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JobID: EXAMPLE_plasmaTypes

***  human-mouse-bovine plasma AbsIDQ  ***

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Running METAP SERVER
Fri Feb  5 21:16:02 CET 2010
ID=EXAMPLE_plasmaTypes
/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_plasmaTypes
+ 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=n
OUTLIER=n
MISSING=n
DATADIR=/home/metap2/data
SHELL=/bin/sh
JOBID=human-mouse-bovine plasma AbsIDQ
REFERENCE=y
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_plasmaTypes
PRIVAT=0
HOME=/home/metap2
SHLVL=4
ID=EXAMPLE_plasmaTypes
DEL_METABS=y
FORMAT=absoluteIDQ
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 4239640 Feb  5 21:20 .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 18452
-rw-r--r--   1 wwwrun www      6719 Feb  5 21:15 phenotypes.txt.tmp
-rw-r--r--   1 wwwrun www      6719 Feb  5 21:15 phenotypes.txt
-rw-r--r--   1 wwwrun www       268 Feb  5 21:15 options
-rwxr-xr-x   1 wwwrun www       611 Feb  5 21:15 metaPjob.cmd
-rw-r--r--   1 wwwrun www   1107844 Feb  5 21:15 input.tmp
-rw-r--r--   1 wwwrun www   1107844 Feb  5 21:15 input
-rw-r--r--   1 wwwrun www         0 Feb  5 21:15 aux.txt
-rw-r--r--   1 metap2 users       1 Feb  5 21:16 out_params.txt
-rw-r--r--   1 metap2 users 1107578 Feb  5 21:16 input_4R
-rw-r--r--   1 metap2 users    4634 Feb  5 21:16 metabNamesMapping.csv
-rw-r--r--   1 metap2 users    8271 Feb  5 21:16 keggMapping.csv
-rw-r--r--   1 metap2 users  695819 Feb  5 21:16 data_beforeCheck.csv
-rw-r--r--   1 metap2 users   11262 Feb  5 21:16 phenotypes_beforeCheck.csv
-rw-r--r--   1 metap2 users      88 Feb  5 21:16 metabolitesForDropping.csv
-rw-r--r--   1 metap2 users  704319 Feb  5 21:16 data_all_beforeCheck.csv
-rw-r--r--   1 metap2 users    2990 Feb  5 21:16 cv_average.csv
-rw-r--r--   1 metap2 users   36751 Feb  5 21:16 cv.pdf
-rw-r--r--   1 metap2 users       2 Feb  5 21:16 cv.ok
-rw-r--r--   1 metap2 users    5689 Feb  5 21:16 QC_cv.csv
-rw-r--r--   1 metap2 users 1260431 Feb  5 21:16 refBatchBoxplot.pdf
-rw-r--r--   1 metap2 users    4340 Feb  5 21:16 sample_description.csv
-rw-r--r--   1 metap2 users    3213 Feb  5 21:16 rowsToMark.csv
-rw-r--r--   1 metap2 users    4013 Feb  5 21:16 phenotypes_for_QC.csv
-rw-r--r--   1 metap2 users    5873 Feb  5 21:16 phenotypes.csv
-rw-r--r--   1 metap2 users    5168 Feb  5 21:16 pValuesForAllMetabolites__Batch.key.csv
-rw-r--r--   1 metap2 users  629931 Feb  5 21:16 data.csv
-rw-r--r--   1 metap2 users    2246 Feb  5 21:16 colsToMark.x.csv
-rw-r--r--   1 metap2 users      81 Feb  5 21:16 colsToMark.csv
-rw-r--r--   1 metap2 users  461306 Feb  5 21:16 batchBoxplot.pdf
-rw-r--r--   1 metap2 users   23559 Feb  5 21:16 summary.csv
-rw-r--r--   1 metap2 users    5873 Feb  5 21:16 phenotypes_nominal.csv
-rw-r--r--   1 metap2 users  636982 Feb  5 21:16 data_all.csv
-rw-r--r--   1 metap2 users 5141788 Feb  5 21:16 histograms.pdf
drwxrwxrwx 426 metap2 users   40960 Feb  5 21:17 ..
drwxrwxrwx   2 wwwrun www     65536 Feb  5 21:20 barplots
-rw-r--r--   1 metap2 users    5428 Feb  5 21:20 pValuesForAllMetabolites__plasma.type.csv
-rw-r--r--   1 metap2 users  554751 Feb  5 21:20 hypothesisTests_complete_data.pdf
-rw-r--r--   1 metap2 users    5753 Feb  5 21:20 PCA_PC1_PC2.png
-rw-r--r--   1 metap2 users   24260 Feb  5 21:20 PCA_PC1_PC2.map
-rw-r--r--   1 metap2 users  459276 Feb  5 21:20 pca.rotations.csv
-rw-r--r--   1 metap2 users   10612 Feb  5 21:20 PCAplasma.type_PC1_PC2.png
-rw-r--r--   1 metap2 users   24293 Feb  5 21:20 PCAplasma.type_PC1_PC2.map
-rw-r--r--   1 metap2 users    7451 Feb  5 21:20 PCA_PC2_PC3.png
-rw-r--r--   1 metap2 users   24335 Feb  5 21:20 PCA_PC2_PC3.map
-rw-r--r--   1 metap2 users    6772 Feb  5 21:20 PCA_PC1_PC3.png
-rw-r--r--   1 metap2 users   24275 Feb  5 21:20 PCA_PC1_PC3.map
-rw-r--r--   1 metap2 users   51092 Feb  5 21:20 PCA.pdf
-rw-r--r--   1 metap2 users    1850 Feb  5 21:20 server_log.txt
-rw-r--r--   1 metap2 users    1321 Feb  5 21:20 processing_log.txt
-rw-r--r--   1 metap2 users   10011 Feb  5 21:20 PCAplasma.type_propOfVar.png
-rw-r--r--   1 metap2 users   14662 Feb  5 21:20 PCAplasma.type_PC2_PC3.png
-rw-r--r--   1 metap2 users   24368 Feb  5 21:20 PCAplasma.type_PC2_PC3.map
-rw-r--r--   1 metap2 users   12970 Feb  5 21:20 PCAplasma.type_PC1_PC3.png
-rw-r--r--   1 metap2 users   24308 Feb  5 21:20 PCAplasma.type_PC1_PC3.map
-rw-r--r--   1 metap2 users   77433 Feb  5 21:20 PCAplasma.type.pdf
-rw-r--r--   1 metap2 users    4197 Feb  5 21:20 PCA_propOfVar.png
-rw-r--r--   1 metap2 users 4239640 Feb  5 21:20 .R.Rout
drwxrwxrwx   3 wwwrun www      4096 Feb  5 21:20 .
+ set -
Finishing METAP SERVER


-----

OPTION:FORMAT:data format: ' absoluteIDQ ' OPTION:MISSING:treat LOD/out of quant. data as missing: ' n ' OPTION:OUTLIER:drop outliers : ' n ' OPTION:REFERENCE:drop reference samples : ' y ' OPTION:DEL_METABS:drop metabolites with cv > 0.25 : ' y ' OPTION:RATIOS:calculate metabolite ratios : ' n ' AUX:Barplots of each metabolite class have equal y axis: TRUE Fileformat MetIQ - original Read MetIQ dataset with 334 columns and 243 rows AbsoluteIDQ data format Keeping data annotated as non-valid EXTRACT: 243 samples and 162 metabolites extracted AbsoluteIDQ data format Non-valid data annotated as missing PHENOTYPES_UPLOAD:Found 243 matched lines with 2 phenotypes specified
REPLICATES:Found REPLICATES as a phenotype for data quality checks PHENOTYPES_UPLOAD:Found plasma.type as non-data quality phenotypes
BATCHES:Added Plate.bar.code as a phenotypes for data quality checks Wrote machted dataset to data_all_beforeCheck.csv DEL_METAB:Found 9 metabolites with cv above 0.25 Boxplots generated No extreme outliers identified No extreme outliers identified 234 samples and 153 metabolites in checked data set Wrote machted dataset to data_all.csv Phenotype plasma.type is nominal Wrote summary.csv file 153 Distribution plots generated Boxplots generated 1 phenotypes processed for PCA






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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