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JobID: 17080815075421423

***  MH resistant TIC  ***

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Running METAP SERVER
Tue Aug  8 15:08:02 CEST 2017
ID=17080815075421423
/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/17080815075421423
+ 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 resistant 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/17080815075421423
PRIVAT=0
LANG=en_US.UTF-8
SHLVL=1
HOME=/home/metap2
ID=17080815075421423
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 32575 Aug  8 15:08 .R.Rout
  adding: kendall.csv (deflated 74%)
  adding: KL_cv.csv (deflated 47%)
  adding: PCA_PC1_PC3.map (deflated 76%)
  adding: summary.csv (deflated 53%)
  adding: colsToMark.x.csv (deflated 36%)
  adding: phenotypes.csv (deflated 61%)
  adding: kendall.pdf (deflated 72%)
  adding: data_all.csv (deflated 57%)
  adding: PCA_PC1_PC2.png (deflated 25%)
  adding: PCAtreatment_PC1_PC2.png (deflated 25%)
  adding: PCAtreatment_propOfVar.png (deflated 19%)
  adding: cv_average.csv (deflated 50%)
  adding: processing_log.txt (deflated 55%)
  adding: options (deflated 39%)
  adding: PCAtreatment_PC1_PC2.map (deflated 76%)
  adding: colsToMark.csv (deflated 13%)
  adding: PCAtreatment_PC1_PC3.png (deflated 28%)
  adding: phenotypes_numeric.csv (deflated 61%)
  adding: cv.pdf (deflated 83%)
  adding: PCA_PC1_PC2.map (deflated 76%)
  adding: PCA_PC2_PC3.map (deflated 75%)
  adding: PCAtreatment_PC2_PC3.png (deflated 27%)
  adding: hypothesisTests_complete_data.pdf (deflated 86%)
  adding: pValuesForAllMetabolites__treatment.csv (deflated 52%)
  adding: PCAtreatment.pdf (deflated 79%)
  adding: bonferroni.csv (deflated 32%)
  adding: rowsToMark.csv (deflated 70%)
  adding: metabNamesMapping.csv (deflated 49%)
  adding: PCA.pdf (deflated 78%)
  adding: out_params.txt (stored 0%)
  adding: input (deflated 57%)
  adding: KD_cv.csv (deflated 45%)
  adding: data.csv (deflated 57%)
  adding: phenotypes.txt (deflated 45%)
  adding: phenotypes_for_QC.csv (deflated 62%)
  adding: histograms.pdf (deflated 90%)
  adding: barplots/1022149992_sbarplot.map (deflated 74%)
  adding: barplots/Cit_barplot_treatment.png (deflated 21%)
  adding: barplots/1022150687_sbarplot.map (deflated 74%)
  adding: barplots/Ala_barplot.map (deflated 77%)
  adding: barplots/Trp_barplot.map (deflated 77%)
  adding: barplots/1022150668_sbarplot.map (deflated 74%)
  adding: barplots/1022149988_sbarplot.png (deflated 50%)
  adding: barplots/Val_barplot.map (deflated 76%)
  adding: barplots/Pro_barplot_treatment.png (deflated 25%)
  adding: barplots/Ile_barplot_treatment.png (deflated 19%)
  adding: barplots/Lys_barplot.map (deflated 77%)
  adding: barplots/Asn_barplot.map (deflated 77%)
  adding: barplots/Gln_barplot.png (deflated 34%)
  adding: barplots/1022150620_sbarplot.png (deflated 49%)
  adding: barplots/1022150736_sbarplot.png (deflated 50%)
  adding: barplots/1022150649_sbarplot.map (deflated 74%)
  adding: barplots/Ala_barplot.png (deflated 33%)
  adding: barplots/Ala_barplot_treatment.png (deflated 24%)
  adding: barplots/Phe_barplot_treatment.png (deflated 21%)
  adding: barplots/Tyr_barplot_treatment.png (deflated 24%)
  adding: barplots/1022150634_sbarplot.png (deflated 49%)
  adding: barplots/Asp_barplot_treatment.png (deflated 20%)
  adding: barplots/Gly_barplot.map (deflated 77%)
  adding: barplots/1022150000_sbarplot.png (deflated 50%)
  adding: barplots/1022150717_sbarplot.png (deflated 52%)
  adding: barplots/1022149992_sbarplot.png (deflated 52%)
  adding: barplots/Met_barplot.png (deflated 34%)
  adding: barplots/Thr_barplot.map (deflated 77%)
  adding: barplots/Val_barplot_treatment.png (deflated 24%)
  adding: barplots/Thr_barplot_treatment.png (deflated 24%)
  adding: barplots/1022150620_sbarplot.map (deflated 74%)
  adding: barplots/Asn_barplot_treatment.png (deflated 23%)
  adding: barplots/Asn_barplot.png (deflated 26%)
  adding: barplots/Ile_barplot.png (deflated 29%)
  adding: barplots/1022150634_sbarplot.map (deflated 74%)
  adding: barplots/1022150615_sbarplot.png (deflated 53%)
  adding: barplots/1022150691_sbarplot.map (deflated 74%)
  adding: barplots/His_barplot.map (deflated 77%)
  adding: barplots/Lys_barplot.png (deflated 30%)
  adding: barplots/Orn_barplot.png (deflated 29%)
  adding: barplots/Tyr_barplot.map (deflated 77%)
  adding: barplots/Orn_barplot.map (deflated 77%)
  adding: barplots/Glu_barplot.png (deflated 30%)
  adding: barplots/1022150721_sbarplot.map (deflated 73%)
  adding: barplots/Glu_barplot.map (deflated 77%)
  adding: barplots/1022149973_sbarplot.map (deflated 74%)
  adding: barplots/Tyr_barplot.png (deflated 35%)
  adding: barplots/Trp_barplot_treatment.png (deflated 21%)
  adding: barplots/Pro_barplot.png (deflated 37%)
  adding: barplots/Leu_barplot.map (deflated 77%)
  adding: barplots/1022150702_sbarplot.png (deflated 53%)
  adding: barplots/Trp_barplot.png (deflated 29%)
  adding: barplots/1022150736_sbarplot.map (deflated 74%)
  adding: barplots/1022150668_sbarplot.png (deflated 51%)
  adding: barplots/1022149973_sbarplot.png (deflated 50%)
  adding: barplots/1022150672_sbarplot.map (deflated 74%)
  adding: barplots/Lys_barplot_treatment.png (deflated 23%)
  adding: barplots/Orn_barplot_treatment.png (deflated 20%)
  adding: barplots/Gln_barplot.map (deflated 78%)
  adding: barplots/Leu_barplot_treatment.png (deflated 22%)
  adding: barplots/Arg_barplot_treatment.png (deflated 21%)
  adding: barplots/Gly_barplot.png (deflated 33%)
  adding: barplots/1022150717_sbarplot.map (deflated 74%)
  adding: barplots/Cit_barplot.png (deflated 26%)
  adding: barplots/Phe_barplot.map (deflated 77%)
  adding: barplots/1022150687_sbarplot.png (deflated 51%)
  adding: barplots/Leu_barplot.png (deflated 33%)
  adding: barplots/Val_barplot.png (deflated 33%)
  adding: barplots/1022150014_sbarplot.map (deflated 74%)
  adding: barplots/Met_barplot_treatment.png (deflated 22%)
  adding: barplots/1022150649_sbarplot.png (deflated 51%)
  adding: barplots/Gln_barplot_treatment.png (deflated 22%)
  adding: barplots/1022150653_sbarplot.map (deflated 74%)
  adding: barplots/1022150653_sbarplot.png (deflated 51%)
  adding: barplots/Cit_barplot.map (deflated 77%)
  adding: barplots/Arg_barplot.map (deflated 77%)
  adding: barplots/1022150000_sbarplot.map (deflated 74%)
  adding: barplots/Arg_barplot.png (deflated 33%)
  adding: barplots/Glu_barplot_treatment.png (deflated 25%)
  adding: barplots/1022150691_sbarplot.png (deflated 50%)
  adding: barplots/1022150014_sbarplot.png (deflated 51%)
  adding: barplots/1022150615_sbarplot.map (deflated 74%)
  adding: barplots/Ile_barplot.map (deflated 77%)
  adding: barplots/Phe_barplot.png (deflated 34%)
  adding: barplots/His_barplot.png (deflated 29%)
  adding: barplots/Gly_barplot_treatment.png (deflated 19%)
  adding: barplots/1022149988_sbarplot.map (deflated 74%)
  adding: barplots/1022150702_sbarplot.map (deflated 74%)
  adding: barplots/Pro_barplot.map (deflated 77%)
  adding: barplots/1022150721_sbarplot.png (deflated 52%)
  adding: barplots/Ser_barplot_treatment.png (deflated 22%)
  adding: barplots/Ser_barplot.png (deflated 35%)
  adding: barplots/Met_barplot.map (deflated 77%)
  adding: barplots/His_barplot_treatment.png (deflated 23%)
  adding: barplots/Asp_barplot.map (deflated 77%)
  adding: barplots/Thr_barplot.png (deflated 29%)
  adding: barplots/1022150672_sbarplot.png (deflated 51%)
  adding: barplots/Ser_barplot.map (deflated 77%)
  adding: barplots/Asp_barplot.png (deflated 32%)
  adding: data_all_beforeCheck.csv (deflated 57%)
  adding: PCA:treatment.pdf (deflated 77%)
  adding: data_beforeCheck.csv (deflated 58%)
  adding: PCA_PC1_PC3.png (deflated 28%)
  adding: phenotypes_nominal.csv (deflated 61%)
  adding: pca.rotations.csv (deflated 51%)
  adding: PCA_propOfVar.png (deflated 25%)
  adding: PCAtreatment_PC2_PC3.map (deflated 75%)
  adding: aux.txt (stored 0%)
  adding: PCAtreatment_PC1_PC3.map (deflated 76%)
  adding: kendall.png (deflated 77%)
  adding: server_log.txt (deflated 81%)
  adding: pca.rotations_treatment.csv (deflated 49%)
  adding: metabolitesForDropping.csv (stored 0%)
  adding: PCA_PC2_PC3.png (deflated 28%)
  adding: phenotypes_beforeCheck.csv (deflated 68%)
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 1000
-rw-r--r--    1 www-data www-data   4787 Aug  8 15:07 input.tmp
-rw-r--r--    1 www-data www-data    207 Aug  8 15:07 phenotypes.txt.tmp
-rw-r--r--    1 www-data www-data   4787 Aug  8 15:07 input
-rw-r--r--    1 www-data www-data    207 Aug  8 15:07 phenotypes.txt
-rw-r--r--    1 www-data www-data      0 Aug  8 15:07 aux.txt
-rw-r--r--    1 www-data www-data    242 Aug  8 15:07 options
-rwxr-xr-x    1 www-data www-data    609 Aug  8 15:07 metaPjob.cmd
drwxrwxrwx 2080 metap2   metap2   258048 Aug  8 15:08 ..
-rw-rw-r--    1 metap2   metap2        1 Aug  8 15:08 out_params.txt
-rw-rw-r--    1 metap2   metap2     4786 Aug  8 15:08 input_4R
-rw-rw-r--    1 metap2   metap2      200 Aug  8 15:08 metabNamesMapping.csv
-rw-rw-r--    1 metap2   metap2     4830 Aug  8 15:08 data_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2     5016 Aug  8 15:08 data_all_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2      444 Aug  8 15:08 phenotypes_beforeCheck.csv
-rw-rw-r--    1 metap2   metap2      649 Aug  8 15:08 KD_cv.csv
-rw-rw-r--    1 metap2   metap2      651 Aug  8 15:08 KL_cv.csv
-rw-rw-r--    1 metap2   metap2    12414 Aug  8 15:08 cv.pdf
-rw-rw-r--    1 metap2   metap2        2 Aug  8 15:08 cv.ok
-rw-rw-r--    1 metap2   metap2        4 Aug  8 15:08 metabolitesForDropping.csv
-rw-rw-r--    1 metap2   metap2      388 Aug  8 15:08 cv_average.csv
-rw-rw-r--    1 metap2   metap2      173 Aug  8 15:08 colsToMark.x.csv
-rw-rw-r--    1 metap2   metap2      252 Aug  8 15:08 rowsToMark.csv
-rw-rw-r--    1 metap2   metap2     4786 Aug  8 15:08 data.csv
-rw-rw-r--    1 metap2   metap2       61 Aug  8 15:08 colsToMark.csv
-rw-rw-r--    1 metap2   metap2      277 Aug  8 15:08 phenotypes_for_QC.csv
-rw-rw-r--    1 metap2   metap2      282 Aug  8 15:08 phenotypes.csv
-rw-rw-r--    1 metap2   metap2     4859 Aug  8 15:08 data_all.csv
-rw-rw-r--    1 metap2   metap2      282 Aug  8 15:08 phenotypes_numeric.csv
-rw-rw-r--    1 metap2   metap2      282 Aug  8 15:08 phenotypes_nominal.csv
-rw-rw-r--    1 metap2   metap2     2623 Aug  8 15:08 summary.csv
-rw-rw-r--    1 metap2   metap2   130120 Aug  8 15:08 histograms.pdf
drwxrwxrwx    2 www-data www-data   4096 Aug  8 15:08 barplots
-rw-rw-r--    1 metap2   metap2      114 Aug  8 15:08 bonferroni.csv
-rw-rw-r--    1 metap2   metap2      279 Aug  8 15:08 pValuesForAllMetabolites__treatment.csv
-rw-rw-r--    1 metap2   metap2    54861 Aug  8 15:08 hypothesisTests_complete_data.pdf
-rw-rw-r--    1 metap2   metap2     2007 Aug  8 15:08 PCA_PC1_PC2.map
-rw-rw-r--    1 metap2   metap2     1924 Aug  8 15:08 PCA_PC1_PC2.png
-rw-rw-r--    1 metap2   metap2     2017 Aug  8 15:08 PCA_PC1_PC3.map
-rw-rw-r--    1 metap2   metap2     1988 Aug  8 15:08 PCA_PC1_PC3.png
-rw-rw-r--    1 metap2   metap2     2020 Aug  8 15:08 PCA_PC2_PC3.map
-rw-rw-r--    1 metap2   metap2     2020 Aug  8 15:08 PCA_PC2_PC3.png
-rw-rw-r--    1 metap2   metap2    11241 Aug  8 15:08 PCA.pdf
-rw-rw-r--    1 metap2   metap2     7349 Aug  8 15:08 pca.rotations.csv
-rw-rw-r--    1 metap2   metap2     2034 Aug  8 15:08 PCAtreatment_PC1_PC2.map
-rw-rw-r--    1 metap2   metap2     1936 Aug  8 15:08 PCAtreatment_PC1_PC2.png
-rw-rw-r--    1 metap2   metap2     2044 Aug  8 15:08 PCAtreatment_PC1_PC3.map
-rw-rw-r--    1 metap2   metap2     2010 Aug  8 15:08 PCAtreatment_PC1_PC3.png
-rw-rw-r--    1 metap2   metap2     2047 Aug  8 15:08 PCAtreatment_PC2_PC3.map
-rw-rw-r--    1 metap2   metap2     2053 Aug  8 15:08 PCAtreatment_PC2_PC3.png
-rw-rw-r--    1 metap2   metap2    12045 Aug  8 15:08 PCAtreatment.pdf
-rw-rw-r--    1 metap2   metap2     9637 Aug  8 15:08 PCA:treatment.pdf
-rw-rw-r--    1 metap2   metap2     2535 Aug  8 15:08 pca.rotations_treatment.csv
-rw-rw-r--    1 metap2   metap2     5193 Aug  8 15:08 kendall.pdf
-rw-rw-r--    1 metap2   metap2      931 Aug  8 15:08 kendall.csv
-rw-rw-r--    1 metap2   metap2    32575 Aug  8 15:08 .R.Rout
-rw-rw-r--    1 metap2   metap2     3577 Aug  8 15:08 kendall.png
-rw-rw-r--    1 metap2   metap2     2351 Aug  8 15:08 PCAtreatment_propOfVar.png
-rw-rw-r--    1 metap2   metap2     2029 Aug  8 15:08 PCA_propOfVar.png
-rw-rw-r--    1 metap2   metap2     1474 Aug  8 15:08 processing_log.txt
-rw-rw-r--    1 metap2   metap2     9507 Aug  8 15:08 server_log.txt
-rw-rw-r--    1 metap2   metap2   226251 Aug  8 15:08 download.zip
drwxrwxrwx    3 www-data www-data   4096 Aug  8 15:08 .
+ 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 18 rows Data format: csv EXTRACT: 18 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 1 metabolites with cv above 0.25 No extreme outliers identified No extreme outliers identified 18 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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