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JobID: 17080815561328758

***  MH U266 sh and Len TIC  ***

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Running METAP SERVER
Tue Aug  8 15:57:01 CEST 2017
ID=17080815561328758
/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/17080815561328758
+ 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 U266 sh and Len 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/17080815561328758
PRIVAT=0
LANG=en_US.UTF-8
SHLVL=1
HOME=/home/metap2
ID=17080815561328758
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 36953 Aug  8 15:57 .R.Rout
  adding: kendall.csv (deflated 73%)
  adding: PCA_PC1_PC3.map (deflated 73%)
  adding: Ush_cv.csv (deflated 46%)
  adding: PCAcell.line_PC2_PC3.png (deflated 31%)
  adding: summary.csv (deflated 53%)
  adding: colsToMark.x.csv (deflated 36%)
  adding: phenotypes.csv (deflated 60%)
  adding: kendall.pdf (deflated 72%)
  adding: data_all.csv (deflated 57%)
  adding: PCA_PC1_PC2.png (deflated 31%)
  adding: PCAtreatment_PC1_PC2.png (deflated 32%)
  adding: PCAtreatment_propOfVar.png (deflated 14%)
  adding: cv_average.csv (deflated 50%)
  adding: processing_log.txt (deflated 58%)
  adding: options (deflated 39%)
  adding: PCAtreatment_PC1_PC2.map (deflated 73%)
  adding: colsToMark.csv (deflated 18%)
  adding: PCAtreatment_PC1_PC3.png (deflated 32%)
  adding: phenotypes_numeric.csv (deflated 63%)
  adding: PCAcell.line.pdf (deflated 77%)
  adding: cv.pdf (deflated 88%)
  adding: hypothesisTests_separated_for_treatment.pdf (deflated 88%)
  adding: PCA_PC1_PC2.map (deflated 73%)
  adding: PCA_PC2_PC3.map (deflated 73%)
  adding: PCAtreatment_PC2_PC3.png (deflated 33%)
  adding: hypothesisTests_complete_data.pdf (deflated 86%)
  adding: pValuesForAllMetabolites__treatment.csv (deflated 54%)
  adding: pValuesForAllMetabolites_cell.line_treatment.csv (deflated 58%)
  adding: PCAcell.line_PC1_PC3.map (deflated 73%)
  adding: PCAtreatment.pdf (deflated 78%)
  adding: bonferroni.csv (deflated 32%)
  adding: rowsToMark.csv (deflated 66%)
  adding: metabNamesMapping.csv (deflated 49%)
  adding: PCA.pdf (deflated 77%)
  adding: out_params.txt (stored 0%)
  adding: input (deflated 57%)
  adding: data.csv (deflated 57%)
  adding: phenotypes.txt (deflated 59%)
  adding: DU_cv.csv (deflated 45%)
  adding: phenotypes_for_QC.csv (deflated 55%)
  adding: histograms.pdf (deflated 90%)
  adding: PCAcell.line_PC2_PC3.map (deflated 73%)
  adding: pValuesForAllMetabolites__cell.line.csv (deflated 71%)
  adding: barplots/Thr_barplot_cell.line.png (deflated 25%)
  adding: barplots/Cit_barplot_treatment.png (deflated 21%)
  adding: barplots/1022150464_sbarplot.map (deflated 74%)
  adding: barplots/Pro_barplot_cell.line.png (deflated 32%)
  adding: barplots/Ala_barplot.map (deflated 74%)
  adding: barplots/Val_barplot_cell.line.png (deflated 27%)
  adding: barplots/Trp_barplot.map (deflated 75%)
  adding: barplots/Val_barplot.map (deflated 75%)
  adding: barplots/Pro_barplot_treatment.png (deflated 23%)
  adding: barplots/Ile_barplot_treatment.png (deflated 21%)
  adding: barplots/Lys_barplot.map (deflated 74%)
  adding: barplots/Asn_barplot.map (deflated 74%)
  adding: barplots/Gln_barplot.png (deflated 34%)
  adding: barplots/1022150071_sbarplot.png (deflated 51%)
  adding: barplots/Ala_barplot.png (deflated 32%)
  adding: barplots/Ala_barplot_treatment.png (deflated 21%)
  adding: barplots/Trp_barplot_cell.line.png (deflated 25%)
  adding: barplots/Arg_barplot_cell.line.png (deflated 31%)
  adding: barplots/Phe_barplot_treatment.png (deflated 19%)
  adding: barplots/Ser_barplot_cell.line.png (deflated 28%)
  adding: barplots/Gly_barplot_cell.line.png (deflated 25%)
  adding: barplots/Tyr_barplot_treatment.png (deflated 23%)
  adding: barplots/Asp_barplot_treatment.png (deflated 22%)
  adding: barplots/Gly_barplot.map (deflated 74%)
  adding: barplots/Met_barplot.png (deflated 31%)
  adding: barplots/Thr_barplot.map (deflated 74%)
  adding: barplots/Val_barplot_treatment.png (deflated 20%)
  adding: barplots/Thr_barplot_treatment.png (deflated 22%)
  adding: barplots/Met_barplot_cell.line.png (deflated 27%)
  adding: barplots/1022150048_sbarplot.map (deflated 74%)
  adding: barplots/Gln_barplot_cell.line.png (deflated 24%)
  adding: barplots/Asn_barplot_treatment.png (deflated 21%)
  adding: barplots/Asn_barplot.png (deflated 32%)
  adding: barplots/1022150479_sbarplot.map (deflated 74%)
  adding: barplots/Ile_barplot.png (deflated 35%)
  adding: barplots/Asn_barplot_cell.line.png (deflated 26%)
  adding: barplots/Lys_barplot_cell.line.png (deflated 29%)
  adding: barplots/His_barplot.map (deflated 75%)
  adding: barplots/1022150450_sbarplot.png (deflated 53%)
  adding: barplots/Cit_barplot_cell.line.png (deflated 29%)
  adding: barplots/1022150067_sbarplot.map (deflated 74%)
  adding: barplots/Lys_barplot.png (deflated 32%)
  adding: barplots/Orn_barplot.png (deflated 33%)
  adding: barplots/1022150445_sbarplot.png (deflated 50%)
  adding: barplots/Tyr_barplot.map (deflated 74%)
  adding: barplots/Orn_barplot.map (deflated 74%)
  adding: barplots/Glu_barplot.png (deflated 27%)
  adding: barplots/Glu_barplot.map (deflated 74%)
  adding: barplots/Tyr_barplot.png (deflated 35%)
  adding: barplots/His_barplot_cell.line.png (deflated 33%)
  adding: barplots/Ala_barplot_cell.line.png (deflated 26%)
  adding: barplots/1022150033_sbarplot.png (deflated 50%)
  adding: barplots/Trp_barplot_treatment.png (deflated 19%)
  adding: barplots/Pro_barplot.png (deflated 38%)
  adding: barplots/Leu_barplot.map (deflated 75%)
  adding: barplots/Trp_barplot.png (deflated 30%)
  adding: barplots/Orn_barplot_cell.line.png (deflated 30%)
  adding: barplots/1022150479_sbarplot.png (deflated 53%)
  adding: barplots/1022150445_sbarplot.map (deflated 74%)
  adding: barplots/Lys_barplot_treatment.png (deflated 19%)
  adding: barplots/Orn_barplot_treatment.png (deflated 23%)
  adding: barplots/Gln_barplot.map (deflated 74%)
  adding: barplots/Leu_barplot_treatment.png (deflated 22%)
  adding: barplots/Arg_barplot_treatment.png (deflated 22%)
  adding: barplots/1022150431_sbarplot.png (deflated 49%)
  adding: barplots/Gly_barplot.png (deflated 30%)
  adding: barplots/1022150052_sbarplot.png (deflated 49%)
  adding: barplots/Phe_barplot_cell.line.png (deflated 24%)
  adding: barplots/Cit_barplot.png (deflated 33%)
  adding: barplots/1022150071_sbarplot.map (deflated 74%)
  adding: barplots/1022150431_sbarplot.map (deflated 74%)
  adding: barplots/Phe_barplot.map (deflated 75%)
  adding: barplots/Leu_barplot.png (deflated 34%)
  adding: barplots/1022150086_sbarplot.map (deflated 74%)
  adding: barplots/Val_barplot.png (deflated 32%)
  adding: barplots/Asp_barplot_cell.line.png (deflated 29%)
  adding: barplots/Met_barplot_treatment.png (deflated 19%)
  adding: barplots/1022150067_sbarplot.png (deflated 51%)
  adding: barplots/Gln_barplot_treatment.png (deflated 20%)
  adding: barplots/Leu_barplot_cell.line.png (deflated 31%)
  adding: barplots/Ile_barplot_cell.line.png (deflated 31%)
  adding: barplots/Cit_barplot.map (deflated 74%)
  adding: barplots/Arg_barplot.map (deflated 75%)
  adding: barplots/Tyr_barplot_cell.line.png (deflated 28%)
  adding: barplots/1022150464_sbarplot.png (deflated 49%)
  adding: barplots/1022150426_sbarplot.png (deflated 51%)
  adding: barplots/1022150426_sbarplot.map (deflated 74%)
  adding: barplots/Arg_barplot.png (deflated 36%)
  adding: barplots/Glu_barplot_treatment.png (deflated 19%)
  adding: barplots/1022150086_sbarplot.png (deflated 50%)
  adding: barplots/Ile_barplot.map (deflated 75%)
  adding: barplots/Phe_barplot.png (deflated 29%)
  adding: barplots/His_barplot.png (deflated 40%)
  adding: barplots/Gly_barplot_treatment.png (deflated 23%)
  adding: barplots/1022150052_sbarplot.map (deflated 74%)
  adding: barplots/Pro_barplot.map (deflated 75%)
  adding: barplots/1022150033_sbarplot.map (deflated 74%)
  adding: barplots/Ser_barplot_treatment.png (deflated 25%)
  adding: barplots/Ser_barplot.png (deflated 35%)
  adding: barplots/1022150048_sbarplot.png (deflated 51%)
  adding: barplots/Met_barplot.map (deflated 74%)
  adding: barplots/His_barplot_treatment.png (deflated 21%)
  adding: barplots/Asp_barplot.map (deflated 75%)
  adding: barplots/Thr_barplot.png (deflated 31%)
  adding: barplots/Glu_barplot_cell.line.png (deflated 24%)
  adding: barplots/1022150450_sbarplot.map (deflated 74%)
  adding: barplots/Ser_barplot.map (deflated 74%)
  adding: barplots/Asp_barplot.png (deflated 35%)
  adding: data_all_beforeCheck.csv (deflated 57%)
  adding: data_beforeCheck.csv (deflated 57%)
  adding: PCA_PC1_PC3.png (deflated 33%)
  adding: phenotypes_nominal.csv (deflated 60%)
  adding: pca.rotations.csv (deflated 50%)
  adding: hypothesisTests_separated_for_cell.line.pdf (deflated 87%)
  adding: PCA_propOfVar.png (deflated 21%)
  adding: PCAtreatment_PC2_PC3.map (deflated 73%)
  adding: PCAcell.line_PC1_PC2.map (deflated 73%)
  adding: aux.txt (stored 0%)
  adding: PCAtreatment_PC1_PC3.map (deflated 73%)
  adding: kendall.png (deflated 76%)
  adding: server_log.txt (deflated 81%)
  adding: metabolitesForDropping.csv (stored 0%)
  adding: Uscr_cv.csv (deflated 45%)
  adding: PCAcell.line_PC1_PC2.png (deflated 32%)
  adding: UL_cv.csv (deflated 46%)
  adding: pValuesForAllMetabolites_treatment_cell.line.csv (deflated 68%)
  adding: PCAcell.line_PC1_PC3.png (deflated 33%)
  adding: PCA_PC2_PC3.png (deflated 31%)
  adding: PCAcell.line_propOfVar.png (deflated 16%)
  adding: phenotypes_beforeCheck.csv (deflated 61%)
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 1424
-rw-r--r--    1 www-data www-data   3223 Aug  8 15:56 input.tmp
-rw-r--r--    1 www-data www-data    372 Aug  8 15:56 phenotypes.txt.tmp
-rw-r--r--    1 www-data www-data   3223 Aug  8 15:56 input
-rw-r--r--    1 www-data www-data    372 Aug  8 15:56 phenotypes.txt
-rw-r--r--    1 www-data www-data      0 Aug  8 15:56 aux.txt
-rw-r--r--    1 www-data www-data    248 Aug  8 15:56 options
-rwxr-xr-x    1 www-data www-data    609 Aug  8 15:56 metaPjob.cmd
drwxrwxrwx 2087 metap2   metap2   258048 Aug  8 15:57 ..
-rw-rw-r--    1 metap2   metap2        1 Aug  8 15:57 out_params.txt
-rw-rw-r--    1 metap2   metap2     3222 Aug  8 15:57 input_4R
-rw-rw-r--    1 metap2   metap2      200 Aug  8 15:57 metabNamesMapping.csv
-rw-rw-r--    1 metap2   metap2     3268 Aug  8 15:57 data_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2      369 Aug  8 15:57 phenotypes_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2     3445 Aug  8 15:57 data_all_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2      650 Aug  8 15:57 DU_cv.csv
-rw-rw-r--    1 metap2   metap2      646 Aug  8 15:57 UL_cv.csv
-rw-rw-r--    1 metap2   metap2      644 Aug  8 15:57 Uscr_cv.csv
-rw-rw-r--    1 metap2   metap2      645 Aug  8 15:57 Ush_cv.csv
-rw-rw-r--    1 metap2   metap2    23852 Aug  8 15:57 cv.pdf
-rw-rw-r--    1 metap2   metap2        2 Aug  8 15:57 cv.ok
-rw-rw-r--    1 metap2   metap2        8 Aug  8 15:57 metabolitesForDropping.csv
-rw-rw-r--    1 metap2   metap2      386 Aug  8 15:57 cv_average.csv
-rw-rw-r--    1 metap2   metap2      168 Aug  8 15:57 rowsToMark.csv
-rw-rw-r--    1 metap2   metap2      180 Aug  8 15:57 colsToMark.x.csv
-rw-rw-r--    1 metap2   metap2       57 Aug  8 15:57 colsToMark.csv
-rw-rw-r--    1 metap2   metap2      202 Aug  8 15:57 phenotypes_for_QC.csv
-rw-rw-r--    1 metap2   metap2      310 Aug  8 15:57 phenotypes.csv
-rw-rw-r--    1 metap2   metap2     3224 Aug  8 15:57 data.csv
-rw-rw-r--    1 metap2   metap2     3391 Aug  8 15:57 data_all.csv
-rw-rw-r--    1 metap2   metap2      225 Aug  8 15:57 phenotypes_numeric.csv
-rw-rw-r--    1 metap2   metap2      310 Aug  8 15:57 phenotypes_nominal.csv
-rw-rw-r--    1 metap2   metap2     2643 Aug  8 15:57 summary.csv
-rw-rw-r--    1 metap2   metap2   119619 Aug  8 15:57 histograms.pdf
drwxrwxrwx    2 www-data www-data   4096 Aug  8 15:57 barplots
-rw-rw-r--    1 metap2   metap2      610 Aug  8 15:57 pValuesForAllMetabolites__cell.line.csv
-rw-rw-r--    1 metap2   metap2      593 Aug  8 15:57 pValuesForAllMetabolites__treatment.csv
-rw-rw-r--    1 metap2   metap2   127722 Aug  8 15:57 hypothesisTests_complete_data.pdf
-rw-rw-r--    1 metap2   metap2      395 Aug  8 15:57 pValuesForAllMetabolites_cell.line_treatment.c...
-rw-rw-r--    1 metap2   metap2   104504 Aug  8 15:57 hypothesisTests_separated_for_cell.line.pdf
-rw-rw-r--    1 metap2   metap2      424 Aug  8 15:57 pValuesForAllMetabolites_treatment_cell.line.c...
-rw-rw-r--    1 metap2   metap2   138587 Aug  8 15:57 hypothesisTests_separated_for_treatment.pdf
-rw-rw-r--    1 metap2   metap2      114 Aug  8 15:57 bonferroni.csv
-rw-rw-r--    1 metap2   metap2     1380 Aug  8 15:57 PCA_PC1_PC2.map
-rw-rw-r--    1 metap2   metap2     1810 Aug  8 15:57 PCA_PC1_PC2.png
-rw-rw-r--    1 metap2   metap2     1379 Aug  8 15:57 PCA_PC1_PC3.map
-rw-rw-r--    1 metap2   metap2     1760 Aug  8 15:57 PCA_PC1_PC3.png
-rw-rw-r--    1 metap2   metap2     1379 Aug  8 15:57 PCA_PC2_PC3.map
-rw-rw-r--    1 metap2   metap2     1828 Aug  8 15:57 PCA_PC2_PC3.png
-rw-rw-r--    1 metap2   metap2     4700 Aug  8 15:57 pca.rotations.csv
-rw-rw-r--    1 metap2   metap2     9827 Aug  8 15:57 PCA.pdf
-rw-rw-r--    1 metap2   metap2     1407 Aug  8 15:57 PCAcell.line_PC1_PC2.map
-rw-rw-r--    1 metap2   metap2     1835 Aug  8 15:57 PCAcell.line_PC1_PC2.png
-rw-rw-r--    1 metap2   metap2     1406 Aug  8 15:57 PCAcell.line_PC1_PC3.map
-rw-rw-r--    1 metap2   metap2     1784 Aug  8 15:57 PCAcell.line_PC1_PC3.png
-rw-rw-r--    1 metap2   metap2     1406 Aug  8 15:57 PCAcell.line_PC2_PC3.map
-rw-rw-r--    1 metap2   metap2     1832 Aug  8 15:57 PCAcell.line_PC2_PC3.png
-rw-rw-r--    1 metap2   metap2    10508 Aug  8 15:57 PCAcell.line.pdf
-rw-rw-r--    1 metap2   metap2     1407 Aug  8 15:57 PCAtreatment_PC1_PC2.map
-rw-rw-r--    1 metap2   metap2     1849 Aug  8 15:57 PCAtreatment_PC1_PC2.png
-rw-rw-r--    1 metap2   metap2     1406 Aug  8 15:57 PCAtreatment_PC1_PC3.map
-rw-rw-r--    1 metap2   metap2     1803 Aug  8 15:57 PCAtreatment_PC1_PC3.png
-rw-rw-r--    1 metap2   metap2     1406 Aug  8 15:57 PCAtreatment_PC2_PC3.map
-rw-rw-r--    1 metap2   metap2     1856 Aug  8 15:57 PCAtreatment_PC2_PC3.png
-rw-rw-r--    1 metap2   metap2    11112 Aug  8 15:57 PCAtreatment.pdf
-rw-rw-r--    1 metap2   metap2     5256 Aug  8 15:57 kendall.pdf
-rw-rw-r--    1 metap2   metap2      960 Aug  8 15:57 kendall.csv
-rw-rw-r--    1 metap2   metap2    36953 Aug  8 15:57 .R.Rout
-rw-rw-r--    1 metap2   metap2     3580 Aug  8 15:57 kendall.png
-rw-rw-r--    1 metap2   metap2     2727 Aug  8 15:57 PCAtreatment_propOfVar.png
-rw-rw-r--    1 metap2   metap2     2504 Aug  8 15:57 PCAcell.line_propOfVar.png
-rw-rw-r--    1 metap2   metap2     2158 Aug  8 15:57 PCA_propOfVar.png
-rw-rw-r--    1 metap2   metap2     1586 Aug  8 15:57 processing_log.txt
-rw-rw-r--    1 metap2   metap2    10799 Aug  8 15:57 server_log.txt
-rw-rw-r--    1 metap2   metap2   316506 Aug  8 15:57 download.zip
drwxrwxrwx    3 www-data www-data   4096 Aug  8 15:57 .
+ 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 12 rows Data format: csv EXTRACT: 12 samples and 21 metabolites extracted PHENOTYPES_UPLOAD:Found 12 matched lines with 3 phenotypes specified
REPLICATES:Found REPLICATES as a phenotype for data quality checks PHENOTYPES_UPLOAD:Found cell.line treatment as non-data quality phenotypes
BATCHES:No batches Wrote machted dataset to data_all_beforeCheck.csv DEL_METAB:Found 2 metabolites with cv above 0.25 No extreme outliers identified No extreme outliers identified 12 samples and 21 metabolites in checked data set Wrote machted dataset to data_all.csv Phenotype cell.line is nominal Phenotype cell.line added to numeric phenotypes also Phenotype treatment is nominal Wrote summary.csv file 21 Distribution plots generated Boxplots generated Boxplots generated Boxplots and hypothesis tests depending on cell.line Boxplots generated Boxplots and hypothesis tests depending on treatment 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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