Running METAP SERVER Wed Aug 2 22:12:01 CEST 2017 ID=1708022211463594 /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/1708022211463594 + 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/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 aa dmso len with replicates REFERENCE=n PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/home/metap2/public_html/users/1708022211463594 PRIVAT=0 LANG=en_US.UTF-8 SHLVL=1 HOME=/home/metap2 ID=1708022211463594 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 37772 Aug 2 22:12 .R.Rout adding: kendall.csv (deflated 44%) adding: PCA_PC1_PC3.map (deflated 80%) adding: PCAcell.line_PC2_PC3.png (deflated 21%) adding: summary.csv (deflated 48%) adding: colsToMark.x.csv (deflated 40%) adding: phenotypes.csv (deflated 74%) adding: kendall.pdf (deflated 73%) adding: data_all.csv (deflated 56%) adding: PCA_PC1_PC2.png (deflated 21%) adding: PCAtreatment_PC1_PC2.png (deflated 20%) adding: PCAtreatment_propOfVar.png (deflated 16%) adding: processing_log.txt (deflated 58%) adding: options (deflated 37%) adding: PCAtreatment_PC1_PC2.map (deflated 80%) adding: colsToMark.csv (deflated 8%) adding: PCAtreatment_PC1_PC3.png (deflated 21%) adding: phenotypes_numeric.csv (deflated 75%) adding: PCAcell.line.pdf (deflated 81%) adding: hypothesisTests_separated_for_treatment.pdf (deflated 85%) adding: PCA_PC1_PC2.map (deflated 80%) adding: PCA:cell.line.pdf (deflated 81%) adding: PCA_PC2_PC3.map (deflated 80%) adding: PCAtreatment_PC2_PC3.png (deflated 20%) adding: hypothesisTests_complete_data.pdf (deflated 86%) adding: pValuesForAllMetabolites__treatment.csv (deflated 42%) adding: pValuesForAllMetabolites_cell.line_treatment.csv (deflated 68%) adding: PCAcell.line_PC1_PC3.map (deflated 80%) adding: PCAtreatment.pdf (deflated 82%) adding: bonferroni.csv (deflated 37%) adding: rowsToMark.csv (deflated 77%) adding: metabNamesMapping.csv (deflated 51%) adding: PCA.pdf (deflated 81%) adding: out_params.txt (stored 0%) adding: input (deflated 55%) adding: data.csv (deflated 55%) adding: phenotypes.txt (deflated 69%) adding: phenotypes_for_QC.csv (deflated 71%) adding: histograms.pdf (deflated 89%) adding: PCAcell.line_PC2_PC3.map (deflated 80%) adding: upperOutliers.csv (deflated 43%) adding: pValuesForAllMetabolites__cell.line.csv (deflated 43%) adding: barplots/Thr_barplot_cell.line.png (deflated 17%) adding: barplots/Cit_barplot_treatment.png (deflated 18%) adding: barplots/Pro_barplot_cell.line.png (deflated 16%) adding: barplots/Ala_barplot.map (deflated 80%) adding: barplots/Val_barplot_cell.line.png (deflated 18%) adding: barplots/Trp_barplot.map (deflated 80%) adding: barplots/Val_barplot.map (deflated 80%) adding: barplots/Pro_barplot_treatment.png (deflated 18%) adding: barplots/Ile_barplot_treatment.png (deflated 23%) adding: barplots/Lys_barplot.map (deflated 80%) adding: barplots/Asn_barplot.map (deflated 80%) adding: barplots/Gln_barplot.png (deflated 29%) adding: barplots/Ala_barplot.png (deflated 24%) adding: barplots/Ala_barplot_treatment.png (deflated 19%) adding: barplots/Trp_barplot_cell.line.png (deflated 16%) adding: barplots/Arg_barplot_cell.line.png (deflated 18%) adding: barplots/Phe_barplot_treatment.png (deflated 24%) adding: barplots/Ser_barplot_cell.line.png (deflated 21%) adding: barplots/Gly_barplot_cell.line.png (deflated 19%) adding: barplots/Tyr_barplot_treatment.png (deflated 20%) adding: barplots/Asp_barplot_treatment.png (deflated 21%) adding: barplots/Gly_barplot.map (deflated 80%) adding: barplots/Met_barplot.png (deflated 23%) adding: barplots/Thr_barplot.map (deflated 81%) adding: barplots/Val_barplot_treatment.png (deflated 24%) adding: barplots/Thr_barplot_treatment.png (deflated 22%) adding: barplots/Met_barplot_cell.line.png (deflated 15%) adding: barplots/Gln_barplot_cell.line.png (deflated 17%) adding: barplots/Asn_barplot_treatment.png (deflated 23%) adding: barplots/Asn_barplot.png (deflated 26%) adding: barplots/Ile_barplot.png (deflated 27%) adding: barplots/Asn_barplot_cell.line.png (deflated 17%) adding: barplots/Lys_barplot_cell.line.png (deflated 20%) adding: barplots/His_barplot.map (deflated 80%) adding: barplots/Cit_barplot_cell.line.png (deflated 15%) adding: barplots/Lys_barplot.png (deflated 29%) adding: barplots/Orn_barplot.png (deflated 30%) adding: barplots/Tyr_barplot.map (deflated 80%) adding: barplots/Orn_barplot.map (deflated 80%) adding: barplots/Glu_barplot.png (deflated 24%) adding: barplots/Glu_barplot.map (deflated 80%) adding: barplots/Tyr_barplot.png (deflated 26%) adding: barplots/His_barplot_cell.line.png (deflated 18%) adding: barplots/Ala_barplot_cell.line.png (deflated 16%) adding: barplots/Trp_barplot_treatment.png (deflated 20%) adding: barplots/Pro_barplot.png (deflated 24%) adding: barplots/Leu_barplot.map (deflated 81%) adding: barplots/Trp_barplot.png (deflated 26%) adding: barplots/Orn_barplot_cell.line.png (deflated 18%) adding: barplots/Lys_barplot_treatment.png (deflated 23%) adding: barplots/Orn_barplot_treatment.png (deflated 23%) adding: barplots/Gln_barplot.map (deflated 81%) adding: barplots/Leu_barplot_treatment.png (deflated 22%) adding: barplots/Arg_barplot_treatment.png (deflated 22%) adding: barplots/Gly_barplot.png (deflated 28%) adding: barplots/Phe_barplot_cell.line.png (deflated 18%) adding: barplots/Cit_barplot.png (deflated 22%) adding: barplots/Phe_barplot.map (deflated 81%) adding: barplots/Leu_barplot.png (deflated 28%) adding: barplots/Val_barplot.png (deflated 32%) adding: barplots/Asp_barplot_cell.line.png (deflated 18%) adding: barplots/Met_barplot_treatment.png (deflated 21%) adding: barplots/Gln_barplot_treatment.png (deflated 22%) adding: barplots/Leu_barplot_cell.line.png (deflated 16%) adding: barplots/Ile_barplot_cell.line.png (deflated 18%) adding: barplots/Cit_barplot.map (deflated 80%) adding: barplots/Arg_barplot.map (deflated 80%) adding: barplots/Tyr_barplot_cell.line.png (deflated 16%) adding: barplots/Arg_barplot.png (deflated 27%) adding: barplots/Glu_barplot_treatment.png (deflated 21%) 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 23%) adding: barplots/Pro_barplot.map (deflated 81%) adding: barplots/Ser_barplot_treatment.png (deflated 26%) adding: barplots/Ser_barplot.png (deflated 32%) adding: barplots/Met_barplot.map (deflated 81%) adding: barplots/His_barplot_treatment.png (deflated 21%) adding: barplots/Asp_barplot.map (deflated 81%) adding: barplots/Thr_barplot.png (deflated 24%) adding: barplots/Glu_barplot_cell.line.png (deflated 17%) 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 81%) adding: lowerOutliers.csv (deflated 49%) adding: data_beforeCheck.csv (deflated 55%) adding: PCA_PC1_PC3.png (deflated 22%) 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 19%) 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 80%) adding: kendall.png (deflated 77%) adding: server_log.txt (deflated 81%) adding: PCAcell.line_PC1_PC2.png (deflated 20%) adding: pca.rotations_cell.line.csv (deflated 51%) adding: pValuesForAllMetabolites_treatment_cell.line.csv (deflated 50%) adding: PCAcell.line_PC1_PC3.png (deflated 21%) adding: PCA_PC2_PC3.png (deflated 20%) adding: PCAcell.line_propOfVar.png (deflated 13%) adding: pca.rotations_cell.line_treatment.csv (deflated 51%) 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 1904 -rw-r--r-- 1 www-data www-data 5808 Aug 2 22:11 input.tmp -rw-r--r-- 1 www-data www-data 817 Aug 2 22:11 phenotypes.txt.tmp -rw-r--r-- 1 www-data www-data 5808 Aug 2 22:11 input -rw-r--r-- 1 www-data www-data 817 Aug 2 22:11 phenotypes.txt -rw-r--r-- 1 www-data www-data 0 Aug 2 22:11 aux.txt -rw-r--r-- 1 www-data www-data 255 Aug 2 22:11 options -rwxr-xr-x 1 www-data www-data 603 Aug 2 22:11 metaPjob.cmd drwxrwxrwx 2312 metap2 metap2 258048 Aug 2 22:12 .. -rw-rw-r-- 1 metap2 metap2 1 Aug 2 22:12 out_params.txt -rw-rw-r-- 1 metap2 metap2 5807 Aug 2 22:12 input_4R -rw-rw-r-- 1 metap2 metap2 222 Aug 2 22:12 metabNamesMapping.csv -rw-rw-r-- 1 metap2 metap2 5530 Aug 2 22:12 data_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 913 Aug 2 22:12 phenotypes_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 5919 Aug 2 22:12 data_all_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 2 Aug 2 22:12 cv.ok -rw-rw-r-- 1 metap2 metap2 883 Aug 2 22:12 lowerOutliers.csv -rw-rw-r-- 1 metap2 metap2 698 Aug 2 22:12 upperOutliers.csv -rw-rw-r-- 1 metap2 metap2 588 Aug 2 22:12 rowsToMark.csv -rw-rw-r-- 1 metap2 metap2 180 Aug 2 22:12 colsToMark.x.csv -rw-rw-r-- 1 metap2 metap2 40 Aug 2 22:12 colsToMark.csv -rw-rw-r-- 1 metap2 metap2 473 Aug 2 22:12 phenotypes_for_QC.csv -rw-rw-r-- 1 metap2 metap2 913 Aug 2 22:12 phenotypes.csv -rw-rw-r-- 1 metap2 metap2 5484 Aug 2 22:12 data.csv -rw-rw-r-- 1 metap2 metap2 5924 Aug 2 22:12 data_all.csv -rw-rw-r-- 1 metap2 metap2 663 Aug 2 22:12 phenotypes_numeric.csv -rw-rw-r-- 1 metap2 metap2 913 Aug 2 22:12 phenotypes_nominal.csv -rw-rw-r-- 1 metap2 metap2 1865 Aug 2 22:12 summary.csv -rw-rw-r-- 1 metap2 metap2 192710 Aug 2 22:12 histograms.pdf drwxrwxrwx 2 www-data www-data 4096 Aug 2 22:12 barplots -rw-rw-r-- 1 metap2 metap2 641 Aug 2 22:12 pValuesForAllMetabolites__cell.line.csv -rw-rw-r-- 1 metap2 metap2 585 Aug 2 22:12 pValuesForAllMetabolites__treatment.csv -rw-rw-r-- 1 metap2 metap2 149936 Aug 2 22:12 hypothesisTests_complete_data.pdf -rw-rw-r-- 1 metap2 metap2 992 Aug 2 22:12 pValuesForAllMetabolites_cell.line_treatment.csv -rw-rw-r-- 1 metap2 metap2 299907 Aug 2 22:12 hypothesisTests_separated_for_cell.line.pdf -rw-rw-r-- 1 metap2 metap2 114 Aug 2 22:12 bonferroni.csv -rw-rw-r-- 1 metap2 metap2 1046 Aug 2 22:12 pValuesForAllMetabolites_treatment_cell.line.csv -rw-rw-r-- 1 metap2 metap2 174806 Aug 2 22:12 hypothesisTests_separated_for_treatment.pdf -rw-rw-r-- 1 metap2 metap2 4593 Aug 2 22:12 PCA_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 2159 Aug 2 22:12 PCA_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 4583 Aug 2 22:12 PCA_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 2143 Aug 2 22:12 PCA_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 4579 Aug 2 22:12 PCA_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2125 Aug 2 22:12 PCA_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 8586 Aug 2 22:12 pca.rotations.csv -rw-rw-r-- 1 metap2 metap2 14831 Aug 2 22:12 PCA.pdf -rw-rw-r-- 1 metap2 metap2 4620 Aug 2 22:12 PCAcell.line_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 2148 Aug 2 22:12 PCAcell.line_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 4610 Aug 2 22:12 PCAcell.line_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 2154 Aug 2 22:12 PCAcell.line_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 4606 Aug 2 22:12 PCAcell.line_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2167 Aug 2 22:12 PCAcell.line_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 16826 Aug 2 22:12 PCAcell.line.pdf -rw-rw-r-- 1 metap2 metap2 8551 Aug 2 22:12 pca.rotations_cell.line.csv -rw-rw-r-- 1 metap2 metap2 15714 Aug 2 22:12 PCA:cell.line.pdf -rw-rw-r-- 1 metap2 metap2 4620 Aug 2 22:12 PCAtreatment_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 2147 Aug 2 22:12 PCAtreatment_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 4610 Aug 2 22:12 PCAtreatment_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 2124 Aug 2 22:12 PCAtreatment_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 4606 Aug 2 22:12 PCAtreatment_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 2127 Aug 2 22:12 PCAtreatment_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 16894 Aug 2 22:12 PCAtreatment.pdf -rw-rw-r-- 1 metap2 metap2 15782 Aug 2 22:12 PCA:treatment.pdf -rw-rw-r-- 1 metap2 metap2 8551 Aug 2 22:12 pca.rotations_cell.line_treatment.csv -rw-rw-r-- 1 metap2 metap2 5399 Aug 2 22:12 kendall.pdf -rw-rw-r-- 1 metap2 metap2 941 Aug 2 22:12 kendall.csv -rw-rw-r-- 1 metap2 metap2 37772 Aug 2 22:12 .R.Rout -rw-rw-r-- 1 metap2 metap2 3583 Aug 2 22:12 kendall.png -rw-rw-r-- 1 metap2 metap2 2515 Aug 2 22:12 PCAtreatment_propOfVar.png -rw-rw-r-- 1 metap2 metap2 3007 Aug 2 22:12 PCAcell.line_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2172 Aug 2 22:12 PCA_propOfVar.png -rw-rw-r-- 1 metap2 metap2 1546 Aug 2 22:12 processing_log.txt -rw-rw-r-- 1 metap2 metap2 9433 Aug 2 22:12 server_log.txt -rw-rw-r-- 1 metap2 metap2 375899 Aug 2 22:12 download.zip drwxrwxrwx 3 www-data www-data 4096 Aug 2 22:12 . + set - Finishing METAP SERVER