Running METAP SERVER
Sun Jan 31 00:38:02 CET 2010
ID=EXAMPLE_drugTesting
/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/1001310037296616
+ hostname
ibis12
+ uname -a
Linux ibis12 2.6.27.29-0.1-default #1 SMP 2009-08-15 17:53:59 +0200 x86_64 x86_64 x86_64 GNU/Linux
+ echo 'this is the environment'
this is the environment
+ env
RATIOS=y
OUTLIER=n
MISSING=n
DATADIR=/home/metap2/data
SHELL=/bin/sh
JOBID=drug dosing study in liver tissue
REFERENCE=n
USER=metap2
PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PWD=/home/metap2/public_html/users/EXAMPLE_drugTesting
PRIVAT=on
HOME=/home/metap2
SHLVL=4
ID=EXAMPLE_drugTesting
DEL_METABS=n
FORMAT=csv_kegg
LOGNAME=metap2
EMAIL=testUser
USERID=testUser
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-r--r-- 1 metap2 users 459474 Jan 31 01:08 .R.Rout
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 43416
-rw-r--r--   1 wwwrun www       1366 Jan 31 00:37 phenotypes.txt.tmp
-rw-r--r--   1 wwwrun www       1366 Jan 31 00:37 phenotypes.txt
-rw-r--r--   1 wwwrun www        266 Jan 31 00:37 options
-rwxr-xr-x   1 wwwrun www        490 Jan 31 00:37 metaPjob.cmd
-rw-r--r--   1 wwwrun www      66723 Jan 31 00:37 input.tmp
-rw-r--r--   1 wwwrun www      66714 Jan 31 00:37 input
-rw-r--r--   1 wwwrun www          0 Jan 31 00:37 aux.txt
drwxrwxrwx 372 metap2 users    36864 Jan 31 00:38 ..
-rw-r--r--   1 metap2 users      336 Jan 31 00:38 rowsToMark.csv
-rw-r--r--   1 metap2 users     1312 Jan 31 00:38 phenotypes_beforeCheck.csv
-rw-r--r--   1 metap2 users        1 Jan 31 00:38 out_params.txt
-rw-r--r--   1 metap2 users     6643 Jan 31 00:38 metabNamesMapping.csv
-rw-r--r--   1 metap2 users     4322 Jan 31 00:38 keggMapping.csv
-rw-r--r--   1 metap2 users    65673 Jan 31 00:38 input_4R
-rw-r--r--   1 metap2 users    67535 Jan 31 00:38 data_beforeCheck.csv
-rw-r--r--   1 metap2 users    68177 Jan 31 00:38 data_all_beforeCheck.csv
-rw-r--r--   1 metap2 users        2 Jan 31 00:38 cv.ok
-rw-r--r--   1 metap2 users     3903 Jan 31 00:38 colsToMark.x.csv
-rw-r--r--   1 metap2 users       74 Jan 31 00:38 colsToMark.csv
-rw-r--r--   1 metap2 users      635 Jan 31 00:38 phenotypes_numeric.csv
-rw-r--r--   1 metap2 users      728 Jan 31 00:38 phenotypes_nominal.csv
-rw-r--r--   1 metap2 users      203 Jan 31 00:38 phenotypes_for_QC.csv
-rw-r--r--   1 metap2 users      927 Jan 31 00:38 phenotypes.csv
-rw-r--r--   1 metap2 users    67783 Jan 31 00:38 data_all.csv
-rw-r--r--   1 metap2 users    67059 Jan 31 00:38 data.csv
-rw-r--r--   1 metap2 users      927 Jan 31 01:05 phenotypes_ratios.csv
-rw-r--r--   1 metap2 users 14112827 Jan 31 01:05 data_ratios.csv
-rw-r--r--   1 metap2 users 14113551 Jan 31 01:05 data_all_ratios.csv
-rw-r--r--   1 metap2 users  3283226 Jan 31 01:05 summary_ratios.csv
-rw-r--r--   1 metap2 users    20563 Jan 31 01:05 summary.csv
-rw-r--r--   1 metap2 users  1772989 Jan 31 01:05 histograms.pdf
drwxrwxrwx   2 wwwrun www      69632 Jan 31 01:06 barplots
-rw-r--r--   1 metap2 users     7557 Jan 31 01:06 pValuesForAllMetabolites__DAY.csv
-rw-r--r--   1 metap2 users     7733 Jan 31 01:06 pValuesForAllMetabolites__DOSE_MG_KG.csv
-rw-r--r--   1 metap2 users   124084 Jan 31 01:06 pca.rotations.csv
-rw-r--r--   1 metap2 users     7795 Jan 31 01:06 pValuesForAllMetabolites__GROUP.csv
-rw-r--r--   1 metap2 users  1745998 Jan 31 01:06 hypothesisTests_complete_data.pdf
-rw-r--r--   1 metap2 users     5577 Jan 31 01:06 PCA_PC2_PC3.png
-rw-r--r--   1 metap2 users     4221 Jan 31 01:06 PCA_PC2_PC3.map
-rw-r--r--   1 metap2 users     5716 Jan 31 01:06 PCA_PC1_PC3.png
-rw-r--r--   1 metap2 users     4215 Jan 31 01:06 PCA_PC1_PC3.map
-rw-r--r--   1 metap2 users     5332 Jan 31 01:06 PCA_PC1_PC2.png
-rw-r--r--   1 metap2 users     4216 Jan 31 01:06 PCA_PC1_PC2.map
-rw-r--r--   1 metap2 users     4245 Jan 31 01:06 PCADOSE_MG_KG_PC1_PC3.map
-rw-r--r--   1 metap2 users     9707 Jan 31 01:06 PCADOSE_MG_KG_PC1_PC2.png
-rw-r--r--   1 metap2 users     4246 Jan 31 01:06 PCADOSE_MG_KG_PC1_PC2.map
-rw-r--r--   1 metap2 users    10263 Jan 31 01:06 PCADAY_PC2_PC3.png
-rw-r--r--   1 metap2 users     4230 Jan 31 01:06 PCADAY_PC2_PC3.map
-rw-r--r--   1 metap2 users    10508 Jan 31 01:06 PCADAY_PC1_PC3.png
-rw-r--r--   1 metap2 users     4224 Jan 31 01:06 PCADAY_PC1_PC3.map
-rw-r--r--   1 metap2 users     9602 Jan 31 01:06 PCADAY_PC1_PC2.png
-rw-r--r--   1 metap2 users     4225 Jan 31 01:06 PCADAY_PC1_PC2.map
-rw-r--r--   1 metap2 users    17371 Jan 31 01:06 PCADAY.pdf
-rw-r--r--   1 metap2 users    16340 Jan 31 01:06 PCA.pdf
-rw-r--r--   1 metap2 users     9874 Jan 31 01:06 PCAGROUP_PC2_PC3.png
-rw-r--r--   1 metap2 users     4236 Jan 31 01:06 PCAGROUP_PC2_PC3.map
-rw-r--r--   1 metap2 users    10108 Jan 31 01:06 PCAGROUP_PC1_PC3.png
-rw-r--r--   1 metap2 users     4230 Jan 31 01:06 PCAGROUP_PC1_PC3.map
-rw-r--r--   1 metap2 users     9187 Jan 31 01:06 PCAGROUP_PC1_PC2.png
-rw-r--r--   1 metap2 users     4231 Jan 31 01:06 PCAGROUP_PC1_PC2.map
-rw-r--r--   1 metap2 users    17854 Jan 31 01:06 PCAGROUP.pdf
-rw-r--r--   1 metap2 users    10411 Jan 31 01:06 PCADOSE_MG_KG_PC2_PC3.png
-rw-r--r--   1 metap2 users     4251 Jan 31 01:06 PCADOSE_MG_KG_PC2_PC3.map
-rw-r--r--   1 metap2 users    10701 Jan 31 01:06 PCADOSE_MG_KG_PC1_PC3.png
-rw-r--r--   1 metap2 users    17518 Jan 31 01:06 PCADOSE_MG_KG.pdf
-rw-r--r--   1 metap2 users    47059 Jan 31 01:06 kendall.pdf
-rw-r--r--   1 metap2 users    25122 Jan 31 01:06 kendall.csv
-rw-r--r--   1 metap2 users  2715755 Jan 31 01:08 kendall_ratios.csv
-rw-r--r--   1 metap2 users     1844 Jan 31 01:08 server_log.txt
-rw-r--r--   1 metap2 users     1942 Jan 31 01:08 processing_log.txt
-rw-r--r--   1 metap2 users  4829662 Jan 31 01:08 kendall_ratios.pdf
-rw-r--r--   1 metap2 users     4644 Jan 31 01:08 PCA_propOfVar.png
-rw-r--r--   1 metap2 users    11049 Jan 31 01:08 PCAGROUP_propOfVar.png
-rw-r--r--   1 metap2 users    11184 Jan 31 01:08 PCADOSE_MG_KG_propOfVar.png
-rw-r--r--   1 metap2 users    10903 Jan 31 01:08 PCADAY_propOfVar.png
-rw-r--r--   1 metap2 users   459474 Jan 31 01:08 .R.Rout
drwxrwxrwx   3 wwwrun www       4096 Jan 31 01:08 .
+ set -
Finishing METAP SERVER


-----

OPTION:FORMAT:data format: ' csv_kegg '
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 : ' y '
AUX:Barplots of each metabolite class have equal y axis: TRUE 
Read CSV dataset with 190 columns and 48 rows
Data format:  csv_kegg 
EXTRACT: 48  samples and  189  metabolites extracted
PHENOTYPES_UPLOAD:Found  48  matched lines with  5  phenotypes specified

PHENOTYPES_UPLOAD:Ignored  CLIENT_ID  column as each sample has its own phenotype specification while being non-numeric

PHENOTYPES_UPLOAD:Found  DAY DOSE_MG_KG GROUP WEIGHT_MG as non-data quality phenotypes

REPLICATES:No replicates
BATCHES:No batches
Wrote machted dataset to data_all_beforeCheck.csv
No replicates in data
No extreme outliers identified
No extreme outliers identified
 48  samples and  189  metabolites in checked data set
Wrote machted dataset to data_all.csv
Phenotype  DAY  is nominal
Phenotype  DOSE_MG_KG  is numeric
Phenotype  DOSE_MG_KG  added to nominal phenotypes also
Phenotype  GROUP  is numeric
Phenotype  GROUP  added to nominal phenotypes also
Phenotype  WEIGHT_MG  is numeric
NA_COLS:For following ratios, all values are missing: deoxycholate.div.ursodeoxycholate caprylate..8.0..div.F.045.30. gamma.glutamylglutamate.div.F.045.30. . Have been deleted
 48  samples and  17763  ratios in checked data set
Wrote machted dataset to data_all_ratios.csv
 Wrote summary.csv file
 Wrote summary_ratios.csv file
 189 Distribution plots generated
Boxplots generated
Boxplots generated
Boxplots generated
 1 phenotypes processed for PCA
Wrote kendall correlation table with 189 rows and 6 columns in  kendall.csv 
Correlation plot generated
Wrote kendall correlation table with 17763 rows and 6 columns in  kendall_ratios.csv 
Correlation plot generated

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

Visit our NAR-web server: