Running METAP SERVER
Wed Aug  2 16:29:01 CEST 2017
ID=1708021628379756
/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/1708021628379756
+ hostname
metap
+ uname -a
Linux metap 4.4.0-65-generic #86-Ubuntu SMP Thu Feb 23 17:49:58 UTC 2017 x86_64 x86_64 x86_64 GNU/Li...
+ 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 aa 01.08.
REFERENCE=y
PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PWD=/home/metap2/public_html/users/1708021628379756
PRIVAT=0
LANG=en_US.UTF-8
SHLVL=1
HOME=/home/metap2
ID=1708021628379756
DEL_METABS=n
FORMAT=absoluteIDQ
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 5284 Aug  2 16:29 .R.Rout
  adding: processing_log.txt (deflated 39%)
  adding: options (deflated 38%)
  adding: metabNamesMapping.csv (deflated 68%)
  adding: out_params.txt (stored 0%)
  adding: input (deflated 74%)
  adding: phenotypes.txt (deflated 63%)
  adding: aux.txt (stored 0%)
  adding: server_log.txt (deflated 58%)
  adding: keggMapping.csv (deflated 84%)
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 440
drwxrwxrwx    2 www-data www-data   4096 Aug  2 16:28 barplots
-rw-r--r--    1 www-data www-data  33544 Aug  2 16:28 input.tmp
-rw-r--r--    1 www-data www-data    406 Aug  2 16:28 phenotypes.txt.tmp
-rw-r--r--    1 www-data www-data  33544 Aug  2 16:28 input
-rw-r--r--    1 www-data www-data    406 Aug  2 16:28 phenotypes.txt
-rw-r--r--    1 www-data www-data      0 Aug  2 16:28 aux.txt
-rw-r--r--    1 www-data www-data    245 Aug  2 16:28 options
-rwxr-xr-x    1 www-data www-data    603 Aug  2 16:28 metaPjob.cmd
drwxrwxrwx 2308 metap2   metap2   258048 Aug  2 16:29 ..
-rw-rw-r--    1 metap2   metap2        1 Aug  2 16:29 out_params.txt
-rw-rw-r--    1 metap2   metap2    33466 Aug  2 16:29 input_4R
-rw-rw-r--    1 metap2   metap2     8271 Aug  2 16:29 keggMapping.csv
-rw-rw-r--    1 metap2   metap2     5284 Aug  2 16:29 .R.Rout
-rw-rw-r--    1 metap2   metap2     1092 Aug  2 16:29 metabNamesMapping.csv
-rw-rw-r--    1 metap2   metap2      566 Aug  2 16:29 processing_log.txt
-rw-rw-r--    1 metap2   metap2     2175 Aug  2 16:29 server_log.txt
-rw-rw-r--    1 metap2   metap2    13161 Aug  2 16:29 download.zip
drwxrwxrwx    3 www-data www-data   4096 Aug  2 16:29 .
+ 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 : ' n '
OPTION:RATIOS:calculate metabolite ratios : ' n '
AUX:Barplots of each metabolite class have equal y axis: TRUE 
Fileformat MetIQ - original - win-lin
Read MetIQ dataset with 59 columns and 59 rows
AbsoluteIDQ data format
EXTRACT:ERROR:Don't know which column is the first one with concentration/intensity information

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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