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JobID: 17080815561328758*** MH U266 sh and Len TIC ***
LOGFILESIn case of trouble, check out our FAQs!Running METAP SERVER Tue Aug 8 15:57:01 CEST 2017 ID=17080815561328758 /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/17080815561328758 + hostname metap + uname -a Linux metap 4.4.0-87-generic #110-Ubuntu SMP Tue Jul 18 12:55:35 UTC 2017 x86_64 x86_64 x86_64 GNU/L... + 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 U266 sh and Len TIC REFERENCE=n PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/home/metap2/public_html/users/17080815561328758 PRIVAT=0 LANG=en_US.UTF-8 SHLVL=1 HOME=/home/metap2 ID=17080815561328758 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 36953 Aug 8 15:57 .R.Rout adding: kendall.csv (deflated 73%) adding: PCA_PC1_PC3.map (deflated 73%) adding: Ush_cv.csv (deflated 46%) adding: PCAcell.line_PC2_PC3.png (deflated 31%) adding: summary.csv (deflated 53%) adding: colsToMark.x.csv (deflated 36%) adding: phenotypes.csv (deflated 60%) adding: kendall.pdf (deflated 72%) adding: data_all.csv (deflated 57%) adding: PCA_PC1_PC2.png (deflated 31%) adding: PCAtreatment_PC1_PC2.png (deflated 32%) adding: PCAtreatment_propOfVar.png (deflated 14%) adding: cv_average.csv (deflated 50%) adding: processing_log.txt (deflated 58%) adding: options (deflated 39%) adding: PCAtreatment_PC1_PC2.map (deflated 73%) adding: colsToMark.csv (deflated 18%) adding: PCAtreatment_PC1_PC3.png (deflated 32%) adding: phenotypes_numeric.csv (deflated 63%) adding: PCAcell.line.pdf (deflated 77%) adding: cv.pdf (deflated 88%) adding: hypothesisTests_separated_for_treatment.pdf (deflated 88%) adding: PCA_PC1_PC2.map (deflated 73%) adding: PCA_PC2_PC3.map (deflated 73%) adding: PCAtreatment_PC2_PC3.png (deflated 33%) adding: hypothesisTests_complete_data.pdf (deflated 86%) adding: pValuesForAllMetabolites__treatment.csv (deflated 54%) adding: pValuesForAllMetabolites_cell.line_treatment.csv (deflated 58%) adding: PCAcell.line_PC1_PC3.map (deflated 73%) adding: PCAtreatment.pdf (deflated 78%) adding: bonferroni.csv (deflated 32%) adding: rowsToMark.csv (deflated 66%) adding: metabNamesMapping.csv (deflated 49%) adding: PCA.pdf (deflated 77%) adding: out_params.txt (stored 0%) adding: input (deflated 57%) adding: data.csv (deflated 57%) adding: phenotypes.txt (deflated 59%) adding: DU_cv.csv (deflated 45%) adding: phenotypes_for_QC.csv (deflated 55%) adding: histograms.pdf (deflated 90%) adding: PCAcell.line_PC2_PC3.map (deflated 73%) adding: pValuesForAllMetabolites__cell.line.csv (deflated 71%) adding: barplots/Thr_barplot_cell.line.png (deflated 25%) adding: barplots/Cit_barplot_treatment.png (deflated 21%) adding: barplots/1022150464_sbarplot.map (deflated 74%) adding: barplots/Pro_barplot_cell.line.png (deflated 32%) adding: barplots/Ala_barplot.map (deflated 74%) adding: barplots/Val_barplot_cell.line.png (deflated 27%) adding: barplots/Trp_barplot.map (deflated 75%) adding: barplots/Val_barplot.map (deflated 75%) adding: barplots/Pro_barplot_treatment.png (deflated 23%) adding: barplots/Ile_barplot_treatment.png (deflated 21%) adding: barplots/Lys_barplot.map (deflated 74%) adding: barplots/Asn_barplot.map (deflated 74%) adding: barplots/Gln_barplot.png (deflated 34%) adding: barplots/1022150071_sbarplot.png (deflated 51%) adding: barplots/Ala_barplot.png (deflated 32%) adding: barplots/Ala_barplot_treatment.png (deflated 21%) adding: barplots/Trp_barplot_cell.line.png (deflated 25%) adding: barplots/Arg_barplot_cell.line.png (deflated 31%) adding: barplots/Phe_barplot_treatment.png (deflated 19%) adding: barplots/Ser_barplot_cell.line.png (deflated 28%) adding: barplots/Gly_barplot_cell.line.png (deflated 25%) adding: barplots/Tyr_barplot_treatment.png (deflated 23%) adding: barplots/Asp_barplot_treatment.png (deflated 22%) adding: barplots/Gly_barplot.map (deflated 74%) adding: barplots/Met_barplot.png (deflated 31%) adding: barplots/Thr_barplot.map (deflated 74%) adding: barplots/Val_barplot_treatment.png (deflated 20%) adding: barplots/Thr_barplot_treatment.png (deflated 22%) adding: barplots/Met_barplot_cell.line.png (deflated 27%) adding: barplots/1022150048_sbarplot.map (deflated 74%) adding: barplots/Gln_barplot_cell.line.png (deflated 24%) adding: barplots/Asn_barplot_treatment.png (deflated 21%) adding: barplots/Asn_barplot.png (deflated 32%) adding: barplots/1022150479_sbarplot.map (deflated 74%) adding: barplots/Ile_barplot.png (deflated 35%) adding: barplots/Asn_barplot_cell.line.png (deflated 26%) adding: barplots/Lys_barplot_cell.line.png (deflated 29%) adding: barplots/His_barplot.map (deflated 75%) adding: barplots/1022150450_sbarplot.png (deflated 53%) adding: barplots/Cit_barplot_cell.line.png (deflated 29%) adding: barplots/1022150067_sbarplot.map (deflated 74%) adding: barplots/Lys_barplot.png (deflated 32%) adding: barplots/Orn_barplot.png (deflated 33%) adding: barplots/1022150445_sbarplot.png (deflated 50%) adding: barplots/Tyr_barplot.map (deflated 74%) adding: barplots/Orn_barplot.map (deflated 74%) adding: barplots/Glu_barplot.png (deflated 27%) adding: barplots/Glu_barplot.map (deflated 74%) adding: barplots/Tyr_barplot.png (deflated 35%) adding: barplots/His_barplot_cell.line.png (deflated 33%) adding: barplots/Ala_barplot_cell.line.png (deflated 26%) adding: barplots/1022150033_sbarplot.png (deflated 50%) adding: barplots/Trp_barplot_treatment.png (deflated 19%) adding: barplots/Pro_barplot.png (deflated 38%) adding: barplots/Leu_barplot.map (deflated 75%) adding: barplots/Trp_barplot.png (deflated 30%) adding: barplots/Orn_barplot_cell.line.png (deflated 30%) adding: barplots/1022150479_sbarplot.png (deflated 53%) adding: barplots/1022150445_sbarplot.map (deflated 74%) adding: barplots/Lys_barplot_treatment.png (deflated 19%) adding: barplots/Orn_barplot_treatment.png (deflated 23%) adding: barplots/Gln_barplot.map (deflated 74%) adding: barplots/Leu_barplot_treatment.png (deflated 22%) adding: barplots/Arg_barplot_treatment.png (deflated 22%) adding: barplots/1022150431_sbarplot.png (deflated 49%) adding: barplots/Gly_barplot.png (deflated 30%) adding: barplots/1022150052_sbarplot.png (deflated 49%) adding: barplots/Phe_barplot_cell.line.png (deflated 24%) adding: barplots/Cit_barplot.png (deflated 33%) adding: barplots/1022150071_sbarplot.map (deflated 74%) adding: barplots/1022150431_sbarplot.map (deflated 74%) adding: barplots/Phe_barplot.map (deflated 75%) adding: barplots/Leu_barplot.png (deflated 34%) adding: barplots/1022150086_sbarplot.map (deflated 74%) adding: barplots/Val_barplot.png (deflated 32%) adding: barplots/Asp_barplot_cell.line.png (deflated 29%) adding: barplots/Met_barplot_treatment.png (deflated 19%) adding: barplots/1022150067_sbarplot.png (deflated 51%) adding: barplots/Gln_barplot_treatment.png (deflated 20%) adding: barplots/Leu_barplot_cell.line.png (deflated 31%) adding: barplots/Ile_barplot_cell.line.png (deflated 31%) adding: barplots/Cit_barplot.map (deflated 74%) adding: barplots/Arg_barplot.map (deflated 75%) adding: barplots/Tyr_barplot_cell.line.png (deflated 28%) adding: barplots/1022150464_sbarplot.png (deflated 49%) adding: barplots/1022150426_sbarplot.png (deflated 51%) adding: barplots/1022150426_sbarplot.map (deflated 74%) adding: barplots/Arg_barplot.png (deflated 36%) adding: barplots/Glu_barplot_treatment.png (deflated 19%) adding: barplots/1022150086_sbarplot.png (deflated 50%) adding: barplots/Ile_barplot.map (deflated 75%) adding: barplots/Phe_barplot.png (deflated 29%) adding: barplots/His_barplot.png (deflated 40%) adding: barplots/Gly_barplot_treatment.png (deflated 23%) adding: barplots/1022150052_sbarplot.map (deflated 74%) adding: barplots/Pro_barplot.map (deflated 75%) adding: barplots/1022150033_sbarplot.map (deflated 74%) adding: barplots/Ser_barplot_treatment.png (deflated 25%) adding: barplots/Ser_barplot.png (deflated 35%) adding: barplots/1022150048_sbarplot.png (deflated 51%) adding: barplots/Met_barplot.map (deflated 74%) adding: barplots/His_barplot_treatment.png (deflated 21%) adding: barplots/Asp_barplot.map (deflated 75%) adding: barplots/Thr_barplot.png (deflated 31%) adding: barplots/Glu_barplot_cell.line.png (deflated 24%) adding: barplots/1022150450_sbarplot.map (deflated 74%) adding: barplots/Ser_barplot.map (deflated 74%) adding: barplots/Asp_barplot.png (deflated 35%) adding: data_all_beforeCheck.csv (deflated 57%) adding: data_beforeCheck.csv (deflated 57%) adding: PCA_PC1_PC3.png (deflated 33%) adding: phenotypes_nominal.csv (deflated 60%) adding: pca.rotations.csv (deflated 50%) adding: hypothesisTests_separated_for_cell.line.pdf (deflated 87%) adding: PCA_propOfVar.png (deflated 21%) adding: PCAtreatment_PC2_PC3.map (deflated 73%) adding: PCAcell.line_PC1_PC2.map (deflated 73%) adding: aux.txt (stored 0%) adding: PCAtreatment_PC1_PC3.map (deflated 73%) adding: kendall.png (deflated 76%) adding: server_log.txt (deflated 81%) adding: metabolitesForDropping.csv (stored 0%) adding: Uscr_cv.csv (deflated 45%) adding: PCAcell.line_PC1_PC2.png (deflated 32%) adding: UL_cv.csv (deflated 46%) adding: pValuesForAllMetabolites_treatment_cell.line.csv (deflated 68%) adding: PCAcell.line_PC1_PC3.png (deflated 33%) adding: PCA_PC2_PC3.png (deflated 31%) adding: PCAcell.line_propOfVar.png (deflated 16%) adding: phenotypes_beforeCheck.csv (deflated 61%) 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 1424 -rw-r--r-- 1 www-data www-data 3223 Aug 8 15:56 input.tmp -rw-r--r-- 1 www-data www-data 372 Aug 8 15:56 phenotypes.txt.tmp -rw-r--r-- 1 www-data www-data 3223 Aug 8 15:56 input -rw-r--r-- 1 www-data www-data 372 Aug 8 15:56 phenotypes.txt -rw-r--r-- 1 www-data www-data 0 Aug 8 15:56 aux.txt -rw-r--r-- 1 www-data www-data 248 Aug 8 15:56 options -rwxr-xr-x 1 www-data www-data 609 Aug 8 15:56 metaPjob.cmd drwxrwxrwx 2087 metap2 metap2 258048 Aug 8 15:57 .. -rw-rw-r-- 1 metap2 metap2 1 Aug 8 15:57 out_params.txt -rw-rw-r-- 1 metap2 metap2 3222 Aug 8 15:57 input_4R -rw-rw-r-- 1 metap2 metap2 200 Aug 8 15:57 metabNamesMapping.csv -rw-rw-r-- 1 metap2 metap2 3268 Aug 8 15:57 data_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 369 Aug 8 15:57 phenotypes_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 3445 Aug 8 15:57 data_all_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 650 Aug 8 15:57 DU_cv.csv -rw-rw-r-- 1 metap2 metap2 646 Aug 8 15:57 UL_cv.csv -rw-rw-r-- 1 metap2 metap2 644 Aug 8 15:57 Uscr_cv.csv -rw-rw-r-- 1 metap2 metap2 645 Aug 8 15:57 Ush_cv.csv -rw-rw-r-- 1 metap2 metap2 23852 Aug 8 15:57 cv.pdf -rw-rw-r-- 1 metap2 metap2 2 Aug 8 15:57 cv.ok -rw-rw-r-- 1 metap2 metap2 8 Aug 8 15:57 metabolitesForDropping.csv -rw-rw-r-- 1 metap2 metap2 386 Aug 8 15:57 cv_average.csv -rw-rw-r-- 1 metap2 metap2 168 Aug 8 15:57 rowsToMark.csv -rw-rw-r-- 1 metap2 metap2 180 Aug 8 15:57 colsToMark.x.csv -rw-rw-r-- 1 metap2 metap2 57 Aug 8 15:57 colsToMark.csv -rw-rw-r-- 1 metap2 metap2 202 Aug 8 15:57 phenotypes_for_QC.csv -rw-rw-r-- 1 metap2 metap2 310 Aug 8 15:57 phenotypes.csv -rw-rw-r-- 1 metap2 metap2 3224 Aug 8 15:57 data.csv -rw-rw-r-- 1 metap2 metap2 3391 Aug 8 15:57 data_all.csv -rw-rw-r-- 1 metap2 metap2 225 Aug 8 15:57 phenotypes_numeric.csv -rw-rw-r-- 1 metap2 metap2 310 Aug 8 15:57 phenotypes_nominal.csv -rw-rw-r-- 1 metap2 metap2 2643 Aug 8 15:57 summary.csv -rw-rw-r-- 1 metap2 metap2 119619 Aug 8 15:57 histograms.pdf drwxrwxrwx 2 www-data www-data 4096 Aug 8 15:57 barplots -rw-rw-r-- 1 metap2 metap2 610 Aug 8 15:57 pValuesForAllMetabolites__cell.line.csv -rw-rw-r-- 1 metap2 metap2 593 Aug 8 15:57 pValuesForAllMetabolites__treatment.csv -rw-rw-r-- 1 metap2 metap2 127722 Aug 8 15:57 hypothesisTests_complete_data.pdf -rw-rw-r-- 1 metap2 metap2 395 Aug 8 15:57 pValuesForAllMetabolites_cell.line_treatment.c... -rw-rw-r-- 1 metap2 metap2 104504 Aug 8 15:57 hypothesisTests_separated_for_cell.line.pdf -rw-rw-r-- 1 metap2 metap2 424 Aug 8 15:57 pValuesForAllMetabolites_treatment_cell.line.c... -rw-rw-r-- 1 metap2 metap2 138587 Aug 8 15:57 hypothesisTests_separated_for_treatment.pdf -rw-rw-r-- 1 metap2 metap2 114 Aug 8 15:57 bonferroni.csv -rw-rw-r-- 1 metap2 metap2 1380 Aug 8 15:57 PCA_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1810 Aug 8 15:57 PCA_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 1379 Aug 8 15:57 PCA_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1760 Aug 8 15:57 PCA_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 1379 Aug 8 15:57 PCA_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 1828 Aug 8 15:57 PCA_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 4700 Aug 8 15:57 pca.rotations.csv -rw-rw-r-- 1 metap2 metap2 9827 Aug 8 15:57 PCA.pdf -rw-rw-r-- 1 metap2 metap2 1407 Aug 8 15:57 PCAcell.line_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1835 Aug 8 15:57 PCAcell.line_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 1406 Aug 8 15:57 PCAcell.line_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1784 Aug 8 15:57 PCAcell.line_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 1406 Aug 8 15:57 PCAcell.line_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 1832 Aug 8 15:57 PCAcell.line_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 10508 Aug 8 15:57 PCAcell.line.pdf -rw-rw-r-- 1 metap2 metap2 1407 Aug 8 15:57 PCAtreatment_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1849 Aug 8 15:57 PCAtreatment_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 1406 Aug 8 15:57 PCAtreatment_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1803 Aug 8 15:57 PCAtreatment_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 1406 Aug 8 15:57 PCAtreatment_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 1856 Aug 8 15:57 PCAtreatment_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 11112 Aug 8 15:57 PCAtreatment.pdf -rw-rw-r-- 1 metap2 metap2 5256 Aug 8 15:57 kendall.pdf -rw-rw-r-- 1 metap2 metap2 960 Aug 8 15:57 kendall.csv -rw-rw-r-- 1 metap2 metap2 36953 Aug 8 15:57 .R.Rout -rw-rw-r-- 1 metap2 metap2 3580 Aug 8 15:57 kendall.png -rw-rw-r-- 1 metap2 metap2 2727 Aug 8 15:57 PCAtreatment_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2504 Aug 8 15:57 PCAcell.line_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2158 Aug 8 15:57 PCA_propOfVar.png -rw-rw-r-- 1 metap2 metap2 1586 Aug 8 15:57 processing_log.txt -rw-rw-r-- 1 metap2 metap2 10799 Aug 8 15:57 server_log.txt -rw-rw-r-- 1 metap2 metap2 316506 Aug 8 15:57 download.zip drwxrwxrwx 3 www-data www-data 4096 Aug 8 15:57 . + 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.
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