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JobID: 150527164019600*** Protocol Test ***
LOGFILESIn case of trouble, check out our FAQs!Running METAP SERVER Wed May 27 16:41:01 CEST 2015 ID=150527164019600 /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/150527164019600 + hostname metap + uname -a Linux metap 3.13.0-43-generic #72-Ubuntu SMP Mon Dec 8 19:35:06 UTC 2014 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=Protocol Test REFERENCE=n PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/home/metap2/public_html/users/150527164019600 PRIVAT=0 LANG=en_US.UTF-8 SHLVL=1 HOME=/home/metap2 ID=150527164019600 DEL_METABS=n FORMAT=csv LOGNAME=metap2 EMAIL=HB USERID=HB 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 48027 May 27 16:41 .R.Rout adding: PCAID_propOfVar.png (deflated 16%) adding: PCA_PC1_PC3.map (deflated 79%) adding: PCAID_PC2_PC3.png (deflated 26%) adding: summary.csv (deflated 58%) adding: colsToMark.x.csv (deflated 71%) adding: phenotypes.csv (deflated 78%) adding: data_all.csv (deflated 67%) adding: PCAPhase_PC1_PC3.png (deflated 24%) adding: pValuesForAllMetabolites__ID.csv (deflated 58%) adding: PCA_PC1_PC2.png (deflated 29%) adding: processing_log.txt (deflated 53%) adding: options (deflated 39%) adding: colsToMark.csv (deflated 10%) adding: PCAPhase_PC2_PC3.map (deflated 79%) adding: PCAPhase_PC1_PC2.png (deflated 30%) adding: PCA_PC1_PC2.map (deflated 79%) adding: PCAID.pdf (deflated 79%) adding: PCA_PC2_PC3.map (deflated 79%) adding: hypothesisTests_complete_data.pdf (deflated 88%) adding: pValuesForAllMetabolites_ID_Phase.csv (deflated 74%) adding: pValuesForAllMetabolites__Phase.csv (deflated 64%) adding: PCAID_PC2_PC3.map (deflated 79%) adding: bonferroni.csv (deflated 20%) adding: hypothesisTests_separated_for_Phase.pdf (deflated 89%) adding: PCAPhase_PC2_PC3.png (deflated 26%) adding: rowsToMark.csv (deflated 75%) adding: metabNamesMapping.csv (deflated 68%) adding: PCA.pdf (deflated 79%) adding: out_params.txt (stored 0%) adding: input (deflated 66%) adding: PCAID_PC1_PC2.png (deflated 29%) adding: data.csv (deflated 66%) adding: PCAPhase_PC1_PC3.map (deflated 79%) adding: phenotypes.txt (deflated 79%) adding: phenotypes_for_QC.csv (deflated 71%) adding: histograms.pdf (deflated 91%) adding: PCAPhase.pdf (deflated 79%) adding: barplots/C18OH.Conc_barplot.png (deflated 30%) adding: barplots/Val.Conc_barplot_ID.png (deflated 20%) adding: barplots/Phe.Conc_barplot.png (deflated 35%) adding: barplots/C5.Conc_barplot_Phase.png (deflated 26%) adding: barplots/C5OH.Conc_barplot_ID.png (deflated 24%) adding: barplots/C10.1.Conc_barplot.png (deflated 27%) adding: barplots/C18.Conc_barplot_Phase.png (deflated 22%) adding: barplots/C14.1.Conc_barplot_Phase.png (deflated 22%) adding: barplots/C3DC.Conc_barplot_ID.png (deflated 21%) adding: barplots/C18.1.Conc_barplot.png (deflated 35%) adding: barplots/Ala.Conc_barplot_ID.png (deflated 25%) adding: barplots/C16OH.Conc_barplot.png (deflated 25%) adding: barplots/Arg.Conc_barplot.map (deflated 81%) adding: barplots/C10.1.Conc_barplot_Phase.png (deflated 23%) adding: barplots/C5DC.Conc_barplot.map (deflated 80%) adding: barplots/C3.Conc_barplot.png (deflated 30%) adding: barplots/C18OH.Conc_barplot_ID.png (deflated 23%) adding: barplots/Cit.Conc_barplot.map (deflated 80%) adding: barplots/C4.Conc_barplot_ID.png (deflated 23%) adding: barplots/Asp.Conc_barplot_ID.png (deflated 25%) adding: barplots/Gly.Conc_barplot_ID.png (deflated 22%) adding: barplots/C8.Conc_barplot_ID.png (deflated 21%) adding: barplots/Met.Conc_barplot_ID.png (deflated 28%) adding: barplots/C10.1.Conc_barplot_ID.png (deflated 23%) adding: barplots/C16OH.Conc_barplot_ID.png (deflated 20%) adding: barplots/C16.Conc_barplot_Phase.png (deflated 19%) adding: barplots/C16.1OH.Conc_barplot.png (deflated 30%) adding: barplots/C4.Conc_barplot.png (deflated 34%) adding: barplots/Gly.Conc_barplot.map (deflated 81%) adding: barplots/C6.Conc_barplot_ID.png (deflated 19%) adding: barplots/C18OH.Conc_barplot_Phase.png (deflated 23%) adding: barplots/C4DC.Conc_barplot.png (deflated 29%) adding: barplots/C5DC.Conc_barplot.png (deflated 27%) adding: barplots/Orn.Conc_barplot.png (deflated 32%) adding: barplots/C18.2OH.Conc_barplot.map (deflated 81%) adding: barplots/C16OH.Conc_barplot_Phase.png (deflated 18%) adding: barplots/C10.Conc_barplot.map (deflated 81%) adding: barplots/C10.Conc_barplot_ID.png (deflated 23%) adding: barplots/C14.2.Conc_barplot.map (deflated 80%) adding: barplots/C6.Conc_barplot.png (deflated 25%) adding: barplots/Leu.Conc_barplot.map (deflated 81%) adding: barplots/C8.Conc_barplot_Phase.png (deflated 21%) adding: barplots/C18.2OH.Conc_barplot_ID.png (deflated 20%) adding: barplots/Met.Conc_barplot.png (deflated 33%) adding: barplots/C18.Conc_barplot_ID.png (deflated 25%) adding: barplots/C16.Conc_barplot.map (deflated 80%) adding: barplots/C14.Conc_barplot_Phase.png (deflated 21%) adding: barplots/Asp.Conc_barplot_Phase.png (deflated 32%) adding: barplots/C16.1.Conc_barplot.map (deflated 81%) adding: barplots/C0.Conc_barplot_Phase.png (deflated 25%) adding: barplots/C3DC.Conc_barplot_Phase.png (deflated 20%) adding: barplots/C18.1.Conc_barplot_ID.png (deflated 26%) adding: barplots/C5.Conc_barplot_ID.png (deflated 22%) adding: barplots/Arg.Conc_barplot_ID.png (deflated 28%) adding: barplots/C8.1.Conc_barplot.map (deflated 80%) adding: barplots/Glu.Conc_barplot_Phase.png (deflated 32%) adding: barplots/C14.Conc_barplot.map (deflated 80%) adding: barplots/C18.Conc_barplot.map (deflated 81%) adding: barplots/C18.2OH.Conc_barplot.png (deflated 25%) adding: barplots/Met.Conc_barplot.map (deflated 81%) adding: barplots/C6.Conc_barplot_Phase.png (deflated 21%) adding: barplots/C8.1.Conc_barplot.png (deflated 26%) adding: barplots/Tyr.Conc_barplot.png (deflated 34%) adding: barplots/C16.Conc_barplot.png (deflated 25%) adding: barplots/C4DC.Conc_barplot.map (deflated 80%) adding: barplots/C3DC.Conc_barplot.png (deflated 25%) adding: barplots/C14.2.Conc_barplot_Phase.png (deflated 23%) adding: barplots/C10.1.Conc_barplot.map (deflated 81%) adding: barplots/C5DC.Conc_barplot_ID.png (deflated 22%) adding: barplots/C16OH.Conc_barplot.map (deflated 81%) adding: barplots/Orn.Conc_barplot.map (deflated 80%) adding: barplots/C16.1OH.Conc_barplot.map (deflated 81%) adding: barplots/C3DC.Conc_barplot.map (deflated 80%) adding: barplots/C14.1.Conc_barplot_ID.png (deflated 22%) adding: barplots/Cit.Conc_barplot.png (deflated 29%) adding: barplots/Orn.Conc_barplot_Phase.png (deflated 27%) adding: barplots/C14.2.Conc_barplot_ID.png (deflated 23%) adding: barplots/C5.1.Conc_barplot_Phase.png (deflated 22%) adding: barplots/C18.1OH.Conc_barplot.png (deflated 29%) adding: barplots/C18.1OH.Conc_barplot_Phase.png (deflated 22%) adding: barplots/C4.Conc_barplot_Phase.png (deflated 30%) adding: barplots/Arg.Conc_barplot.png (deflated 37%) adding: barplots/Phe.Conc_barplot_Phase.png (deflated 30%) adding: barplots/Asp.Conc_barplot.map (deflated 80%) adding: barplots/C14OH.Conc_barplot_ID.png (deflated 24%) adding: barplots/C0.Conc_barplot.map (deflated 80%) adding: barplots/Tyr.Conc_barplot_ID.png (deflated 31%) adding: barplots/C4.Conc_barplot.map (deflated 81%) adding: barplots/Glu.Conc_barplot_ID.png (deflated 25%) adding: barplots/Leu.Conc_barplot.png (deflated 37%) adding: barplots/C12.Conc_barplot_Phase.png (deflated 19%) adding: barplots/C16.1OH.Conc_barplot_ID.png (deflated 21%) adding: barplots/Gly.Conc_barplot_Phase.png (deflated 29%) adding: barplots/C14OH.Conc_barplot_Phase.png (deflated 24%) adding: barplots/C4OH.Conc_barplot_Phase.png (deflated 21%) adding: barplots/Met.Conc_barplot_Phase.png (deflated 26%) adding: barplots/C3.Conc_barplot.map (deflated 81%) adding: barplots/C18.2OH.Conc_barplot_Phase.png (deflated 18%) adding: barplots/C12.Conc_barplot.map (deflated 81%) adding: barplots/C5DC.Conc_barplot_Phase.png (deflated 23%) adding: barplots/C0.Conc_barplot.png (deflated 32%) adding: barplots/C12.Conc_barplot_ID.png (deflated 22%) adding: barplots/Ala.Conc_barplot.png (deflated 38%) adding: barplots/Tyr.Conc_barplot_Phase.png (deflated 28%) adding: barplots/C3.Conc_barplot_Phase.png (deflated 22%) adding: barplots/C5.1.Conc_barplot.png (deflated 28%) adding: barplots/C14.Conc_barplot.png (deflated 26%) adding: barplots/C18.1.Conc_barplot_Phase.png (deflated 24%) adding: barplots/C18.1OH.Conc_barplot_ID.png (deflated 24%) adding: barplots/C14OH.Conc_barplot.map (deflated 81%) adding: barplots/C5OH.Conc_barplot_Phase.png (deflated 24%) adding: barplots/Glu.Conc_barplot.png (deflated 40%) adding: barplots/C5.Conc_barplot.map (deflated 81%) adding: barplots/C16.1.Conc_barplot_Phase.png (deflated 20%) adding: barplots/C14OH.Conc_barplot.png (deflated 28%) adding: barplots/Phe.Conc_barplot.map (deflated 81%) adding: barplots/C16.Conc_barplot_ID.png (deflated 22%) adding: barplots/C8.Conc_barplot.map (deflated 81%) adding: barplots/Ala.Conc_barplot.map (deflated 81%) adding: barplots/C14.2.Conc_barplot.png (deflated 29%) adding: barplots/C14.Conc_barplot_ID.png (deflated 20%) adding: barplots/C14.1.Conc_barplot.png (deflated 37%) adding: barplots/C5.Conc_barplot.png (deflated 30%) adding: barplots/Leu.Conc_barplot_Phase.png (deflated 31%) adding: barplots/C18.Conc_barplot.png (deflated 30%) adding: barplots/C16.1.Conc_barplot_ID.png (deflated 20%) adding: barplots/C8.1.Conc_barplot_Phase.png (deflated 21%) adding: barplots/Cit.Conc_barplot_Phase.png (deflated 24%) adding: barplots/C4OH.Conc_barplot.png (deflated 28%) adding: barplots/C5.1.Conc_barplot_ID.png (deflated 20%) adding: barplots/C3.Conc_barplot_ID.png (deflated 20%) adding: barplots/C4DC.Conc_barplot_ID.png (deflated 26%) adding: barplots/C2.Conc_barplot.png (deflated 37%) adding: barplots/C6.Conc_barplot.map (deflated 80%) adding: barplots/Phe.Conc_barplot_ID.png (deflated 22%) adding: barplots/C5.1.Conc_barplot.map (deflated 81%) adding: barplots/Leu.Conc_barplot_ID.png (deflated 24%) adding: barplots/Gly.Conc_barplot.png (deflated 32%) adding: barplots/Ala.Conc_barplot_Phase.png (deflated 30%) adding: barplots/C4DC.Conc_barplot_Phase.png (deflated 25%) adding: barplots/C2.Conc_barplot.map (deflated 81%) adding: barplots/Val.Conc_barplot.map (deflated 80%) adding: barplots/C5OH.Conc_barplot.png (deflated 27%) adding: barplots/C12.Conc_barplot.png (deflated 26%) adding: barplots/Val.Conc_barplot.png (deflated 29%) adding: barplots/C18OH.Conc_barplot.map (deflated 81%) adding: barplots/C2.Conc_barplot_Phase.png (deflated 30%) adding: barplots/C0.Conc_barplot_ID.png (deflated 24%) adding: barplots/C16.1OH.Conc_barplot_Phase.png (deflated 21%) adding: barplots/C8.1.Conc_barplot_ID.png (deflated 23%) adding: barplots/C10.Conc_barplot_Phase.png (deflated 23%) adding: barplots/C18.1.Conc_barplot.map (deflated 81%) adding: barplots/Orn.Conc_barplot_ID.png (deflated 21%) adding: barplots/Arg.Conc_barplot_Phase.png (deflated 34%) adding: barplots/C4OH.Conc_barplot.map (deflated 80%) adding: barplots/C4OH.Conc_barplot_ID.png (deflated 23%) adding: barplots/C2.Conc_barplot_ID.png (deflated 23%) adding: barplots/Asp.Conc_barplot.png (deflated 41%) adding: barplots/Val.Conc_barplot_Phase.png (deflated 26%) adding: barplots/Tyr.Conc_barplot.map (deflated 81%) adding: barplots/C8.Conc_barplot.png (deflated 28%) adding: barplots/C16.1.Conc_barplot.png (deflated 27%) adding: barplots/Glu.Conc_barplot.map (deflated 81%) adding: barplots/Cit.Conc_barplot_ID.png (deflated 22%) adding: barplots/C18.1OH.Conc_barplot.map (deflated 81%) adding: barplots/C14.1.Conc_barplot.map (deflated 81%) adding: barplots/C10.Conc_barplot.png (deflated 28%) adding: barplots/C5OH.Conc_barplot.map (deflated 81%) adding: data_all_beforeCheck.csv (deflated 67%) adding: data_beforeCheck.csv (deflated 67%) adding: PCAID_PC1_PC3.map (deflated 79%) adding: PCA_PC1_PC3.png (deflated 25%) adding: phenotypes_nominal.csv (deflated 78%) adding: pca.rotations.csv (deflated 52%) adding: PCAPhase_PC1_PC2.map (deflated 79%) adding: PCA_propOfVar.png (deflated 21%) adding: PCAID_PC1_PC2.map (deflated 79%) adding: aux.txt (stored 0%) adding: PCAPhase_propOfVar.png (deflated 16%) adding: server_log.txt (deflated 85%) adding: PCAID_PC1_PC3.png (deflated 25%) adding: hypothesisTests_separated_for_ID.pdf (deflated 89%) adding: PCA_PC2_PC3.png (deflated 24%) adding: pValuesForAllMetabolites_Phase_ID.csv (deflated 73%) adding: phenotypes_beforeCheck.csv (deflated 78%) 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 2052 -rw-r--r-- 1 www-data www-data 5490 May 27 16:40 input.tmp -rw-r--r-- 1 www-data www-data 5490 May 27 16:40 input -rw-r--r-- 1 www-data www-data 639 May 27 16:40 phenotypes.txt.tmp -rw-r--r-- 1 www-data www-data 639 May 27 16:40 phenotypes.txt -rw-r--r-- 1 www-data www-data 0 May 27 16:40 aux.txt -rw-r--r-- 1 www-data www-data 227 May 27 16:40 options -rwxr-xr-x 1 www-data www-data 587 May 27 16:40 metaPjob.cmd drwxrwxrwx 1096 metap2 metap2 122880 May 27 16:41 .. -rw-rw-r-- 1 metap2 metap2 1 May 27 16:41 out_params.txt -rw-rw-r-- 1 metap2 metap2 5470 May 27 16:41 input_4R -rw-rw-r-- 1 metap2 metap2 841 May 27 16:41 metabNamesMapping.csv -rw-rw-r-- 1 metap2 metap2 5501 May 27 16:41 data_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 5677 May 27 16:41 data_all_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 620 May 27 16:41 phenotypes_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 2 May 27 16:41 cv.ok -rw-rw-r-- 1 metap2 metap2 551 May 27 16:41 colsToMark.x.csv -rw-rw-r-- 1 metap2 metap2 29 May 27 16:41 colsToMark.csv -rw-rw-r-- 1 metap2 metap2 366 May 27 16:41 rowsToMark.csv -rw-rw-r-- 1 metap2 metap2 5377 May 27 16:41 data.csv -rw-rw-r-- 1 metap2 metap2 323 May 27 16:41 phenotypes_for_QC.csv -rw-rw-r-- 1 metap2 metap2 620 May 27 16:41 phenotypes.csv -rw-rw-r-- 1 metap2 metap2 5676 May 27 16:41 data_all.csv -rw-rw-r-- 1 metap2 metap2 620 May 27 16:41 phenotypes_nominal.csv -rw-rw-r-- 1 metap2 metap2 4131 May 27 16:41 summary.csv -rw-rw-r-- 1 metap2 metap2 258642 May 27 16:41 histograms.pdf drwxrwxrwx 2 www-data www-data 12288 May 27 16:41 barplots -rw-rw-r-- 1 metap2 metap2 1311 May 27 16:41 pValuesForAllMetabolites__ID.csv -rw-rw-r-- 1 metap2 metap2 1428 May 27 16:41 pValuesForAllMetabolites__Phase.csv -rw-rw-r-- 1 metap2 metap2 253682 May 27 16:41 hypothesisTests_complete_data.pdf -rw-rw-r-- 1 metap2 metap2 1573 May 27 16:41 pValuesForAllMetabolites_ID_Phase.csv -rw-rw-r-- 1 metap2 metap2 269089 May 27 16:41 hypothesisTests_separated_for_ID.pdf -rw-rw-r-- 1 metap2 metap2 114 May 27 16:41 bonferroni.csv -rw-rw-r-- 1 metap2 metap2 1593 May 27 16:41 pValuesForAllMetabolites_Phase_ID.csv -rw-rw-r-- 1 metap2 metap2 270212 May 27 16:41 hypothesisTests_separated_for_Phase.pdf -rw-rw-r-- 1 metap2 metap2 2364 May 27 16:41 PCA_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1930 May 27 16:41 PCA_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 2359 May 27 16:41 PCA_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1999 May 27 16:41 PCA_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 2356 May 27 16:41 PCA_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2004 May 27 16:41 PCA_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 11807 May 27 16:41 PCA.pdf -rw-rw-r-- 1 metap2 metap2 15031 May 27 16:41 pca.rotations.csv -rw-rw-r-- 1 metap2 metap2 2370 May 27 16:41 PCAID_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1963 May 27 16:41 PCAID_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 2365 May 27 16:41 PCAID_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 2022 May 27 16:41 PCAID_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 2362 May 27 16:41 PCAID_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2027 May 27 16:41 PCAID_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 12806 May 27 16:41 PCAID.pdf -rw-rw-r-- 1 metap2 metap2 2379 May 27 16:41 PCAPhase_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1971 May 27 16:41 PCAPhase_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 2374 May 27 16:41 PCAPhase_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 2029 May 27 16:41 PCAPhase_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 2371 May 27 16:41 PCAPhase_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2032 May 27 16:41 PCAPhase_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 13038 May 27 16:41 PCAPhase.pdf -rw-rw-r-- 1 metap2 metap2 48027 May 27 16:41 .R.Rout -rw-rw-r-- 1 metap2 metap2 2543 May 27 16:41 PCAPhase_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2520 May 27 16:41 PCAID_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2120 May 27 16:41 PCA_propOfVar.png -rw-rw-r-- 1 metap2 metap2 1245 May 27 16:41 processing_log.txt -rw-rw-r-- 1 metap2 metap2 13934 May 27 16:41 server_log.txt -rw-rw-r-- 1 metap2 metap2 538161 May 27 16:41 download.zip drwxrwxrwx 3 www-data www-data 4096 May 27 16:41 . + set - Finishing METAP SERVER 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.
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