Running METAP SERVER Tue Aug 8 15:35:01 CEST 2017 ID=17080815344323456 /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/17080815344323456 + 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/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=MH resistant TIC2 REFERENCE=n PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/home/metap2/public_html/users/17080815344323456 PRIVAT=0 LANG=en_US.UTF-8 SHLVL=1 HOME=/home/metap2 ID=17080815344323456 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 69. Use of uninitialized value $max_length in numeric lt (<) at /home/metap2/exec/readAux.pl line 71. -rw-rw-r-- 1 metap2 metap2 37106 Aug 8 15:35 .R.Rout adding: kendall.csv (deflated 57%) adding: KL_cv.csv (deflated 47%) adding: PCA_PC1_PC3.map (deflated 76%) adding: PCAcell.line_PC2_PC3.png (deflated 29%) adding: summary.csv (deflated 53%) adding: colsToMark.x.csv (deflated 40%) adding: phenotypes.csv (deflated 67%) adding: kendall.pdf (deflated 72%) adding: data_all.csv (deflated 57%) adding: PCA_PC1_PC2.png (deflated 25%) adding: PCAtreatment_PC1_PC2.png (deflated 26%) adding: PCAtreatment_propOfVar.png (deflated 19%) adding: cv_average.csv (deflated 51%) adding: processing_log.txt (deflated 58%) adding: options (deflated 39%) adding: PCAtreatment_PC1_PC2.map (deflated 76%) adding: colsToMark.csv (deflated 18%) adding: PCAtreatment_PC1_PC3.png (deflated 27%) adding: phenotypes_numeric.csv (deflated 63%) adding: PCAcell.line.pdf (deflated 79%) adding: cv.pdf (deflated 90%) adding: hypothesisTests_separated_for_treatment.pdf (deflated 87%) adding: PCA_PC1_PC2.map (deflated 76%) adding: JL_cv.csv (deflated 47%) adding: PCA_PC2_PC3.map (deflated 75%) adding: PCAtreatment_PC2_PC3.png (deflated 29%) adding: hypothesisTests_complete_data.pdf (deflated 87%) adding: pValuesForAllMetabolites__treatment.csv (deflated 53%) adding: pValuesForAllMetabolites_cell.line_treatment.csv (deflated 64%) adding: PCAcell.line_PC1_PC3.map (deflated 76%) adding: PCAtreatment.pdf (deflated 79%) adding: bonferroni.csv (deflated 32%) adding: rowsToMark.csv (deflated 70%) adding: RL_cv.csv (deflated 45%) adding: metabNamesMapping.csv (deflated 49%) adding: PCA.pdf (deflated 78%) adding: out_params.txt (stored 0%) adding: input (deflated 57%) adding: KD_cv.csv (deflated 45%) adding: data.csv (deflated 57%) adding: phenotypes.txt (deflated 64%) adding: phenotypes_for_QC.csv (deflated 60%) adding: histograms.pdf (deflated 90%) adding: PCAcell.line_PC2_PC3.map (deflated 75%) adding: pValuesForAllMetabolites__cell.line.csv (deflated 53%) adding: barplots/1022149992_sbarplot.map (deflated 74%) adding: barplots/Thr_barplot_cell.line.png (deflated 22%) adding: barplots/Cit_barplot_treatment.png (deflated 18%) adding: barplots/1022150687_sbarplot.map (deflated 74%) adding: barplots/Pro_barplot_cell.line.png (deflated 31%) adding: barplots/Ala_barplot.map (deflated 77%) adding: barplots/Val_barplot_cell.line.png (deflated 21%) adding: barplots/Trp_barplot.map (deflated 77%) adding: barplots/1022150668_sbarplot.map (deflated 74%) adding: barplots/1022149988_sbarplot.png (deflated 50%) adding: barplots/Val_barplot.map (deflated 76%) adding: barplots/Pro_barplot_treatment.png (deflated 26%) adding: barplots/Ile_barplot_treatment.png (deflated 22%) adding: barplots/Lys_barplot.map (deflated 77%) adding: barplots/Asn_barplot.map (deflated 77%) adding: barplots/Gln_barplot.png (deflated 34%) adding: barplots/1022150620_sbarplot.png (deflated 49%) adding: barplots/1022150736_sbarplot.png (deflated 50%) adding: barplots/1022150649_sbarplot.map (deflated 74%) adding: barplots/Ala_barplot.png (deflated 33%) adding: barplots/Ala_barplot_treatment.png (deflated 27%) adding: barplots/Trp_barplot_cell.line.png (deflated 22%) adding: barplots/Arg_barplot_cell.line.png (deflated 24%) adding: barplots/Phe_barplot_treatment.png (deflated 27%) adding: barplots/Ser_barplot_cell.line.png (deflated 25%) adding: barplots/Gly_barplot_cell.line.png (deflated 23%) adding: barplots/Tyr_barplot_treatment.png (deflated 29%) adding: barplots/1022150634_sbarplot.png (deflated 49%) adding: barplots/Asp_barplot_treatment.png (deflated 21%) adding: barplots/Gly_barplot.map (deflated 77%) adding: barplots/1022150000_sbarplot.png (deflated 50%) adding: barplots/1022150717_sbarplot.png (deflated 52%) adding: barplots/1022149992_sbarplot.png (deflated 52%) adding: barplots/Met_barplot.png (deflated 34%) adding: barplots/Thr_barplot.map (deflated 77%) adding: barplots/Val_barplot_treatment.png (deflated 24%) adding: barplots/Thr_barplot_treatment.png (deflated 24%) adding: barplots/Met_barplot_cell.line.png (deflated 19%) adding: barplots/Gln_barplot_cell.line.png (deflated 28%) adding: barplots/1022150620_sbarplot.map (deflated 74%) adding: barplots/Asn_barplot_treatment.png (deflated 24%) adding: barplots/Asn_barplot.png (deflated 26%) adding: barplots/Ile_barplot.png (deflated 29%) adding: barplots/1022150634_sbarplot.map (deflated 74%) adding: barplots/1022150615_sbarplot.png (deflated 53%) adding: barplots/Asn_barplot_cell.line.png (deflated 19%) adding: barplots/1022150691_sbarplot.map (deflated 74%) adding: barplots/Lys_barplot_cell.line.png (deflated 21%) adding: barplots/His_barplot.map (deflated 77%) adding: barplots/Cit_barplot_cell.line.png (deflated 16%) adding: barplots/Lys_barplot.png (deflated 30%) adding: barplots/Orn_barplot.png (deflated 29%) adding: barplots/Tyr_barplot.map (deflated 77%) adding: barplots/Orn_barplot.map (deflated 77%) adding: barplots/Glu_barplot.png (deflated 30%) adding: barplots/1022150721_sbarplot.map (deflated 73%) adding: barplots/Glu_barplot.map (deflated 77%) adding: barplots/1022149973_sbarplot.map (deflated 74%) adding: barplots/Tyr_barplot.png (deflated 35%) adding: barplots/His_barplot_cell.line.png (deflated 20%) adding: barplots/Ala_barplot_cell.line.png (deflated 23%) adding: barplots/Trp_barplot_treatment.png (deflated 23%) adding: barplots/Pro_barplot.png (deflated 37%) adding: barplots/Leu_barplot.map (deflated 77%) adding: barplots/1022150702_sbarplot.png (deflated 53%) adding: barplots/Trp_barplot.png (deflated 29%) adding: barplots/Orn_barplot_cell.line.png (deflated 22%) adding: barplots/1022150736_sbarplot.map (deflated 74%) adding: barplots/1022150668_sbarplot.png (deflated 51%) adding: barplots/1022149973_sbarplot.png (deflated 50%) adding: barplots/1022150672_sbarplot.map (deflated 74%) adding: barplots/Lys_barplot_treatment.png (deflated 29%) adding: barplots/Orn_barplot_treatment.png (deflated 20%) adding: barplots/Gln_barplot.map (deflated 78%) adding: barplots/Leu_barplot_treatment.png (deflated 24%) adding: barplots/Arg_barplot_treatment.png (deflated 24%) adding: barplots/Gly_barplot.png (deflated 33%) adding: barplots/Phe_barplot_cell.line.png (deflated 23%) adding: barplots/1022150717_sbarplot.map (deflated 74%) adding: barplots/Cit_barplot.png (deflated 26%) adding: barplots/Phe_barplot.map (deflated 77%) adding: barplots/1022150687_sbarplot.png (deflated 51%) adding: barplots/Leu_barplot.png (deflated 33%) adding: barplots/Val_barplot.png (deflated 33%) adding: barplots/1022150014_sbarplot.map (deflated 74%) adding: barplots/Asp_barplot_cell.line.png (deflated 24%) adding: barplots/Met_barplot_treatment.png (deflated 24%) adding: barplots/1022150649_sbarplot.png (deflated 51%) adding: barplots/Gln_barplot_treatment.png (deflated 30%) adding: barplots/Leu_barplot_cell.line.png (deflated 22%) adding: barplots/1022150653_sbarplot.map (deflated 74%) adding: barplots/1022150653_sbarplot.png (deflated 51%) adding: barplots/Ile_barplot_cell.line.png (deflated 19%) adding: barplots/Cit_barplot.map (deflated 77%) adding: barplots/Arg_barplot.map (deflated 77%) adding: barplots/Tyr_barplot_cell.line.png (deflated 24%) adding: barplots/1022150000_sbarplot.map (deflated 74%) adding: barplots/Arg_barplot.png (deflated 33%) adding: barplots/Glu_barplot_treatment.png (deflated 23%) adding: barplots/1022150691_sbarplot.png (deflated 50%) adding: barplots/1022150014_sbarplot.png (deflated 51%) adding: barplots/1022150615_sbarplot.map (deflated 74%) adding: barplots/Ile_barplot.map (deflated 77%) adding: barplots/Phe_barplot.png (deflated 34%) adding: barplots/His_barplot.png (deflated 29%) adding: barplots/Gly_barplot_treatment.png (deflated 21%) adding: barplots/1022149988_sbarplot.map (deflated 74%) adding: barplots/1022150702_sbarplot.map (deflated 74%) adding: barplots/Pro_barplot.map (deflated 77%) adding: barplots/1022150721_sbarplot.png (deflated 52%) adding: barplots/Ser_barplot_treatment.png (deflated 24%) adding: barplots/Ser_barplot.png (deflated 35%) adding: barplots/Met_barplot.map (deflated 77%) adding: barplots/His_barplot_treatment.png (deflated 25%) adding: barplots/Asp_barplot.map (deflated 77%) adding: barplots/Thr_barplot.png (deflated 29%) adding: barplots/Glu_barplot_cell.line.png (deflated 24%) adding: barplots/1022150672_sbarplot.png (deflated 51%) adding: barplots/Ser_barplot.map (deflated 77%) adding: barplots/Asp_barplot.png (deflated 32%) adding: data_all_beforeCheck.csv (deflated 57%) adding: data_beforeCheck.csv (deflated 58%) adding: JD_cv.csv (deflated 45%) adding: PCA_PC1_PC3.png (deflated 28%) adding: phenotypes_nominal.csv (deflated 67%) adding: pca.rotations.csv (deflated 51%) adding: hypothesisTests_separated_for_cell.line.pdf (deflated 88%) adding: PCA_propOfVar.png (deflated 25%) adding: PCAtreatment_PC2_PC3.map (deflated 75%) adding: PCAcell.line_PC1_PC2.map (deflated 76%) adding: aux.txt (stored 0%) adding: PCAtreatment_PC1_PC3.map (deflated 76%) adding: kendall.png (deflated 76%) adding: server_log.txt (deflated 82%) adding: PCAcell.line_PC1_PC2.png (deflated 26%) adding: pValuesForAllMetabolites_treatment_cell.line.csv (deflated 71%) adding: PCAcell.line_PC1_PC3.png (deflated 27%) adding: PCA_PC2_PC3.png (deflated 28%) adding: PCAcell.line_propOfVar.png (deflated 16%) adding: phenotypes_beforeCheck.csv (deflated 67%) adding: RD_cv.csv (deflated 46%) 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 1548 -rw-r--r-- 1 www-data www-data 4787 Aug 8 15:34 input.tmp -rw-r--r-- 1 www-data www-data 513 Aug 8 15:34 phenotypes.txt.tmp -rw-r--r-- 1 www-data www-data 4787 Aug 8 15:34 input -rw-r--r-- 1 www-data www-data 513 Aug 8 15:34 phenotypes.txt -rw-r--r-- 1 www-data www-data 0 Aug 8 15:34 aux.txt -rw-r--r-- 1 www-data www-data 243 Aug 8 15:34 options -rwxr-xr-x 1 www-data www-data 609 Aug 8 15:34 metaPjob.cmd drwxrwxrwx 2081 metap2 metap2 258048 Aug 8 15:35 .. -rw-rw-r-- 1 metap2 metap2 1 Aug 8 15:35 out_params.txt -rw-rw-r-- 1 metap2 metap2 4786 Aug 8 15:35 input_4R -rw-rw-r-- 1 metap2 metap2 200 Aug 8 15:35 metabNamesMapping.csv -rw-rw-r-- 1 metap2 metap2 4830 Aug 8 15:35 data_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 510 Aug 8 15:35 phenotypes_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 5082 Aug 8 15:35 data_all_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 644 Aug 8 15:35 JD_cv.csv -rw-rw-r-- 1 metap2 metap2 649 Aug 8 15:35 JL_cv.csv -rw-rw-r-- 1 metap2 metap2 649 Aug 8 15:35 KD_cv.csv -rw-rw-r-- 1 metap2 metap2 651 Aug 8 15:35 KL_cv.csv -rw-rw-r-- 1 metap2 metap2 650 Aug 8 15:35 RD_cv.csv -rw-rw-r-- 1 metap2 metap2 645 Aug 8 15:35 RL_cv.csv -rw-rw-r-- 1 metap2 metap2 34744 Aug 8 15:35 cv.pdf -rw-rw-r-- 1 metap2 metap2 2 Aug 8 15:35 cv.ok -rw-rw-r-- 1 metap2 metap2 388 Aug 8 15:35 cv_average.csv -rw-rw-r-- 1 metap2 metap2 166 Aug 8 15:35 colsToMark.x.csv -rw-rw-r-- 1 metap2 metap2 57 Aug 8 15:35 colsToMark.csv -rw-rw-r-- 1 metap2 metap2 252 Aug 8 15:35 rowsToMark.csv -rw-rw-r-- 1 metap2 metap2 442 Aug 8 15:35 phenotypes.csv -rw-rw-r-- 1 metap2 metap2 4786 Aug 8 15:35 data.csv -rw-rw-r-- 1 metap2 metap2 277 Aug 8 15:35 phenotypes_for_QC.csv -rw-rw-r-- 1 metap2 metap2 5019 Aug 8 15:35 data_all.csv -rw-rw-r-- 1 metap2 metap2 300 Aug 8 15:35 phenotypes_numeric.csv -rw-rw-r-- 1 metap2 metap2 442 Aug 8 15:35 phenotypes_nominal.csv -rw-rw-r-- 1 metap2 metap2 2623 Aug 8 15:35 summary.csv -rw-rw-r-- 1 metap2 metap2 130120 Aug 8 15:35 histograms.pdf drwxrwxrwx 2 www-data www-data 4096 Aug 8 15:35 barplots -rw-rw-r-- 1 metap2 metap2 609 Aug 8 15:35 pValuesForAllMetabolites__cell.line.csv -rw-rw-r-- 1 metap2 metap2 566 Aug 8 15:35 pValuesForAllMetabolites__treatment.csv -rw-rw-r-- 1 metap2 metap2 120712 Aug 8 15:35 hypothesisTests_complete_data.pdf -rw-rw-r-- 1 metap2 metap2 525 Aug 8 15:35 pValuesForAllMetabolites_cell.line_treatment.csv -rw-rw-r-- 1 metap2 metap2 156795 Aug 8 15:35 hypothesisTests_separated_for_cell.line.pdf -rw-rw-r-- 1 metap2 metap2 114 Aug 8 15:35 bonferroni.csv -rw-rw-r-- 1 metap2 metap2 1023 Aug 8 15:35 pValuesForAllMetabolites_treatment_cell.line.csv -rw-rw-r-- 1 metap2 metap2 125870 Aug 8 15:35 hypothesisTests_separated_for_treatment.pdf -rw-rw-r-- 1 metap2 metap2 2007 Aug 8 15:35 PCA_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1924 Aug 8 15:35 PCA_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 2017 Aug 8 15:35 PCA_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1988 Aug 8 15:35 PCA_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 2020 Aug 8 15:35 PCA_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2020 Aug 8 15:35 PCA_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 7349 Aug 8 15:35 pca.rotations.csv -rw-rw-r-- 1 metap2 metap2 11241 Aug 8 15:35 PCA.pdf -rw-rw-r-- 1 metap2 metap2 2034 Aug 8 15:35 PCAcell.line_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1931 Aug 8 15:35 PCAcell.line_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 2044 Aug 8 15:35 PCAcell.line_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 2030 Aug 8 15:35 PCAcell.line_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 2047 Aug 8 15:35 PCAcell.line_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2065 Aug 8 15:35 PCAcell.line_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 12223 Aug 8 15:35 PCAcell.line.pdf -rw-rw-r-- 1 metap2 metap2 2034 Aug 8 15:35 PCAtreatment_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1935 Aug 8 15:35 PCAtreatment_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 2044 Aug 8 15:35 PCAtreatment_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 2011 Aug 8 15:35 PCAtreatment_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 2047 Aug 8 15:35 PCAtreatment_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2044 Aug 8 15:35 PCAtreatment_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 12423 Aug 8 15:35 PCAtreatment.pdf -rw-rw-r-- 1 metap2 metap2 5298 Aug 8 15:35 kendall.pdf -rw-rw-r-- 1 metap2 metap2 925 Aug 8 15:35 kendall.csv -rw-rw-r-- 1 metap2 metap2 37106 Aug 8 15:35 .R.Rout -rw-rw-r-- 1 metap2 metap2 3585 Aug 8 15:35 kendall.png -rw-rw-r-- 1 metap2 metap2 2351 Aug 8 15:35 PCAtreatment_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2568 Aug 8 15:35 PCAcell.line_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2029 Aug 8 15:35 PCA_propOfVar.png -rw-rw-r-- 1 metap2 metap2 1534 Aug 8 15:35 processing_log.txt -rw-rw-r-- 1 metap2 metap2 11508 Aug 8 15:35 server_log.txt -rw-rw-r-- 1 metap2 metap2 354147 Aug 8 15:35 download.zip drwxrwxrwx 3 www-data www-data 4096 Aug 8 15:35 . + set - Finishing METAP SERVER