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JobID: 17080815412925215

***  MH RPMI TIC  ***

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Running METAP SERVER
Tue Aug  8 15:42:01 CEST 2017
ID=17080815412925215
/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/17080815412925215
+ 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 RPMI 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/17080815412925215
PRIVAT=0
LANG=en_US.UTF-8
SHLVL=1
HOME=/home/metap2
ID=17080815412925215
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 32549 Aug  8 15:42 .R.Rout
  adding: kendall.csv (deflated 73%)
  adding: PCA_PC1_PC3.map (deflated 65%)
  adding: summary.csv (deflated 53%)
  adding: colsToMark.x.csv (deflated 40%)
  adding: phenotypes.csv (deflated 45%)
  adding: kendall.pdf (deflated 72%)
  adding: data_all.csv (deflated 53%)
  adding: PCA_PC1_PC2.png (deflated 39%)
  adding: PCAtreatment_PC1_PC2.png (deflated 40%)
  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 39%)
  adding: phenotypes_numeric.csv (deflated 45%)
  adding: cv.pdf (deflated 83%)
  adding: PCA_PC1_PC2.map (deflated 66%)
  adding: PCA_PC2_PC3.map (deflated 65%)
  adding: PCAtreatment_PC2_PC3.png (deflated 38%)
  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: RL_cv.csv (deflated 45%)
  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 49%)
  adding: phenotypes_for_QC.csv (deflated 45%)
  adding: histograms.pdf (deflated 91%)
  adding: upperOutliers.csv (deflated 42%)
  adding: barplots/Cit_barplot_treatment.png (deflated 24%)
  adding: barplots/Ala_barplot.map (deflated 67%)
  adding: barplots/Trp_barplot.map (deflated 68%)
  adding: barplots/1022150668_sbarplot.map (deflated 74%)
  adding: barplots/Val_barplot.map (deflated 67%)
  adding: barplots/Pro_barplot_treatment.png (deflated 26%)
  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 38%)
  adding: barplots/1022150620_sbarplot.png (deflated 50%)
  adding: barplots/1022150649_sbarplot.map (deflated 74%)
  adding: barplots/Ala_barplot.png (deflated 30%)
  adding: barplots/Ala_barplot_treatment.png (deflated 24%)
  adding: barplots/Phe_barplot_treatment.png (deflated 24%)
  adding: barplots/Tyr_barplot_treatment.png (deflated 20%)
  adding: barplots/1022150634_sbarplot.png (deflated 51%)
  adding: barplots/Asp_barplot_treatment.png (deflated 22%)
  adding: barplots/Gly_barplot.map (deflated 67%)
  adding: barplots/Met_barplot.png (deflated 34%)
  adding: barplots/Thr_barplot.map (deflated 68%)
  adding: barplots/Val_barplot_treatment.png (deflated 22%)
  adding: barplots/Thr_barplot_treatment.png (deflated 29%)
  adding: barplots/1022150620_sbarplot.map (deflated 74%)
  adding: barplots/Asn_barplot_treatment.png (deflated 28%)
  adding: barplots/Asn_barplot.png (deflated 32%)
  adding: barplots/Ile_barplot.png (deflated 33%)
  adding: barplots/1022150634_sbarplot.map (deflated 74%)
  adding: barplots/1022150615_sbarplot.png (deflated 50%)
  adding: barplots/His_barplot.map (deflated 67%)
  adding: barplots/Lys_barplot.png (deflated 32%)
  adding: barplots/Orn_barplot.png (deflated 41%)
  adding: barplots/Tyr_barplot.map (deflated 67%)
  adding: barplots/Orn_barplot.map (deflated 67%)
  adding: barplots/Glu_barplot.png (deflated 39%)
  adding: barplots/Glu_barplot.map (deflated 67%)
  adding: barplots/Tyr_barplot.png (deflated 27%)
  adding: barplots/Trp_barplot_treatment.png (deflated 34%)
  adding: barplots/Pro_barplot.png (deflated 35%)
  adding: barplots/Leu_barplot.map (deflated 67%)
  adding: barplots/Trp_barplot.png (deflated 38%)
  adding: barplots/1022150668_sbarplot.png (deflated 52%)
  adding: barplots/Lys_barplot_treatment.png (deflated 26%)
  adding: barplots/Orn_barplot_treatment.png (deflated 31%)
  adding: barplots/Gln_barplot.map (deflated 67%)
  adding: barplots/Leu_barplot_treatment.png (deflated 26%)
  adding: barplots/Arg_barplot_treatment.png (deflated 29%)
  adding: barplots/Gly_barplot.png (deflated 27%)
  adding: barplots/Cit_barplot.png (deflated 31%)
  adding: barplots/Phe_barplot.map (deflated 67%)
  adding: barplots/Leu_barplot.png (deflated 38%)
  adding: barplots/Val_barplot.png (deflated 27%)
  adding: barplots/Met_barplot_treatment.png (deflated 21%)
  adding: barplots/1022150649_sbarplot.png (deflated 48%)
  adding: barplots/Gln_barplot_treatment.png (deflated 34%)
  adding: barplots/1022150653_sbarplot.map (deflated 74%)
  adding: barplots/1022150653_sbarplot.png (deflated 51%)
  adding: barplots/Cit_barplot.map (deflated 67%)
  adding: barplots/Arg_barplot.map (deflated 67%)
  adding: barplots/Arg_barplot.png (deflated 33%)
  adding: barplots/Glu_barplot_treatment.png (deflated 34%)
  adding: barplots/1022150615_sbarplot.map (deflated 74%)
  adding: barplots/Ile_barplot.map (deflated 67%)
  adding: barplots/Phe_barplot.png (deflated 30%)
  adding: barplots/His_barplot.png (deflated 35%)
  adding: barplots/Gly_barplot_treatment.png (deflated 21%)
  adding: barplots/Pro_barplot.map (deflated 67%)
  adding: barplots/Ser_barplot_treatment.png (deflated 39%)
  adding: barplots/Ser_barplot.png (deflated 47%)
  adding: barplots/Met_barplot.map (deflated 67%)
  adding: barplots/His_barplot_treatment.png (deflated 30%)
  adding: barplots/Asp_barplot.map (deflated 67%)
  adding: barplots/Thr_barplot.png (deflated 35%)
  adding: barplots/Ser_barplot.map (deflated 67%)
  adding: barplots/Asp_barplot.png (deflated 35%)
  adding: data_all_beforeCheck.csv (deflated 54%)
  adding: data_beforeCheck.csv (deflated 55%)
  adding: PCA_PC1_PC3.png (deflated 39%)
  adding: phenotypes_nominal.csv (deflated 45%)
  adding: pca.rotations.csv (deflated 49%)
  adding: PCA_propOfVar.png (deflated 22%)
  adding: PCAtreatment_PC2_PC3.map (deflated 66%)
  adding: aux.txt (stored 0%)
  adding: PCAtreatment_PC1_PC3.map (deflated 66%)
  adding: kendall.png (deflated 76%)
  adding: server_log.txt (deflated 79%)
  adding: PCA_PC2_PC3.png (deflated 39%)
  adding: phenotypes_beforeCheck.csv (deflated 53%)
  adding: RD_cv.csv (deflated 46%)
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 864
-rw-r--r--    1 www-data www-data   1666 Aug  8 15:41 input.tmp
-rw-r--r--    1 www-data www-data    213 Aug  8 15:41 phenotypes.txt.tmp
-rw-r--r--    1 www-data www-data   1666 Aug  8 15:41 input
-rw-r--r--    1 www-data www-data    213 Aug  8 15:41 phenotypes.txt
-rw-r--r--    1 www-data www-data      0 Aug  8 15:41 aux.txt
-rw-r--r--    1 www-data www-data    237 Aug  8 15:41 options
-rwxr-xr-x    1 www-data www-data    609 Aug  8 15:41 metaPjob.cmd
-rw-rw-r--    1 metap2   metap2        1 Aug  8 15:42 out_params.txt
-rw-rw-r--    1 metap2   metap2     1665 Aug  8 15:42 input_4R
-rw-rw-r--    1 metap2   metap2      200 Aug  8 15:42 metabNamesMapping.csv
-rw-rw-r--    1 metap2   metap2     1709 Aug  8 15:42 data_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2      210 Aug  8 15:42 phenotypes_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2     1793 Aug  8 15:42 data_all_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2      650 Aug  8 15:42 RD_cv.csv
-rw-rw-r--    1 metap2   metap2      645 Aug  8 15:42 RL_cv.csv
-rw-rw-r--    1 metap2   metap2    12283 Aug  8 15:42 cv.pdf
-rw-rw-r--    1 metap2   metap2        2 Aug  8 15:42 cv.ok
-rw-rw-r--    1 metap2   metap2      387 Aug  8 15:42 cv_average.csv
-rw-rw-r--    1 metap2   metap2      401 Aug  8 15:42 upperOutliers.csv
-rw-rw-r--    1 metap2   metap2       84 Aug  8 15:42 rowsToMark.csv
-rw-rw-r--    1 metap2   metap2      166 Aug  8 15:42 colsToMark.x.csv
-rw-rw-r--    1 metap2   metap2       61 Aug  8 15:42 colsToMark.csv
-rw-rw-r--    1 metap2   metap2      109 Aug  8 15:42 phenotypes_for_QC.csv
-rw-rw-r--    1 metap2   metap2      114 Aug  8 15:42 phenotypes.csv
-rw-rw-r--    1 metap2   metap2     1665 Aug  8 15:42 data.csv
-rw-rw-r--    1 metap2   metap2     1702 Aug  8 15:42 data_all.csv
-rw-rw-r--    1 metap2   metap2      114 Aug  8 15:42 phenotypes_numeric.csv
-rw-rw-r--    1 metap2   metap2      114 Aug  8 15:42 phenotypes_nominal.csv
-rw-rw-r--    1 metap2   metap2     2557 Aug  8 15:42 summary.csv
-rw-rw-r--    1 metap2   metap2    97925 Aug  8 15:42 histograms.pdf
drwxrwxrwx    2 www-data www-data   4096 Aug  8 15:42 barplots
-rw-rw-r--    1 metap2   metap2      114 Aug  8 15:42 bonferroni.csv
-rw-rw-r--    1 metap2   metap2      281 Aug  8 15:42 pValuesForAllMetabolites__treatment.csv
-rw-rw-r--    1 metap2   metap2    53589 Aug  8 15:42 hypothesisTests_complete_data.pdf
-rw-rw-r--    1 metap2   metap2      739 Aug  8 15:42 PCA_PC1_PC2.map
-rw-rw-r--    1 metap2   metap2     1688 Aug  8 15:42 PCA_PC1_PC2.png
-rw-rw-r--    1 metap2   metap2      741 Aug  8 15:42 PCA_PC1_PC3.map
-rw-rw-r--    1 metap2   metap2     1682 Aug  8 15:42 PCA_PC1_PC3.png
-rw-rw-r--    1 metap2   metap2      741 Aug  8 15:42 PCA_PC2_PC3.map
-rw-rw-r--    1 metap2   metap2     1671 Aug  8 15:42 PCA_PC2_PC3.png
-rw-rw-r--    1 metap2   metap2     2528 Aug  8 15:42 pca.rotations.csv
-rw-rw-r--    1 metap2   metap2     8475 Aug  8 15:42 PCA.pdf
-rw-rw-r--    1 metap2   metap2      766 Aug  8 15:42 PCAtreatment_PC1_PC2.map
-rw-rw-r--    1 metap2   metap2     1701 Aug  8 15:42 PCAtreatment_PC1_PC2.png
-rw-rw-r--    1 metap2   metap2      768 Aug  8 15:42 PCAtreatment_PC1_PC3.map
-rw-rw-r--    1 metap2   metap2     1706 Aug  8 15:42 PCAtreatment_PC1_PC3.png
-rw-rw-r--    1 metap2   metap2      768 Aug  8 15:42 PCAtreatment_PC2_PC3.map
-rw-rw-r--    1 metap2   metap2     1686 Aug  8 15:42 PCAtreatment_PC2_PC3.png
-rw-rw-r--    1 metap2   metap2     9152 Aug  8 15:42 PCAtreatment.pdf
-rw-rw-r--    1 metap2   metap2     5382 Aug  8 15:42 kendall.pdf
-rw-rw-r--    1 metap2   metap2      922 Aug  8 15:42 kendall.csv
-rw-rw-r--    1 metap2   metap2    32549 Aug  8 15:42 .R.Rout
-rw-rw-r--    1 metap2   metap2     3604 Aug  8 15:42 kendall.png
-rw-rw-r--    1 metap2   metap2     2445 Aug  8 15:42 PCAtreatment_propOfVar.png
-rw-rw-r--    1 metap2   metap2     2091 Aug  8 15:42 PCA_propOfVar.png
drwxrwxrwx 2084 metap2   metap2   258048 Aug  8 15:42 ..
-rw-rw-r--    1 metap2   metap2     1436 Aug  8 15:42 processing_log.txt
-rw-rw-r--    1 metap2   metap2   176439 Aug  8 15:42 download.zip
drwxrwxrwx    3 www-data www-data   4096 Aug  8 15:42 .
-rw-rw-r--    1 metap2   metap2     8008 Aug  8 15:42 server_log.txt
+ 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 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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