Running METAP SERVER
Tue Aug  8 12:58:01 CEST 2017
ID=17080812571131782
/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/17080812571131782
+ hostname
metap
+ uname -a
Linux metap 4.4.0-87-generic #110-Ubuntu SMP Tue Jul 18 12:55:35 UTC 2017 x86_64 x86_64 x86_64 GNU/L...
+ echo 'this is the environment'
this is the environment
+ env
RATIOS=n
OUTLIER=n
MISSING=n
DATADIR=/home/metap2/data
SHELL=/bin/sh
JOBID=MH MM1s TIC
REFERENCE=n
PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PWD=/home/metap2/public_html/users/17080812571131782
PRIVAT=0
LANG=en_US.UTF-8
SHLVL=1
HOME=/home/metap2
ID=17080812571131782
DEL_METABS=n
FORMAT=csv
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 32607 Aug  8 12:58 .R.Rout
  adding: kendall.csv (deflated 75%)
  adding: PCA_PC1_PC3.map (deflated 65%)
  adding: summary.csv (deflated 53%)
  adding: colsToMark.x.csv (deflated 37%)
  adding: phenotypes.csv (deflated 44%)
  adding: kendall.pdf (deflated 72%)
  adding: data_all.csv (deflated 54%)
  adding: PCA_PC1_PC2.png (deflated 39%)
  adding: PCAtreatment_PC1_PC2.png (deflated 39%)
  adding: PCAtreatment_propOfVar.png (deflated 18%)
  adding: cv_average.csv (deflated 50%)
  adding: processing_log.txt (deflated 55%)
  adding: options (deflated 41%)
  adding: PCAtreatment_PC1_PC2.map (deflated 66%)
  adding: colsToMark.csv (deflated 13%)
  adding: PCAtreatment_PC1_PC3.png (deflated 36%)
  adding: phenotypes_numeric.csv (deflated 44%)
  adding: cv.pdf (deflated 83%)
  adding: MD_cv.csv (deflated 46%)
  adding: PCA_PC1_PC2.map (deflated 65%)
  adding: PCA_PC2_PC3.map (deflated 65%)
  adding: PCAtreatment_PC2_PC3.png (deflated 35%)
  adding: hypothesisTests_complete_data.pdf (deflated 86%)
  adding: pValuesForAllMetabolites__treatment.csv (deflated 52%)
  adding: PCAtreatment.pdf (deflated 76%)
  adding: bonferroni.csv (deflated 32%)
  adding: rowsToMark.csv (deflated 55%)
  adding: metabNamesMapping.csv (deflated 49%)
  adding: PCA.pdf (deflated 76%)
  adding: out_params.txt (stored 0%)
  adding: input (deflated 54%)
  adding: data.csv (deflated 54%)
  adding: phenotypes.txt (deflated 44%)
  adding: ML_cv.csv (deflated 46%)
  adding: phenotypes_for_QC.csv (deflated 45%)
  adding: histograms.pdf (deflated 91%)
  adding: upperOutliers.csv (deflated 42%)
  adding: barplots/Cit_barplot_treatment.png (deflated 30%)
  adding: barplots/Ala_barplot.map (deflated 67%)
  adding: barplots/Trp_barplot.map (deflated 67%)
  adding: barplots/Val_barplot.map (deflated 67%)
  adding: barplots/Pro_barplot_treatment.png (deflated 30%)
  adding: barplots/Ile_barplot_treatment.png (deflated 29%)
  adding: barplots/Lys_barplot.map (deflated 67%)
  adding: barplots/Asn_barplot.map (deflated 67%)
  adding: barplots/Gln_barplot.png (deflated 36%)
  adding: barplots/Ala_barplot.png (deflated 32%)
  adding: barplots/Ala_barplot_treatment.png (deflated 27%)
  adding: barplots/Phe_barplot_treatment.png (deflated 22%)
  adding: barplots/Tyr_barplot_treatment.png (deflated 23%)
  adding: barplots/Asp_barplot_treatment.png (deflated 32%)
  adding: barplots/Gly_barplot.map (deflated 67%)
  adding: barplots/Met_barplot.png (deflated 34%)
  adding: barplots/Thr_barplot.map (deflated 67%)
  adding: barplots/1022150532_sbarplot.png (deflated 51%)
  adding: barplots/Val_barplot_treatment.png (deflated 23%)
  adding: barplots/Thr_barplot_treatment.png (deflated 30%)
  adding: barplots/1022150498_sbarplot.png (deflated 50%)
  adding: barplots/1022150483_sbarplot.map (deflated 74%)
  adding: barplots/Asn_barplot_treatment.png (deflated 34%)
  adding: barplots/Asn_barplot.png (deflated 40%)
  adding: barplots/Ile_barplot.png (deflated 37%)
  adding: barplots/His_barplot.map (deflated 67%)
  adding: barplots/1022150532_sbarplot.map (deflated 74%)
  adding: barplots/Lys_barplot.png (deflated 36%)
  adding: barplots/Orn_barplot.png (deflated 38%)
  adding: barplots/Tyr_barplot.map (deflated 67%)
  adding: barplots/Orn_barplot.map (deflated 67%)
  adding: barplots/Glu_barplot.png (deflated 36%)
  adding: barplots/1022150509_sbarplot.map (deflated 74%)
  adding: barplots/Glu_barplot.map (deflated 66%)
  adding: barplots/1022150498_sbarplot.map (deflated 74%)
  adding: barplots/Tyr_barplot.png (deflated 31%)
  adding: barplots/Trp_barplot_treatment.png (deflated 25%)
  adding: barplots/Pro_barplot.png (deflated 37%)
  adding: barplots/1022150513_sbarplot.map (deflated 74%)
  adding: barplots/Leu_barplot.map (deflated 67%)
  adding: barplots/Trp_barplot.png (deflated 30%)
  adding: barplots/Lys_barplot_treatment.png (deflated 30%)
  adding: barplots/Orn_barplot_treatment.png (deflated 35%)
  adding: barplots/Gln_barplot.map (deflated 67%)
  adding: barplots/Leu_barplot_treatment.png (deflated 26%)
  adding: barplots/Arg_barplot_treatment.png (deflated 33%)
  adding: barplots/Gly_barplot.png (deflated 39%)
  adding: barplots/Cit_barplot.png (deflated 38%)
  adding: barplots/Phe_barplot.map (deflated 67%)
  adding: barplots/Leu_barplot.png (deflated 30%)
  adding: barplots/Val_barplot.png (deflated 26%)
  adding: barplots/1022150483_sbarplot.png (deflated 50%)
  adding: barplots/Met_barplot_treatment.png (deflated 27%)
  adding: barplots/Gln_barplot_treatment.png (deflated 32%)
  adding: barplots/1022150528_sbarplot.png (deflated 52%)
  adding: barplots/Cit_barplot.map (deflated 66%)
  adding: barplots/Arg_barplot.map (deflated 67%)
  adding: barplots/Arg_barplot.png (deflated 40%)
  adding: barplots/1022150513_sbarplot.png (deflated 51%)
  adding: barplots/1022150528_sbarplot.map (deflated 74%)
  adding: barplots/Glu_barplot_treatment.png (deflated 32%)
  adding: barplots/Ile_barplot.map (deflated 67%)
  adding: barplots/Phe_barplot.png (deflated 24%)
  adding: barplots/His_barplot.png (deflated 33%)
  adding: barplots/Gly_barplot_treatment.png (deflated 30%)
  adding: barplots/Pro_barplot.map (deflated 67%)
  adding: barplots/1022150509_sbarplot.png (deflated 54%)
  adding: barplots/Ser_barplot_treatment.png (deflated 34%)
  adding: barplots/Ser_barplot.png (deflated 41%)
  adding: barplots/Met_barplot.map (deflated 67%)
  adding: barplots/His_barplot_treatment.png (deflated 24%)
  adding: barplots/Asp_barplot.map (deflated 67%)
  adding: barplots/Thr_barplot.png (deflated 37%)
  adding: barplots/Ser_barplot.map (deflated 67%)
  adding: barplots/Asp_barplot.png (deflated 40%)
  adding: data_all_beforeCheck.csv (deflated 54%)
  adding: data_beforeCheck.csv (deflated 55%)
  adding: PCA_PC1_PC3.png (deflated 36%)
  adding: phenotypes_nominal.csv (deflated 44%)
  adding: pca.rotations.csv (deflated 49%)
  adding: PCA_propOfVar.png (deflated 23%)
  adding: PCAtreatment_PC2_PC3.map (deflated 66%)
  adding: aux.txt (stored 0%)
  adding: PCAtreatment_PC1_PC3.map (deflated 66%)
  adding: kendall.png (deflated 75%)
  adding: server_log.txt (deflated 79%)
  adding: metabolitesForDropping.csv (stored 0%)
  adding: PCA_PC2_PC3.png (deflated 37%)
  adding: phenotypes_beforeCheck.csv (deflated 49%)
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 872
-rw-r--r--    1 www-data www-data   1676 Aug  8 12:57 input.tmp
-rw-r--r--    1 www-data www-data    189 Aug  8 12:57 phenotypes.txt.tmp
-rw-r--r--    1 www-data www-data   1676 Aug  8 12:57 input
-rw-r--r--    1 www-data www-data    189 Aug  8 12:57 phenotypes.txt
-rw-r--r--    1 www-data www-data      0 Aug  8 12:57 aux.txt
-rw-r--r--    1 www-data www-data    237 Aug  8 12:57 options
-rwxr-xr-x    1 www-data www-data    609 Aug  8 12:57 metaPjob.cmd
drwxrwxrwx 2074 metap2   metap2   258048 Aug  8 12:58 ..
-rw-rw-r--    1 metap2   metap2        1 Aug  8 12:58 out_params.txt
-rw-rw-r--    1 metap2   metap2     1675 Aug  8 12:58 input_4R
-rw-rw-r--    1 metap2   metap2      200 Aug  8 12:58 metabNamesMapping.csv
-rw-rw-r--    1 metap2   metap2     1719 Aug  8 12:58 data_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2     1779 Aug  8 12:58 data_all_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2      186 Aug  8 12:58 phenotypes_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2      646 Aug  8 12:58 MD_cv.csv
-rw-rw-r--    1 metap2   metap2      648 Aug  8 12:58 ML_cv.csv
-rw-rw-r--    1 metap2   metap2    12592 Aug  8 12:58 cv.pdf
-rw-rw-r--    1 metap2   metap2        2 Aug  8 12:58 cv.ok
-rw-rw-r--    1 metap2   metap2       12 Aug  8 12:58 metabolitesForDropping.csv
-rw-rw-r--    1 metap2   metap2      390 Aug  8 12:58 cv_average.csv
-rw-rw-r--    1 metap2   metap2      406 Aug  8 12:58 upperOutliers.csv
-rw-rw-r--    1 metap2   metap2       84 Aug  8 12:58 rowsToMark.csv
-rw-rw-r--    1 metap2   metap2      187 Aug  8 12:58 colsToMark.x.csv
-rw-rw-r--    1 metap2   metap2       61 Aug  8 12:58 colsToMark.csv
-rw-rw-r--    1 metap2   metap2      109 Aug  8 12:58 phenotypes_for_QC.csv
-rw-rw-r--    1 metap2   metap2      114 Aug  8 12:58 phenotypes.csv
-rw-rw-r--    1 metap2   metap2     1675 Aug  8 12:58 data.csv
-rw-rw-r--    1 metap2   metap2     1712 Aug  8 12:58 data_all.csv
-rw-rw-r--    1 metap2   metap2      114 Aug  8 12:58 phenotypes_numeric.csv
-rw-rw-r--    1 metap2   metap2      114 Aug  8 12:58 phenotypes_nominal.csv
-rw-rw-r--    1 metap2   metap2     2583 Aug  8 12:58 summary.csv
-rw-rw-r--    1 metap2   metap2    98941 Aug  8 12:58 histograms.pdf
drwxrwxrwx    2 www-data www-data   4096 Aug  8 12:58 barplots
-rw-rw-r--    1 metap2   metap2      114 Aug  8 12:58 bonferroni.csv
-rw-rw-r--    1 metap2   metap2      283 Aug  8 12:58 pValuesForAllMetabolites__treatment.csv
-rw-rw-r--    1 metap2   metap2    54336 Aug  8 12:58 hypothesisTests_complete_data.pdf
-rw-rw-r--    1 metap2   metap2      741 Aug  8 12:58 PCA_PC1_PC2.map
-rw-rw-r--    1 metap2   metap2     1643 Aug  8 12:58 PCA_PC1_PC2.png
-rw-rw-r--    1 metap2   metap2      740 Aug  8 12:58 PCA_PC1_PC3.map
-rw-rw-r--    1 metap2   metap2     1682 Aug  8 12:58 PCA_PC1_PC3.png
-rw-rw-r--    1 metap2   metap2      740 Aug  8 12:58 PCA_PC2_PC3.map
-rw-rw-r--    1 metap2   metap2     1688 Aug  8 12:58 PCA_PC2_PC3.png
-rw-rw-r--    1 metap2   metap2     2535 Aug  8 12:58 pca.rotations.csv
-rw-rw-r--    1 metap2   metap2     8482 Aug  8 12:58 PCA.pdf
-rw-rw-r--    1 metap2   metap2      768 Aug  8 12:58 PCAtreatment_PC1_PC2.map
-rw-rw-r--    1 metap2   metap2     1667 Aug  8 12:58 PCAtreatment_PC1_PC2.png
-rw-rw-r--    1 metap2   metap2      767 Aug  8 12:58 PCAtreatment_PC1_PC3.map
-rw-rw-r--    1 metap2   metap2     1714 Aug  8 12:58 PCAtreatment_PC1_PC3.png
-rw-rw-r--    1 metap2   metap2      767 Aug  8 12:58 PCAtreatment_PC2_PC3.map
-rw-rw-r--    1 metap2   metap2     1712 Aug  8 12:58 PCAtreatment_PC2_PC3.png
-rw-rw-r--    1 metap2   metap2     9159 Aug  8 12:58 PCAtreatment.pdf
-rw-rw-r--    1 metap2   metap2     5382 Aug  8 12:58 kendall.pdf
-rw-rw-r--    1 metap2   metap2      928 Aug  8 12:58 kendall.csv
-rw-rw-r--    1 metap2   metap2    32607 Aug  8 12:58 .R.Rout
-rw-rw-r--    1 metap2   metap2     3601 Aug  8 12:58 kendall.png
-rw-rw-r--    1 metap2   metap2     2411 Aug  8 12:58 PCAtreatment_propOfVar.png
-rw-rw-r--    1 metap2   metap2     2075 Aug  8 12:58 PCA_propOfVar.png
-rw-rw-r--    1 metap2   metap2     1488 Aug  8 12:58 processing_log.txt
-rw-rw-r--    1 metap2   metap2     8057 Aug  8 12:58 server_log.txt
-rw-rw-r--    1 metap2   metap2   172653 Aug  8 12:58 download.zip
drwxrwxrwx    3 www-data www-data   4096 Aug  8 12:58 .
+ set -
Finishing METAP SERVER


-----

OPTION:FORMAT:data format: ' csv '
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 CSV - deleted lines - win-lin
Read CSV dataset with 22 columns and 6 rows
Data format:  csv 
EXTRACT: 6  samples and  21  metabolites extracted
PHENOTYPES_UPLOAD:Found  6  matched lines with  3  phenotypes specified

REPLICATES:Found  REPLICATES  as a phenotype for data quality checks
PHENOTYPES_UPLOAD:Ignored  cell.line  column as it contains the same phenotype for all samples

PHENOTYPES_UPLOAD:Found  treatment as non-data quality phenotypes

BATCHES:No batches
Wrote machted dataset to data_all_beforeCheck.csv
DEL_METAB:Found  3 metabolites with cv above  0.25 
No extreme outliers identified
Wrote extreme outliers into  upperOutliers.csv 
 6  samples and  21  metabolites in checked data set
Wrote machted dataset to data_all.csv
Phenotype  treatment  is nominal
Phenotype  treatment  added to numeric phenotypes also
 Wrote summary.csv file
 21 Distribution plots generated
Boxplots generated
 1 phenotypes processed for PCA
Wrote kendall correlation table with 21 rows and 2 columns in  kendall.csv 
Correlation plot generated
Wrote kendall correlation table with 21 rows and 2 columns in  kendall.csv 

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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