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JobID: EXAMPLE_drugTesting_small

***  drug dosing study in liver tissue (2 phenotypes)  ***

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Running METAP SERVER
Wed Feb  3 11:25:02 CET 2010
ID=EXAMPLE_drugTesting_small
/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/EXAMPLE_drugTesting_small
+ 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 (2 phenotypes)
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_small
PRIVAT=0
HOME=/home/metap2
SHLVL=4
ID=EXAMPLE_drugTesting_small
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 481329 Feb  3 11:54 .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 43600
-rw-r--r--   1 wwwrun www       1506 Feb  3 11:24 phenotypes.txt.tmp
-rw-r--r--   1 wwwrun www       1208 Feb  3 11:24 phenotypes.txt
-rw-r--r--   1 wwwrun www        281 Feb  3 11:24 options
-rwxr-xr-x   1 wwwrun www        495 Feb  3 11:24 metaPjob.cmd
-rw-r--r--   1 wwwrun www      66669 Feb  3 11:24 input.tmp
-rw-r--r--   1 wwwrun www      66660 Feb  3 11:24 input
-rw-r--r--   1 wwwrun www          0 Feb  3 11:24 aux.txt
drwxrwxrwx 386 metap2 users    36864 Feb  3 11:25 ..
-rw-r--r--   1 metap2 users     1210 Feb  3 11:25 phenotypes_beforeCheck.csv
-rw-r--r--   1 metap2 users        1 Feb  3 11:25 out_params.txt
-rw-r--r--   1 metap2 users     6643 Feb  3 11:25 metabNamesMapping.csv
-rw-r--r--   1 metap2 users     4322 Feb  3 11:25 keggMapping.csv
-rw-r--r--   1 metap2 users    65670 Feb  3 11:25 input_4R
-rw-r--r--   1 metap2 users    67535 Feb  3 11:25 data_beforeCheck.csv
-rw-r--r--   1 metap2 users    68075 Feb  3 11:25 data_all_beforeCheck.csv
-rw-r--r--   1 metap2 users        2 Feb  3 11:25 cv.ok
-rw-r--r--   1 metap2 users      336 Feb  3 11:25 rowsToMark.csv
-rw-r--r--   1 metap2 users      533 Feb  3 11:25 phenotypes_numeric.csv
-rw-r--r--   1 metap2 users      626 Feb  3 11:25 phenotypes_nominal.csv
-rw-r--r--   1 metap2 users      203 Feb  3 11:25 phenotypes_for_QC.csv
-rw-r--r--   1 metap2 users      825 Feb  3 11:25 phenotypes.csv
-rw-r--r--   1 metap2 users    67681 Feb  3 11:25 data_all.csv
-rw-r--r--   1 metap2 users    67059 Feb  3 11:25 data.csv
-rw-r--r--   1 metap2 users     3903 Feb  3 11:25 colsToMark.x.csv
-rw-r--r--   1 metap2 users       65 Feb  3 11:25 colsToMark.csv
-rw-r--r--   1 metap2 users      825 Feb  3 11:51 phenotypes_ratios.csv
-rw-r--r--   1 metap2 users 14112827 Feb  3 11:51 data_ratios.csv
-rw-r--r--   1 metap2 users 14113449 Feb  3 11:52 data_all_ratios.csv
-rw-r--r--   1 metap2 users  3283226 Feb  3 11:52 summary_ratios.csv
-rw-r--r--   1 metap2 users    20563 Feb  3 11:52 summary.csv
-rw-r--r--   1 metap2 users  1772989 Feb  3 11:52 histograms.pdf
drwxrwxrwx   2 wwwrun www      69632 Feb  3 11:53 barplots
-rw-r--r--   1 metap2 users     7557 Feb  3 11:53 pValuesForAllMetabolites__DAY.csv
-rw-r--r--   1 metap2 users     7733 Feb  3 11:53 pValuesForAllMetabolites__DOSE_MG_KG.csv
-rw-r--r--   1 metap2 users  1082803 Feb  3 11:53 hypothesisTests_complete_data.pdf
-rw-r--r--   1 metap2 users    14772 Feb  3 11:53 pValuesForAllMetabolites_DAY_DOSE_MG_KG.csv
-rw-r--r--   1 metap2 users  1386653 Feb  3 11:53 hypothesisTests_separated_for_DAY.pdf
-rw-r--r--   1 metap2 users   124084 Feb  3 11:53 pca.rotations.csv
-rw-r--r--   1 metap2 users    11276 Feb  3 11:53 pValuesForAllMetabolites_DOSE_MG_KG_DAY.csv
-rw-r--r--   1 metap2 users  1128920 Feb  3 11:53 hypothesisTests_separated_for_DOSE_MG_KG.pdf
-rw-r--r--   1 metap2 users     5577 Feb  3 11:53 PCA_PC2_PC3.png
-rw-r--r--   1 metap2 users     4221 Feb  3 11:53 PCA_PC2_PC3.map
-rw-r--r--   1 metap2 users     5716 Feb  3 11:53 PCA_PC1_PC3.png
-rw-r--r--   1 metap2 users     4215 Feb  3 11:53 PCA_PC1_PC3.map
-rw-r--r--   1 metap2 users     5332 Feb  3 11:53 PCA_PC1_PC2.png
-rw-r--r--   1 metap2 users     4216 Feb  3 11:53 PCA_PC1_PC2.map
-rw-r--r--   1 metap2 users     4224 Feb  3 11:53 PCADAY_PC1_PC3.map
-rw-r--r--   1 metap2 users     9602 Feb  3 11:53 PCADAY_PC1_PC2.png
-rw-r--r--   1 metap2 users     4225 Feb  3 11:53 PCADAY_PC1_PC2.map
-rw-r--r--   1 metap2 users    16340 Feb  3 11:53 PCA.pdf
-rw-r--r--   1 metap2 users    10411 Feb  3 11:53 PCADOSE_MG_KG_PC2_PC3.png
-rw-r--r--   1 metap2 users     4251 Feb  3 11:53 PCADOSE_MG_KG_PC2_PC3.map
-rw-r--r--   1 metap2 users    10701 Feb  3 11:53 PCADOSE_MG_KG_PC1_PC3.png
-rw-r--r--   1 metap2 users     4245 Feb  3 11:53 PCADOSE_MG_KG_PC1_PC3.map
-rw-r--r--   1 metap2 users     9707 Feb  3 11:53 PCADOSE_MG_KG_PC1_PC2.png
-rw-r--r--   1 metap2 users     4246 Feb  3 11:53 PCADOSE_MG_KG_PC1_PC2.map
-rw-r--r--   1 metap2 users    17518 Feb  3 11:53 PCADOSE_MG_KG.pdf
-rw-r--r--   1 metap2 users    10263 Feb  3 11:53 PCADAY_PC2_PC3.png
-rw-r--r--   1 metap2 users     4230 Feb  3 11:53 PCADAY_PC2_PC3.map
-rw-r--r--   1 metap2 users    10508 Feb  3 11:53 PCADAY_PC1_PC3.png
-rw-r--r--   1 metap2 users    17371 Feb  3 11:53 PCADAY.pdf
-rw-r--r--   1 metap2 users    37158 Feb  3 11:53 kendall.pdf
-rw-r--r--   1 metap2 users    17914 Feb  3 11:53 kendall.csv
-rw-r--r--   1 metap2 users     1862 Feb  3 11:54 server_log.txt
-rw-r--r--   1 metap2 users     2021 Feb  3 11:54 processing_log.txt
-rw-r--r--   1 metap2 users  3910448 Feb  3 11:54 kendall_ratios.pdf
-rw-r--r--   1 metap2 users  2042773 Feb  3 11:54 kendall_ratios.csv
-rw-r--r--   1 metap2 users     4644 Feb  3 11:54 PCA_propOfVar.png
-rw-r--r--   1 metap2 users    11184 Feb  3 11:54 PCADOSE_MG_KG_propOfVar.png
-rw-r--r--   1 metap2 users    10903 Feb  3 11:54 PCADAY_propOfVar.png
-rw-r--r--   1 metap2 users   481329 Feb  3 11:54 .R.Rout
drwxrwxrwx   3 wwwrun www       4096 Feb  3 11:54 .
+ 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 Fileformat CSV - deleted lines - win-lin 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 4 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 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 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 and hypothesis tests depending on DAY Boxplots generated Boxplots and hypothesis tests depending on DOSE_MG_KG Boxplots generated 1 phenotypes processed for PCA Wrote kendall correlation table with 189 rows and 4 columns in kendall.csv Correlation plot generated Wrote kendall correlation table with 17763 rows and 4 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

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