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server

JobID: 15081316325326915

***  human-mouse-bovine plasma AbsIDQ  ***

  Metabolites  |  Samples  |  Quality Check  |  PCA  |  Kendall  |  Hypothesis test  |  Logs  |  Input data  |  Download results  

LOGFILES

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Running METAP SERVER
Thu Aug 13 16:33:01 CEST 2015
ID=15081316325326915
/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/15081316325326915
+ 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/Li...
+ echo 'this is the environment'
this is the environment
+ env
RATIOS=n
OUTLIER=n
MISSING=n
DATADIR=/home/metap2/data
SHELL=/bin/sh
JOBID=human-mouse-bovine plasma AbsIDQ
REFERENCE=y
PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PWD=/home/metap2/public_html/users/15081316325326915
PRIVAT=0
LANG=en_US.UTF-8
SHLVL=1
HOME=/home/metap2
ID=15081316325326915
DEL_METABS=y
FORMAT=absoluteIDQ
LOGNAME=metap2
EMAIL=jwt
USERID=jwt
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 4240279 Aug 13 16:37 .R.Rout
  adding: batchBoxplot.pdf (deflated 88%)
  adding: PCA_PC1_PC3.map (deflated 82%)
  adding: PCAplasma.type_PC1_PC3.map (deflated 82%)
  adding: sample_description.csv (deflated 85%)
  adding: summary.csv (deflated 51%)
  adding: colsToMark.x.csv (deflated 77%)
  adding: phenotypes.csv (deflated 85%)
  adding: data_all.csv (deflated 53%)
  adding: PCAplasma.type_PC2_PC3.map (deflated 82%)
  adding: PCA_PC1_PC2.png (deflated 18%)
  adding: cv_average.csv (deflated 52%)
  adding: processing_log.txt (deflated 53%)
  adding: options (deflated 35%)
  adding: colsToMark.csv (deflated 25%)
  adding: cv.pdf (deflated 85%)
  adding: PCAplasma.type_PC1_PC2.png (deflated 18%)
  adding: PCAplasma.type_propOfVar.png (deflated 17%)
  adding: PCA_PC1_PC2.map (deflated 83%)
  adding: PCA_PC2_PC3.map (deflated 82%)
  adding: hypothesisTests_complete_data.pdf (deflated 89%)
  adding: pValuesForAllMetabolites__plasma.type.csv (deflated 63%)
  adding: bonferroni.csv (deflated 19%)
  adding: rowsToMark.csv (deflated 78%)
  adding: metabNamesMapping.csv (deflated 72%)
  adding: PCA.pdf (deflated 86%)
  adding: out_params.txt (stored 0%)
  adding: QC_cv.csv (deflated 63%)
  adding: input (deflated 65%)
  adding: data.csv (deflated 53%)
  adding: PCAplasma.type.pdf (deflated 90%)
  adding: phenotypes.txt (deflated 85%)
  adding: pValuesForAllMetabolites__Batch.key.csv (deflated 60%)
  adding: phenotypes_for_QC.csv (deflated 83%)
  adding: histograms.pdf (deflated 88%)
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  adding: barplots/PC.aa.C36.5_barplot.map (deflated 83%)
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  adding: barplots/Gln.PTC_barplot.map (deflated 82%)
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  adding: barplots/lysoPC.a.C26.0_barplot.png (deflated 14%)
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  adding: barplots/PC.ae.C36.4_barplot.map (deflated 83%)
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  adding: barplots/PC.ae.C40.0_barplot.png (deflated 21%)
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  adding: barplots/400417140_4keggColoring.csv (deflated 93%)
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  adding: barplots/C16.2.OH_barplot.png (deflated 12%)
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  adding: barplots/PC.aa.C38.3_barplot.map (deflated 83%)
  adding: barplots/400417294_4keggColoring.csv (deflated 92%)
  adding: barplots/lysoPC.a.C20.4_barplot_plasma.type.png (deflated 20%)
  adding: barplots/lysoPC.a.C28.1_barplot.map (deflated 82%)
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  adding: barplots/SM.C20.2_barplot.png (deflated 19%)
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  adding: barplots/SM.C22.3_barplot.map (deflated 83%)
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  adding: barplots/C5.1_barplot.map (deflated 82%)
  adding: barplots/400495971_4keggColoring.csv (deflated 92%)
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  adding: barplots/Gly.PTC_barplot.png (deflated 17%)
  adding: barplots/PC.aa.C40.6_barplot_plasma.type.png (deflated 18%)
  adding: barplots/C7.DC_barplot_plasma.type.png (deflated 11%)
  adding: barplots/PC.ae.C44.5_barplot.map (deflated 83%)
  adding: barplots/400419356_4keggColoring.csv (deflated 93%)
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  adding: barplots/C14.1.OH_barplot_plasma.type.png (deflated 11%)
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  adding: barplots/PC.aa.C40.4_barplot_plasma.type.png (deflated 17%)
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  adding: barplots/C18.2_barplot_plasma.type.png (deflated 13%)
  adding: barplots/400419133_sbarplot.map (deflated 83%)
  adding: barplots/400416780_4keggColoring.csv (deflated 93%)
  adding: barplots/Pro.PTC_barplot_plasma.type.png (deflated 15%)
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  adding: barplots/400495724_sbarplot.map (deflated 83%)
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  adding: barplots/400418671_4keggColoring.csv (deflated 93%)
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  adding: barplots/lysoPC.a.C28.0_barplot.map (deflated 82%)
  adding: barplots/400495569_sbarplot.png (deflated 13%)
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  adding: barplots/400417634_sbarplot.png (deflated 13%)
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  adding: barplots/lysoPC.a.C18.1_barplot.png (deflated 19%)
  adding: barplots/400496069_sbarplot.map (deflated 83%)
  adding: barplots/400416998_4keggColoring.csv (deflated 93%)
  adding: barplots/400419031_sbarplot.map (deflated 83%)
  adding: barplots/400496021_4keggColoring.csv (deflated 93%)
  adding: barplots/SM.C20.2_barplot.map (deflated 83%)
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  adding: barplots/PC.ae.C30.0_barplot_plasma.type.png (deflated 13%)
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  adding: barplots/400417431_sbarplot.map (deflated 83%)
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  adding: barplots/PC.aa.C38.0_barplot_plasma.type.png (deflated 14%)
  adding: barplots/400418721_sbarplot.map (deflated 83%)
  adding: barplots/C12.1_barplot_plasma.type.png (deflated 10%)
  adding: barplots/400416775_4keggColoring.csv (deflated 93%)
  adding: barplots/400416877_sbarplot.map (deflated 83%)
  adding: barplots/C0_barplot.map (deflated 83%)
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  adding: barplots/400418880_4keggColoring.csv (deflated 93%)
  adding: barplots/PC.ae.C42.2_barplot.map (deflated 83%)
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  adding: barplots/C8_barplot_plasma.type.png (deflated 11%)
  adding: barplots/400419084_4keggColoring.csv (deflated 92%)
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  adding: barplots/400496205_sbarplot.map (deflated 83%)
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  adding: barplots/Arg.PTC_barplot.map (deflated 82%)
  adding: barplots/PC.ae.C30.1_barplot_plasma.type.png (deflated 18%)
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  adding: barplots/SM..OH..C16.1_barplot_plasma.type.png (deflated 24%)
  adding: barplots/400418735_4keggColoring.csv (deflated 93%)
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  adding: barplots/400416931_sbarplot.png (deflated 14%)
  adding: barplots/PC.ae.C36.0_barplot.png (deflated 16%)
  adding: barplots/C3_barplot_plasma.type.png (deflated 13%)
  adding: barplots/PC.ae.C34.0_barplot.map (deflated 83%)
  adding: barplots/400419191_4keggColoring.csv (deflated 93%)
  adding: barplots/PC.aa.C36.4_barplot.png (deflated 19%)
  adding: barplots/400496069_sbarplot.png (deflated 14%)
  adding: barplots/lysoPC.a.C18.0_barplot.map (deflated 83%)
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  adding: barplots/C8.1_barplot.png (deflated 14%)
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  adding: barplots/400495883_sbarplot.png (deflated 13%)
  adding: barplots/lysoPC.a.C20.4_barplot.png (deflated 20%)
  adding: barplots/C6..C4.1.DC._barplot.map (deflated 82%)
  adding: barplots/PC.ae.C38.5_barplot_plasma.type.png (deflated 14%)
  adding: barplots/400495966_4keggColoring.csv (deflated 93%)
  adding: barplots/Orn.PTC_barplot.map (deflated 82%)
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  adding: barplots/400419240_4keggColoring.csv (deflated 92%)
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  adding: barplots/400418701_4keggColoring.csv (deflated 93%)
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  adding: barplots/SM.C18.1_barplot.map (deflated 83%)
  adding: barplots/C5.DC.C6.OH._barplot.map (deflated 82%)
  adding: barplots/PC.aa.C36.6_barplot_plasma.type.png (deflated 17%)
  adding: barplots/400417339_4keggColoring.csv (deflated 93%)
  adding: barplots/PC.ae.C44.3_barplot.map (deflated 83%)
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  adding: barplots/PC.ae.C44.5_barplot_plasma.type.png (deflated 16%)
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  adding: barplots/PC.aa.C30.0_barplot_plasma.type.png (deflated 15%)
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  adding: barplots/400495932_4keggColoring.csv (deflated 93%)
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  adding: barplots/PC.aa.C42.6_barplot.png (deflated 15%)
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  adding: barplots/C3.OH_barplot.png (deflated 15%)
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  adding: barplots/PC.aa.C40.3_barplot.map (deflated 83%)
  adding: barplots/PC.ae.C32.2_barplot.png (deflated 21%)
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  adding: barplots/PC.aa.C32.0_barplot_plasma.type.png (deflated 13%)
  adding: barplots/lysoPC.a.C18.1_barplot.map (deflated 83%)
  adding: barplots/C16_barplot.map (deflated 83%)
  adding: barplots/400416911_4keggColoring.csv (deflated 93%)
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  adding: barplots/PC.ae.C40.3_barplot.png (deflated 16%)
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  adding: barplots/C14.1_barplot_plasma.type.png (deflated 12%)
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  adding: barplots/PC.aa.C32.0_barplot.map (deflated 83%)
  adding: barplots/C14_barplot.map (deflated 83%)
  adding: barplots/C16.2_barplot_plasma.type.png (deflated 11%)
  adding: barplots/C12.DC_barplot_plasma.type.png (deflated 11%)
  adding: barplots/C0_barplot_plasma.type.png (deflated 12%)
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  adding: barplots/400419221_4keggColoring.csv (deflated 93%)
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  adding: barplots/400418691_sbarplot.png (deflated 14%)
  adding: barplots/400495913_4keggColoring.csv (deflated 92%)
  adding: barplots/PC.aa.C42.1_barplot.png (deflated 17%)
  adding: barplots/Gln.PTC_barplot_plasma.type.png (deflated 11%)
  adding: barplots/400495796_sbarplot.png (deflated 14%)
  adding: barplots/C10_barplot.map (deflated 83%)
  adding: barplots/Gly.PTC_barplot.map (deflated 82%)
  adding: barplots/400419341_sbarplot.map (deflated 83%)
  adding: barplots/400495932_sbarplot.png (deflated 14%)
  adding: barplots/400417411_sbarplot.png (deflated 14%)
  adding: barplots/lysoPC.a.C16.1_barplot_plasma.type.png (deflated 17%)
  adding: barplots/400416839_sbarplot.png (deflated 13%)
  adding: barplots/lysoPC.a.C14.0_barplot_plasma.type.png (deflated 12%)
  adding: barplots/SM..OH..C22.2_barplot.png (deflated 16%)
  adding: barplots/400418667_4keggColoring.csv (deflated 93%)
  adding: barplots/400417649_4keggColoring.csv (deflated 92%)
  adding: barplots/C5.DC.C6.OH._barplot_plasma.type.png (deflated 9%)
  adding: barplots/PC.aa.C34.4_barplot_plasma.type.png (deflated 19%)
  adding: barplots/400418996_sbarplot.png (deflated 14%)
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  adding: barplots/400416983_sbarplot.map (deflated 83%)
  adding: barplots/PC.ae.C42.4_barplot_plasma.type.png (deflated 15%)
  adding: barplots/400418735_sbarplot.png (deflated 13%)
  adding: barplots/C16.2_barplot.map (deflated 82%)
  adding: barplots/400417218_4keggColoring.csv (deflated 93%)
  adding: barplots/lysoPC.a.C26.1_barplot.map (deflated 83%)
  adding: data_all_beforeCheck.csv (deflated 53%)
  adding: data_beforeCheck.csv (deflated 53%)
  adding: PCA_PC1_PC3.png (deflated 16%)
  adding: phenotypes_nominal.csv (deflated 85%)
  adding: pca.rotations.csv (deflated 56%)
  adding: PCAplasma.type_PC1_PC2.map (deflated 83%)
  adding: PCA_propOfVar.png (deflated 24%)
  adding: aux.txt (stored 0%)
  adding: server_log.txt (deflated 90%)
  adding: metabolitesForDropping.csv (deflated 26%)
  adding: PCAplasma.type_PC2_PC3.png (deflated 16%)
  adding: keggMapping.csv (deflated 84%)
  adding: PCAplasma.type_PC1_PC3.png (deflated 16%)
  adding: PCA_PC2_PC3.png (deflated 15%)
  adding: phenotypes_beforeCheck.csv (deflated 90%)
  adding: refBatchBoxplot.pdf (deflated 92%)
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 24740
-rw-r--r--    1 www-data www-data 1107844 Aug 13 16:32 input.tmp
-rw-r--r--    1 www-data www-data    6719 Aug 13 16:32 phenotypes.txt.tmp
-rw-r--r--    1 www-data www-data 1107844 Aug 13 16:32 input
-rw-r--r--    1 www-data www-data    6719 Aug 13 16:32 phenotypes.txt
-rw-r--r--    1 www-data www-data       0 Aug 13 16:32 aux.txt
-rw-r--r--    1 www-data www-data     258 Aug 13 16:32 options
-rwxr-xr-x    1 www-data www-data     601 Aug 13 16:32 metaPjob.cmd
drwxrwxrwx 1313 metap2   metap2    135168 Aug 13 16:33 ..
-rw-rw-r--    1 metap2   metap2         1 Aug 13 16:33 out_params.txt
-rw-rw-r--    1 metap2   metap2   1107578 Aug 13 16:33 input_4R
-rw-rw-r--    1 metap2   metap2      8271 Aug 13 16:33 keggMapping.csv
-rw-rw-r--    1 metap2   metap2      4634 Aug 13 16:33 metabNamesMapping.csv
-rw-rw-r--    1 metap2   metap2    695819 Aug 13 16:33 data_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2    704319 Aug 13 16:33 data_all_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2     11262 Aug 13 16:33 phenotypes_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2      5689 Aug 13 16:33 QC_cv.csv
-rw-rw-r--    1 metap2   metap2     36751 Aug 13 16:33 cv.pdf
-rw-rw-r--    1 metap2   metap2         2 Aug 13 16:33 cv.ok
-rw-rw-r--    1 metap2   metap2        88 Aug 13 16:33 metabolitesForDropping.csv
-rw-rw-r--    1 metap2   metap2      2990 Aug 13 16:33 cv_average.csv
-rw-rw-r--    1 metap2   metap2   1260431 Aug 13 16:33 refBatchBoxplot.pdf
-rw-rw-r--    1 metap2   metap2      5168 Aug 13 16:33 pValuesForAllMetabolites__Batch.key.csv
-rw-rw-r--    1 metap2   metap2    461306 Aug 13 16:33 batchBoxplot.pdf
-rw-rw-r--    1 metap2   metap2      3213 Aug 13 16:33 rowsToMark.csv
-rw-rw-r--    1 metap2   metap2      2246 Aug 13 16:33 colsToMark.x.csv
-rw-rw-r--    1 metap2   metap2        81 Aug 13 16:33 colsToMark.csv
-rw-rw-r--    1 metap2   metap2    629931 Aug 13 16:33 data.csv
-rw-rw-r--    1 metap2   metap2      4340 Aug 13 16:33 sample_description.csv
-rw-rw-r--    1 metap2   metap2      4013 Aug 13 16:33 phenotypes_for_QC.csv
-rw-rw-r--    1 metap2   metap2      5873 Aug 13 16:33 phenotypes.csv
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-rw-rw-r--    1 metap2   metap2     23559 Aug 13 16:33 summary.csv
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drwxrwxrwx    2 www-data www-data   69632 Aug 13 16:37 barplots
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-rw-rw-r--    1 metap2   metap2    554751 Aug 13 16:37 hypothesisTests_complete_data.pdf
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-rw-rw-r--    1 metap2   metap2     51092 Aug 13 16:37 PCA.pdf
-rw-rw-r--    1 metap2   metap2    459276 Aug 13 16:37 pca.rotations.csv
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-rw-rw-r--    1 metap2   metap2     77433 Aug 13 16:37 PCAplasma.type.pdf
-rw-rw-r--    1 metap2   metap2   4240279 Aug 13 16:37 .R.Rout
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-rw-rw-r--    1 metap2   metap2      1321 Aug 13 16:37 processing_log.txt
-rw-rw-r--    1 metap2   metap2   6390423 Aug 13 16:37 download.zip
drwxrwxrwx    3 www-data www-data    4096 Aug 13 16:37 .
-rw-rw-r--    1 metap2   metap2     72954 Aug 13 16:37 server_log.txt
+ set -
Finishing METAP SERVER


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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 : ' y ' OPTION:DEL_METABS:drop metabolites with cv > 0.25 : ' y ' OPTION:RATIOS:calculate metabolite ratios : ' n ' AUX:Barplots of each metabolite class have equal y axis: TRUE Fileformat MetIQ - original Read MetIQ dataset with 334 columns and 243 rows AbsoluteIDQ data format Keeping data annotated as non-valid EXTRACT: 243 samples and 162 metabolites extracted AbsoluteIDQ data format Non-valid data annotated as missing PHENOTYPES_UPLOAD:Found 243 matched lines with 2 phenotypes specified
REPLICATES:Found REPLICATES as a phenotype for data quality checks PHENOTYPES_UPLOAD:Found plasma.type as non-data quality phenotypes
BATCHES:Added Plate.bar.code as a phenotypes for data quality checks Wrote machted dataset to data_all_beforeCheck.csv DEL_METAB:Found 9 metabolites with cv above 0.25 Boxplots generated No extreme outliers identified No extreme outliers identified 234 samples and 153 metabolites in checked data set Wrote machted dataset to data_all.csv Phenotype plasma.type is nominal Wrote summary.csv file 153 Distribution plots generated Boxplots generated 1 phenotypes processed for PCA






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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