Running METAP SERVER Tue Aug 8 15:45:01 CEST 2017 ID=17080815443126613 /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/17080815443126613 + 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 all samples 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/17080815443126613 PRIVAT=0 LANG=en_US.UTF-8 SHLVL=1 HOME=/home/metap2 ID=17080815443126613 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 45601 Aug 8 15:45 .R.Rout adding: PCA_PC1_PC3.map (deflated 79%) adding: PCAcell.line_PC2_PC3.png (deflated 15%) adding: summary.csv (deflated 52%) adding: colsToMark.x.csv (deflated 40%) adding: phenotypes.csv (deflated 74%) adding: data_all.csv (deflated 59%) adding: PCA_PC1_PC2.png (deflated 18%) adding: PCAtreatment_PC1_PC2.png (deflated 18%) adding: PCAtreatment_propOfVar.png (deflated 15%) adding: processing_log.txt (deflated 54%) adding: options (deflated 39%) adding: PCAtreatment_PC1_PC2.map (deflated 80%) adding: colsToMark.csv (deflated 8%) adding: PCAtreatment_PC1_PC3.png (deflated 15%) adding: PCAcell.line.pdf (deflated 81%) adding: hypothesisTests_separated_for_treatment.pdf (deflated 86%) adding: PCA_PC1_PC2.map (deflated 80%) adding: PCA_PC2_PC3.map (deflated 80%) adding: PCAtreatment_PC2_PC3.png (deflated 14%) adding: hypothesisTests_complete_data.pdf (deflated 86%) adding: pValuesForAllMetabolites__treatment.csv (deflated 45%) adding: pValuesForAllMetabolites_cell.line_treatment.csv (deflated 74%) adding: PCAcell.line_PC1_PC3.map (deflated 79%) adding: PCAtreatment.pdf (deflated 82%) 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 59%) adding: data.csv (deflated 59%) adding: phenotypes.txt (deflated 70%) adding: phenotypes_for_QC.csv (deflated 71%) adding: histograms.pdf (deflated 89%) adding: PCAcell.line_PC2_PC3.map (deflated 80%) adding: pValuesForAllMetabolites__cell.line.csv (deflated 44%) adding: barplots/1022149992_sbarplot.map (deflated 74%) adding: barplots/1022150590_sbarplot.map (deflated 74%) adding: barplots/Thr_barplot_cell.line.png (deflated 17%) adding: barplots/Cit_barplot_treatment.png (deflated 16%) adding: barplots/1022150687_sbarplot.map (deflated 74%) adding: barplots/1022150464_sbarplot.map (deflated 74%) adding: barplots/Pro_barplot_cell.line.png (deflated 15%) adding: barplots/Ala_barplot.map (deflated 81%) adding: barplots/Val_barplot_cell.line.png (deflated 16%) 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 52%) adding: barplots/Val_barplot.map (deflated 80%) adding: barplots/Pro_barplot_treatment.png (deflated 17%) adding: barplots/Ile_barplot_treatment.png (deflated 17%) adding: barplots/Lys_barplot.map (deflated 80%) adding: barplots/Asn_barplot.map (deflated 80%) adding: barplots/1022150547_sbarplot.png (deflated 51%) adding: barplots/Gln_barplot.png (deflated 30%) adding: barplots/1022150620_sbarplot.png (deflated 50%) adding: barplots/1022150736_sbarplot.png (deflated 51%) adding: barplots/1022150071_sbarplot.png (deflated 51%) adding: barplots/1022150649_sbarplot.map (deflated 74%) adding: barplots/Ala_barplot.png (deflated 22%) adding: barplots/Ala_barplot_treatment.png (deflated 15%) adding: barplots/Trp_barplot_cell.line.png (deflated 16%) adding: barplots/Arg_barplot_cell.line.png (deflated 16%) adding: barplots/Phe_barplot_treatment.png (deflated 16%) adding: barplots/Ser_barplot_cell.line.png (deflated 16%) adding: barplots/Gly_barplot_cell.line.png (deflated 17%) adding: barplots/Tyr_barplot_treatment.png (deflated 19%) adding: barplots/1022150634_sbarplot.png (deflated 50%) adding: barplots/Asp_barplot_treatment.png (deflated 16%) 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 47%) adding: barplots/Met_barplot.png (deflated 20%) adding: barplots/Thr_barplot.map (deflated 80%) adding: barplots/1022150532_sbarplot.png (deflated 49%) adding: barplots/Val_barplot_treatment.png (deflated 17%) adding: barplots/Thr_barplot_treatment.png (deflated 18%) adding: barplots/1022150498_sbarplot.png (deflated 49%) adding: barplots/Met_barplot_cell.line.png (deflated 13%) adding: barplots/1022150048_sbarplot.map (deflated 74%) adding: barplots/Gln_barplot_cell.line.png (deflated 20%) 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 17%) adding: barplots/Asn_barplot.png (deflated 21%) adding: barplots/1022150479_sbarplot.map (deflated 74%) adding: barplots/Ile_barplot.png (deflated 23%) adding: barplots/1022150634_sbarplot.map (deflated 74%) adding: barplots/1022150615_sbarplot.png (deflated 50%) adding: barplots/Asn_barplot_cell.line.png (deflated 16%) adding: barplots/1022150551_sbarplot.map (deflated 74%) adding: barplots/1022150691_sbarplot.map (deflated 74%) adding: barplots/Lys_barplot_cell.line.png (deflated 14%) adding: barplots/His_barplot.map (deflated 80%) adding: barplots/1022150450_sbarplot.png (deflated 52%) adding: barplots/Cit_barplot_cell.line.png (deflated 16%) adding: barplots/1022150067_sbarplot.map (deflated 74%) adding: barplots/1022150532_sbarplot.map (deflated 74%) adding: barplots/Lys_barplot.png (deflated 24%) adding: barplots/Orn_barplot.png (deflated 27%) 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 23%) adding: barplots/1022150721_sbarplot.map (deflated 74%) adding: barplots/1022150509_sbarplot.map (deflated 73%) adding: barplots/Glu_barplot.map (deflated 80%) adding: barplots/1022150498_sbarplot.map (deflated 73%) adding: barplots/1022149973_sbarplot.map (deflated 74%) adding: barplots/1022150571_sbarplot.png (deflated 53%) adding: barplots/Tyr_barplot.png (deflated 27%) adding: barplots/His_barplot_cell.line.png (deflated 16%) adding: barplots/Ala_barplot_cell.line.png (deflated 13%) adding: barplots/1022150033_sbarplot.png (deflated 53%) adding: barplots/Trp_barplot_treatment.png (deflated 18%) adding: barplots/Pro_barplot.png (deflated 23%) adding: barplots/1022150513_sbarplot.map (deflated 74%) adding: barplots/Leu_barplot.map (deflated 81%) adding: barplots/1022150702_sbarplot.png (deflated 51%) adding: barplots/Trp_barplot.png (deflated 24%) adding: barplots/Orn_barplot_cell.line.png (deflated 15%) 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 51%) adding: barplots/1022149973_sbarplot.png (deflated 53%) adding: barplots/1022150672_sbarplot.map (deflated 74%) adding: barplots/Lys_barplot_treatment.png (deflated 16%) adding: barplots/Orn_barplot_treatment.png (deflated 19%) adding: barplots/Gln_barplot.map (deflated 81%) adding: barplots/Leu_barplot_treatment.png (deflated 17%) adding: barplots/Arg_barplot_treatment.png (deflated 18%) adding: barplots/1022150431_sbarplot.png (deflated 49%) adding: barplots/Gly_barplot.png (deflated 34%) adding: barplots/1022150052_sbarplot.png (deflated 51%) adding: barplots/Phe_barplot_cell.line.png (deflated 15%) adding: barplots/1022150717_sbarplot.map (deflated 74%) adding: barplots/Cit_barplot.png (deflated 21%) adding: barplots/1022150585_sbarplot.png (deflated 51%) adding: barplots/1022150585_sbarplot.map (deflated 74%) adding: barplots/1022150071_sbarplot.map (deflated 74%) adding: barplots/1022150431_sbarplot.map (deflated 74%) adding: barplots/Phe_barplot.map (deflated 80%) adding: barplots/1022150687_sbarplot.png (deflated 54%) adding: barplots/Leu_barplot.png (deflated 23%) adding: barplots/1022150086_sbarplot.map (deflated 74%) adding: barplots/Val_barplot.png (deflated 24%) adding: barplots/1022150014_sbarplot.map (deflated 74%) adding: barplots/Asp_barplot_cell.line.png (deflated 15%) adding: barplots/1022150483_sbarplot.png (deflated 51%) adding: barplots/1022150590_sbarplot.png (deflated 52%) adding: barplots/Met_barplot_treatment.png (deflated 13%) adding: barplots/1022150649_sbarplot.png (deflated 51%) adding: barplots/1022150067_sbarplot.png (deflated 49%) adding: barplots/Gln_barplot_treatment.png (deflated 20%) adding: barplots/1022150528_sbarplot.png (deflated 50%) adding: barplots/Leu_barplot_cell.line.png (deflated 15%) adding: barplots/1022150653_sbarplot.map (deflated 74%) adding: barplots/1022150653_sbarplot.png (deflated 52%) adding: barplots/Ile_barplot_cell.line.png (deflated 15%) adding: barplots/Cit_barplot.map (deflated 80%) adding: barplots/Arg_barplot.map (deflated 80%) adding: barplots/Tyr_barplot_cell.line.png (deflated 18%) adding: barplots/1022150464_sbarplot.png (deflated 53%) adding: barplots/1022150000_sbarplot.map (deflated 74%) adding: barplots/1022150426_sbarplot.png (deflated 52%) adding: barplots/1022150426_sbarplot.map (deflated 74%) adding: barplots/Arg_barplot.png (deflated 29%) adding: barplots/1022150513_sbarplot.png (deflated 49%) adding: barplots/1022150528_sbarplot.map (deflated 74%) adding: barplots/Glu_barplot_treatment.png (deflated 19%) adding: barplots/1022150691_sbarplot.png (deflated 53%) adding: barplots/1022150086_sbarplot.png (deflated 49%) adding: barplots/1022150566_sbarplot.png (deflated 49%) 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 24%) adding: barplots/His_barplot.png (deflated 20%) adding: barplots/Gly_barplot_treatment.png (deflated 20%) adding: barplots/1022150052_sbarplot.map (deflated 74%) adding: barplots/1022149988_sbarplot.map (deflated 74%) adding: barplots/1022150702_sbarplot.map (deflated 74%) adding: barplots/Pro_barplot.map (deflated 80%) adding: barplots/1022150721_sbarplot.png (deflated 51%) adding: barplots/1022150033_sbarplot.map (deflated 74%) adding: barplots/1022150509_sbarplot.png (deflated 49%) adding: barplots/Ser_barplot_treatment.png (deflated 18%) adding: barplots/Ser_barplot.png (deflated 24%) adding: barplots/1022150048_sbarplot.png (deflated 50%) adding: barplots/Met_barplot.map (deflated 80%) adding: barplots/His_barplot_treatment.png (deflated 16%) adding: barplots/Asp_barplot.map (deflated 80%) adding: barplots/Thr_barplot.png (deflated 24%) adding: barplots/1022150571_sbarplot.map (deflated 74%) adding: barplots/1022150547_sbarplot.map (deflated 74%) adding: barplots/Glu_barplot_cell.line.png (deflated 17%) adding: barplots/1022150672_sbarplot.png (deflated 51%) adding: barplots/1022150450_sbarplot.map (deflated 74%) adding: barplots/Ser_barplot.map (deflated 81%) adding: barplots/Asp_barplot.png (deflated 20%) adding: data_all_beforeCheck.csv (deflated 59%) adding: data_beforeCheck.csv (deflated 59%) adding: PCA_PC1_PC3.png (deflated 15%) adding: phenotypes_nominal.csv (deflated 74%) adding: pca.rotations.csv (deflated 51%) adding: hypothesisTests_separated_for_cell.line.pdf (deflated 89%) adding: PCA_propOfVar.png (deflated 23%) adding: PCAtreatment_PC2_PC3.map (deflated 80%) adding: PCAcell.line_PC1_PC2.map (deflated 80%) adding: aux.txt (stored 0%) adding: PCAtreatment_PC1_PC3.map (deflated 79%) adding: server_log.txt (deflated 84%) adding: PCAcell.line_PC1_PC2.png (deflated 18%) adding: pValuesForAllMetabolites_treatment_cell.line.csv (deflated 55%) adding: PCAcell.line_PC1_PC3.png (deflated 15%) adding: PCA_PC2_PC3.png (deflated 14%) adding: PCAcell.line_propOfVar.png (deflated 13%) adding: phenotypes_beforeCheck.csv (deflated 74%) 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 2148 -rw-r--r-- 1 www-data www-data 11046 Aug 8 15:44 input.tmp -rw-r--r-- 1 www-data www-data 973 Aug 8 15:44 phenotypes.txt.tmp -rw-r--r-- 1 www-data www-data 11046 Aug 8 15:44 input -rw-r--r-- 1 www-data www-data 973 Aug 8 15:44 phenotypes.txt -rw-r--r-- 1 www-data www-data 0 Aug 8 15:44 aux.txt -rw-r--r-- 1 www-data www-data 244 Aug 8 15:44 options -rwxr-xr-x 1 www-data www-data 609 Aug 8 15:44 metaPjob.cmd drwxrwxrwx 2086 metap2 metap2 258048 Aug 8 15:45 .. -rw-rw-r-- 1 metap2 metap2 1 Aug 8 15:45 out_params.txt -rw-rw-r-- 1 metap2 metap2 11045 Aug 8 15:45 input_4R -rw-rw-r-- 1 metap2 metap2 200 Aug 8 15:45 metabNamesMapping.csv -rw-rw-r-- 1 metap2 metap2 11091 Aug 8 15:45 data_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 967 Aug 8 15:45 phenotypes_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 11536 Aug 8 15:45 data_all_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 2 Aug 8 15:45 cv.ok -rw-rw-r-- 1 metap2 metap2 588 Aug 8 15:45 rowsToMark.csv -rw-rw-r-- 1 metap2 metap2 166 Aug 8 15:45 colsToMark.x.csv -rw-rw-r-- 1 metap2 metap2 40 Aug 8 15:45 colsToMark.csv -rw-rw-r-- 1 metap2 metap2 967 Aug 8 15:45 phenotypes.csv -rw-rw-r-- 1 metap2 metap2 11047 Aug 8 15:45 data.csv -rw-rw-r-- 1 metap2 metap2 473 Aug 8 15:45 phenotypes_for_QC.csv -rw-rw-r-- 1 metap2 metap2 11541 Aug 8 15:45 data_all.csv -rw-rw-r-- 1 metap2 metap2 967 Aug 8 15:45 phenotypes_nominal.csv -rw-rw-r-- 1 metap2 metap2 2612 Aug 8 15:45 summary.csv -rw-rw-r-- 1 metap2 metap2 192290 Aug 8 15:45 histograms.pdf drwxrwxrwx 2 www-data www-data 12288 Aug 8 15:45 barplots -rw-rw-r-- 1 metap2 metap2 634 Aug 8 15:45 pValuesForAllMetabolites__cell.line.csv -rw-rw-r-- 1 metap2 metap2 610 Aug 8 15:45 pValuesForAllMetabolites__treatment.csv -rw-rw-r-- 1 metap2 metap2 180385 Aug 8 15:45 hypothesisTests_complete_data.pdf -rw-rw-r-- 1 metap2 metap2 1039 Aug 8 15:45 pValuesForAllMetabolites_cell.line_treatment.csv -rw-rw-r-- 1 metap2 metap2 357085 Aug 8 15:45 hypothesisTests_separated_for_cell.line.pdf -rw-rw-r-- 1 metap2 metap2 1180 Aug 8 15:45 pValuesForAllMetabolites_treatment_cell.line.csv -rw-rw-r-- 1 metap2 metap2 240163 Aug 8 15:45 hypothesisTests_separated_for_treatment.pdf -rw-rw-r-- 1 metap2 metap2 114 Aug 8 15:45 bonferroni.csv -rw-rw-r-- 1 metap2 metap2 4583 Aug 8 15:45 PCA_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 2273 Aug 8 15:45 PCA_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 4583 Aug 8 15:45 PCA_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 2373 Aug 8 15:45 PCA_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 4583 Aug 8 15:45 PCA_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2409 Aug 8 15:45 PCA_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 7753 Aug 8 15:45 pca.rotations.csv -rw-rw-r-- 1 metap2 metap2 15681 Aug 8 15:45 PCA.pdf -rw-rw-r-- 1 metap2 metap2 4610 Aug 8 15:45 PCAcell.line_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 2265 Aug 8 15:45 PCAcell.line_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 4610 Aug 8 15:45 PCAcell.line_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 2394 Aug 8 15:45 PCAcell.line_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 4610 Aug 8 15:45 PCAcell.line_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2372 Aug 8 15:45 PCAcell.line_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 17849 Aug 8 15:45 PCAcell.line.pdf -rw-rw-r-- 1 metap2 metap2 4610 Aug 8 15:45 PCAtreatment_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 2276 Aug 8 15:45 PCAtreatment_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 4610 Aug 8 15:45 PCAtreatment_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 2376 Aug 8 15:45 PCAtreatment_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 4610 Aug 8 15:45 PCAtreatment_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2367 Aug 8 15:45 PCAtreatment_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 18225 Aug 8 15:45 PCAtreatment.pdf -rw-rw-r-- 1 metap2 metap2 45601 Aug 8 15:45 .R.Rout -rw-rw-r-- 1 metap2 metap2 2625 Aug 8 15:45 PCAtreatment_propOfVar.png -rw-rw-r-- 1 metap2 metap2 3045 Aug 8 15:45 PCAcell.line_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2078 Aug 8 15:45 PCA_propOfVar.png -rw-rw-r-- 1 metap2 metap2 1278 Aug 8 15:45 processing_log.txt -rw-rw-r-- 1 metap2 metap2 13851 Aug 8 15:45 server_log.txt -rw-rw-r-- 1 metap2 metap2 512628 Aug 8 15:45 download.zip drwxrwxrwx 3 www-data www-data 4096 Aug 8 15:45 . + set - Finishing METAP SERVER