominal
Phenotype  Genotype  added to numeric phenotypes also
 Wrote summary.csv file
 138 Distribution plots generated
Boxplots generated
Boxplots generated
Boxplots generated

KEGG Data is provided by the Kanehisa Laboratories for academic use. Any commercial use of KEGG data requires a license agreement from Pathway Solutions Inc.
The Helmholtz Zentrum München imprint applies.

This page is maintained by Gabi Kastenmüller and Werner Römisch-Margl.
Last modification: 28 December 2009

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