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JobID: 1708022235037397*** MH aa MM1S ***
LOGFILESIn case of trouble, check out our FAQs!Running METAP SERVER Wed Aug 2 22:36:01 CEST 2017 ID=1708022235037397 /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/1708022235037397 + 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 MM1S REFERENCE=n PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/home/metap2/public_html/users/1708022235037397 PRIVAT=0 LANG=en_US.UTF-8 SHLVL=1 HOME=/home/metap2 ID=1708022235037397 DEL_METABS=n FORMAT=csv 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 33942 Aug 2 22:36 .R.Rout adding: kendall.csv (deflated 71%) adding: PCA_PC1_PC3.map (deflated 80%) adding: summary.csv (deflated 48%) adding: colsToMark.x.csv (deflated 41%) adding: phenotypes.csv (deflated 72%) adding: kendall.pdf (deflated 72%) adding: data_all.csv (deflated 55%) adding: PCA_PC1_PC2.png (deflated 21%) adding: PCAtreatment_PC1_PC2.png (deflated 20%) adding: PCAtreatment_propOfVar.png (deflated 16%) adding: cv_average.csv (deflated 50%) adding: processing_log.txt (deflated 56%) adding: options (deflated 40%) adding: PCAtreatment_PC1_PC2.map (deflated 80%) adding: colsToMark.csv (deflated 13%) adding: PCAtreatment_PC1_PC3.png (deflated 22%) adding: phenotypes_numeric.csv (deflated 72%) adding: cv.pdf (deflated 82%) adding: MD_cv.csv (deflated 45%) adding: PCA_PC1_PC2.map (deflated 80%) adding: PCA_PC2_PC3.map (deflated 80%) adding: PCAtreatment_PC2_PC3.png (deflated 21%) adding: hypothesisTests_complete_data.pdf (deflated 86%) adding: pValuesForAllMetabolites__treatment.csv (deflated 49%) adding: PCAtreatment.pdf (deflated 81%) adding: bonferroni.csv (deflated 32%) adding: rowsToMark.csv (deflated 77%) adding: metabNamesMapping.csv (deflated 49%) adding: PCA.pdf (deflated 81%) adding: out_params.txt (stored 0%) adding: input (deflated 55%) adding: data.csv (deflated 55%) adding: phenotypes.txt (deflated 44%) adding: ML_cv.csv (deflated 46%) adding: phenotypes_for_QC.csv (deflated 72%) adding: histograms.pdf (deflated 89%) adding: upperOutliers.csv (deflated 43%) adding: barplots/1022149992_sbarplot.map (deflated 74%) adding: barplots/1022150590_sbarplot.map (deflated 74%) adding: barplots/Cit_barplot_treatment.png (deflated 23%) adding: barplots/1022150687_sbarplot.map (deflated 74%) adding: barplots/1022150464_sbarplot.map (deflated 74%) adding: barplots/Ala_barplot.map (deflated 80%) adding: barplots/Trp_barplot.map (deflated 80%) adding: barplots/1022150551_sbarplot.png (deflated 50%) adding: barplots/1022150668_sbarplot.map (deflated 74%) adding: barplots/1022149988_sbarplot.png (deflated 48%) adding: barplots/Val_barplot.map (deflated 80%) adding: barplots/Pro_barplot_treatment.png (deflated 22%) adding: barplots/Ile_barplot_treatment.png (deflated 27%) adding: barplots/Lys_barplot.map (deflated 80%) adding: barplots/Asn_barplot.map (deflated 80%) adding: barplots/1022150547_sbarplot.png (deflated 52%) adding: barplots/Gln_barplot.png (deflated 29%) adding: barplots/1022150620_sbarplot.png (deflated 51%) adding: barplots/1022150736_sbarplot.png (deflated 53%) adding: barplots/1022150071_sbarplot.png (deflated 58%) adding: barplots/1022150649_sbarplot.map (deflated 74%) adding: barplots/Ala_barplot.png (deflated 24%) adding: barplots/Ala_barplot_treatment.png (deflated 22%) adding: barplots/Phe_barplot_treatment.png (deflated 27%) adding: barplots/Tyr_barplot_treatment.png (deflated 23%) adding: barplots/1022150634_sbarplot.png (deflated 51%) adding: barplots/Asp_barplot_treatment.png (deflated 23%) adding: barplots/Gly_barplot.map (deflated 80%) adding: barplots/1022150000_sbarplot.png (deflated 49%) adding: barplots/1022150717_sbarplot.png (deflated 50%) adding: barplots/1022149992_sbarplot.png (deflated 49%) adding: barplots/Met_barplot.png (deflated 23%) adding: barplots/Thr_barplot.map (deflated 81%) adding: barplots/1022150532_sbarplot.png (deflated 49%) adding: barplots/Val_barplot_treatment.png (deflated 25%) adding: barplots/Thr_barplot_treatment.png (deflated 24%) adding: barplots/1022150498_sbarplot.png (deflated 50%) adding: barplots/1022150048_sbarplot.map (deflated 74%) adding: barplots/1022150566_sbarplot.map (deflated 74%) adding: barplots/1022150483_sbarplot.map (deflated 74%) adding: barplots/1022150620_sbarplot.map (deflated 74%) adding: barplots/Asn_barplot_treatment.png (deflated 27%) adding: barplots/Asn_barplot.png (deflated 26%) adding: barplots/1022150479_sbarplot.map (deflated 74%) adding: barplots/Ile_barplot.png (deflated 27%) adding: barplots/1022150634_sbarplot.map (deflated 74%) adding: barplots/1022150615_sbarplot.png (deflated 53%) adding: barplots/1022150551_sbarplot.map (deflated 74%) adding: barplots/1022150691_sbarplot.map (deflated 74%) adding: barplots/His_barplot.map (deflated 80%) adding: barplots/1022150450_sbarplot.png (deflated 52%) adding: barplots/1022150067_sbarplot.map (deflated 74%) adding: barplots/1022150532_sbarplot.map (deflated 74%) adding: barplots/Lys_barplot.png (deflated 29%) adding: barplots/Orn_barplot.png (deflated 30%) adding: barplots/1022150445_sbarplot.png (deflated 51%) adding: barplots/Tyr_barplot.map (deflated 80%) adding: barplots/Orn_barplot.map (deflated 80%) adding: barplots/Glu_barplot.png (deflated 24%) adding: barplots/1022150721_sbarplot.map (deflated 74%) adding: barplots/1022150509_sbarplot.map (deflated 74%) adding: barplots/Glu_barplot.map (deflated 80%) adding: barplots/1022150498_sbarplot.map (deflated 74%) adding: barplots/1022149973_sbarplot.map (deflated 74%) adding: barplots/1022150571_sbarplot.png (deflated 52%) adding: barplots/Tyr_barplot.png (deflated 26%) adding: barplots/1022150033_sbarplot.png (deflated 58%) adding: barplots/Trp_barplot_treatment.png (deflated 23%) adding: barplots/Pro_barplot.png (deflated 24%) adding: barplots/1022150513_sbarplot.map (deflated 74%) adding: barplots/Leu_barplot.map (deflated 81%) adding: barplots/1022150702_sbarplot.png (deflated 50%) adding: barplots/Trp_barplot.png (deflated 26%) adding: barplots/1022150479_sbarplot.png (deflated 50%) adding: barplots/1022150445_sbarplot.map (deflated 74%) adding: barplots/1022150736_sbarplot.map (deflated 74%) adding: barplots/1022150668_sbarplot.png (deflated 52%) adding: barplots/1022149973_sbarplot.png (deflated 51%) adding: barplots/1022150672_sbarplot.map (deflated 74%) adding: barplots/Lys_barplot_treatment.png (deflated 25%) adding: barplots/Orn_barplot_treatment.png (deflated 24%) adding: barplots/Gln_barplot.map (deflated 81%) adding: barplots/Leu_barplot_treatment.png (deflated 26%) adding: barplots/Arg_barplot_treatment.png (deflated 25%) adding: barplots/1022150431_sbarplot.png (deflated 50%) adding: barplots/Gly_barplot.png (deflated 28%) adding: barplots/1022150052_sbarplot.png (deflated 58%) adding: barplots/1022150717_sbarplot.map (deflated 74%) adding: barplots/Cit_barplot.png (deflated 22%) adding: barplots/1022150585_sbarplot.png (deflated 50%) adding: barplots/1022150585_sbarplot.map (deflated 74%) adding: barplots/1022150071_sbarplot.map (deflated 75%) adding: barplots/1022150431_sbarplot.map (deflated 74%) adding: barplots/Phe_barplot.map (deflated 81%) adding: barplots/1022150687_sbarplot.png (deflated 50%) adding: barplots/Leu_barplot.png (deflated 28%) adding: barplots/1022150086_sbarplot.map (deflated 75%) adding: barplots/Val_barplot.png (deflated 32%) adding: barplots/1022150014_sbarplot.map (deflated 74%) adding: barplots/1022150483_sbarplot.png (deflated 54%) adding: barplots/1022150590_sbarplot.png (deflated 51%) adding: barplots/Met_barplot_treatment.png (deflated 22%) adding: barplots/1022150649_sbarplot.png (deflated 51%) adding: barplots/1022150067_sbarplot.png (deflated 57%) adding: barplots/Gln_barplot_treatment.png (deflated 22%) adding: barplots/1022150528_sbarplot.png (deflated 52%) adding: barplots/1022150653_sbarplot.map (deflated 74%) adding: barplots/1022150653_sbarplot.png (deflated 52%) adding: barplots/Cit_barplot.map (deflated 80%) adding: barplots/Arg_barplot.map (deflated 80%) adding: barplots/1022150464_sbarplot.png (deflated 50%) adding: barplots/1022150000_sbarplot.map (deflated 74%) adding: barplots/1022150426_sbarplot.png (deflated 51%) adding: barplots/1022150426_sbarplot.map (deflated 74%) adding: barplots/Arg_barplot.png (deflated 27%) adding: barplots/1022150513_sbarplot.png (deflated 49%) adding: barplots/1022150528_sbarplot.map (deflated 74%) adding: barplots/Glu_barplot_treatment.png (deflated 22%) adding: barplots/1022150691_sbarplot.png (deflated 51%) adding: barplots/1022150086_sbarplot.png (deflated 58%) adding: barplots/1022150566_sbarplot.png (deflated 50%) adding: barplots/1022150014_sbarplot.png (deflated 48%) adding: barplots/1022150615_sbarplot.map (deflated 74%) adding: barplots/Ile_barplot.map (deflated 80%) adding: barplots/Phe_barplot.png (deflated 26%) adding: barplots/His_barplot.png (deflated 26%) adding: barplots/Gly_barplot_treatment.png (deflated 25%) adding: barplots/1022150052_sbarplot.map (deflated 75%) adding: barplots/1022149988_sbarplot.map (deflated 74%) adding: barplots/1022150702_sbarplot.map (deflated 74%) adding: barplots/Pro_barplot.map (deflated 81%) adding: barplots/1022150721_sbarplot.png (deflated 53%) adding: barplots/1022150033_sbarplot.map (deflated 74%) adding: barplots/1022150509_sbarplot.png (deflated 51%) adding: barplots/Ser_barplot_treatment.png (deflated 24%) adding: barplots/Ser_barplot.png (deflated 32%) adding: barplots/1022150048_sbarplot.png (deflated 54%) adding: barplots/Met_barplot.map (deflated 81%) adding: barplots/His_barplot_treatment.png (deflated 22%) adding: barplots/Asp_barplot.map (deflated 81%) adding: barplots/Thr_barplot.png (deflated 24%) adding: barplots/1022150571_sbarplot.map (deflated 74%) adding: barplots/1022150547_sbarplot.map (deflated 74%) adding: barplots/1022150672_sbarplot.png (deflated 53%) adding: barplots/1022150450_sbarplot.map (deflated 73%) adding: barplots/Ser_barplot.map (deflated 81%) adding: barplots/Asp_barplot.png (deflated 28%) adding: data_all_beforeCheck.csv (deflated 56%) adding: PCA:treatment.pdf (deflated 77%) adding: lowerOutliers.csv (deflated 49%) adding: data_beforeCheck.csv (deflated 55%) adding: PCA_PC1_PC3.png (deflated 22%) adding: phenotypes_nominal.csv (deflated 72%) adding: pca.rotations.csv (deflated 51%) adding: PCA_propOfVar.png (deflated 19%) adding: PCAtreatment_PC2_PC3.map (deflated 80%) adding: aux.txt (stored 0%) adding: PCAtreatment_PC1_PC3.map (deflated 80%) adding: kendall.png (deflated 77%) adding: server_log.txt (deflated 83%) adding: pca.rotations_treatment.csv (deflated 49%) adding: metabolitesForDropping.csv (stored 0%) adding: PCA_PC2_PC3.png (deflated 20%) adding: phenotypes_beforeCheck.csv (deflated 76%) 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 1192 -rw-r--r-- 1 www-data www-data 5348 Aug 2 22:35 input.tmp -rw-r--r-- 1 www-data www-data 189 Aug 2 22:35 phenotypes.txt.tmp -rw-r--r-- 1 www-data www-data 5348 Aug 2 22:35 input -rw-r--r-- 1 www-data www-data 189 Aug 2 22:35 phenotypes.txt -rw-r--r-- 1 www-data www-data 0 Aug 2 22:35 aux.txt -rw-r--r-- 1 www-data www-data 235 Aug 2 22:35 options -rwxr-xr-x 1 www-data www-data 603 Aug 2 22:35 metaPjob.cmd drwxrwxrwx 2315 metap2 metap2 258048 Aug 2 22:36 .. -rw-rw-r-- 1 metap2 metap2 1 Aug 2 22:36 out_params.txt -rw-rw-r-- 1 metap2 metap2 5347 Aug 2 22:36 input_4R -rw-rw-r-- 1 metap2 metap2 200 Aug 2 22:36 metabNamesMapping.csv -rw-rw-r-- 1 metap2 metap2 5391 Aug 2 22:36 data_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 906 Aug 2 22:36 phenotypes_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 5775 Aug 2 22:36 data_all_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 637 Aug 2 22:36 MD_cv.csv -rw-rw-r-- 1 metap2 metap2 638 Aug 2 22:36 ML_cv.csv -rw-rw-r-- 1 metap2 metap2 12925 Aug 2 22:36 cv.pdf -rw-rw-r-- 1 metap2 metap2 2 Aug 2 22:36 cv.ok -rw-rw-r-- 1 metap2 metap2 20 Aug 2 22:36 metabolitesForDropping.csv -rw-rw-r-- 1 metap2 metap2 378 Aug 2 22:36 cv_average.csv -rw-rw-r-- 1 metap2 metap2 852 Aug 2 22:36 lowerOutliers.csv -rw-rw-r-- 1 metap2 metap2 673 Aug 2 22:36 upperOutliers.csv -rw-rw-r-- 1 metap2 metap2 588 Aug 2 22:36 rowsToMark.csv -rw-rw-r-- 1 metap2 metap2 201 Aug 2 22:36 colsToMark.x.csv -rw-rw-r-- 1 metap2 metap2 61 Aug 2 22:36 colsToMark.csv -rw-rw-r-- 1 metap2 metap2 613 Aug 2 22:36 phenotypes_for_QC.csv -rw-rw-r-- 1 metap2 metap2 618 Aug 2 22:36 phenotypes.csv -rw-rw-r-- 1 metap2 metap2 5347 Aug 2 22:36 data.csv -rw-rw-r-- 1 metap2 metap2 5492 Aug 2 22:36 data_all.csv -rw-rw-r-- 1 metap2 metap2 618 Aug 2 22:36 phenotypes_numeric.csv -rw-rw-r-- 1 metap2 metap2 618 Aug 2 22:36 phenotypes_nominal.csv -rw-rw-r-- 1 metap2 metap2 1828 Aug 2 22:36 summary.csv -rw-rw-r-- 1 metap2 metap2 192710 Aug 2 22:36 histograms.pdf drwxrwxrwx 2 www-data www-data 12288 Aug 2 22:36 barplots -rw-rw-r-- 1 metap2 metap2 295 Aug 2 22:36 pValuesForAllMetabolites__treatment.csv -rw-rw-r-- 1 metap2 metap2 52753 Aug 2 22:36 hypothesisTests_complete_data.pdf -rw-rw-r-- 1 metap2 metap2 114 Aug 2 22:36 bonferroni.csv -rw-rw-r-- 1 metap2 metap2 4593 Aug 2 22:36 PCA_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 2159 Aug 2 22:36 PCA_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 4583 Aug 2 22:36 PCA_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 2143 Aug 2 22:36 PCA_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 4579 Aug 2 22:36 PCA_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2125 Aug 2 22:36 PCA_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 8586 Aug 2 22:36 pca.rotations.csv -rw-rw-r-- 1 metap2 metap2 14831 Aug 2 22:36 PCA.pdf -rw-rw-r-- 1 metap2 metap2 4620 Aug 2 22:36 PCAtreatment_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 2174 Aug 2 22:36 PCAtreatment_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 4610 Aug 2 22:36 PCAtreatment_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 2171 Aug 2 22:36 PCAtreatment_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 4606 Aug 2 22:36 PCAtreatment_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2138 Aug 2 22:36 PCAtreatment_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 15760 Aug 2 22:36 PCAtreatment.pdf -rw-rw-r-- 1 metap2 metap2 9436 Aug 2 22:36 PCA:treatment.pdf -rw-rw-r-- 1 metap2 metap2 2531 Aug 2 22:36 pca.rotations_treatment.csv -rw-rw-r-- 1 metap2 metap2 5319 Aug 2 22:36 kendall.pdf -rw-rw-r-- 1 metap2 metap2 926 Aug 2 22:36 kendall.csv -rw-rw-r-- 1 metap2 metap2 33942 Aug 2 22:36 .R.Rout -rw-rw-r-- 1 metap2 metap2 3595 Aug 2 22:36 kendall.png -rw-rw-r-- 1 metap2 metap2 2515 Aug 2 22:36 PCAtreatment_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2172 Aug 2 22:36 PCA_propOfVar.png -rw-rw-r-- 1 metap2 metap2 1508 Aug 2 22:36 processing_log.txt -rw-rw-r-- 1 metap2 metap2 12366 Aug 2 22:36 server_log.txt -rw-rw-r-- 1 metap2 metap2 299415 Aug 2 22:36 download.zip drwxrwxrwx 3 www-data www-data 4096 Aug 2 22:36 . + 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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