Running METAP SERVER Tue Aug 8 13:31:01 CEST 2017 ID=1708081330123853 /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/1708081330123853 + 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=AMO1 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/1708081330123853 PRIVAT=0 LANG=en_US.UTF-8 SHLVL=1 HOME=/home/metap2 ID=1708081330123853 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 32526 Aug 8 13:31 .R.Rout adding: kendall.csv (deflated 73%) adding: PCA_PC1_PC3.map (deflated 65%) adding: summary.csv (deflated 53%) adding: colsToMark.x.csv (deflated 40%) adding: phenotypes.csv (deflated 45%) adding: kendall.pdf (deflated 72%) adding: data_all.csv (deflated 53%) adding: PCA_PC1_PC2.png (deflated 34%) adding: PCAtreatment_PC1_PC2.png (deflated 34%) adding: PCAtreatment_propOfVar.png (deflated 16%) adding: cv_average.csv (deflated 49%) adding: processing_log.txt (deflated 55%) adding: options (deflated 42%) adding: PCAtreatment_PC1_PC2.map (deflated 66%) adding: colsToMark.csv (deflated 13%) adding: PCAtreatment_PC1_PC3.png (deflated 38%) adding: phenotypes_numeric.csv (deflated 45%) adding: cv.pdf (deflated 83%) adding: PCA_PC1_PC2.map (deflated 66%) adding: PCA_PC2_PC3.map (deflated 65%) adding: PCAtreatment_PC2_PC3.png (deflated 35%) adding: hypothesisTests_complete_data.pdf (deflated 86%) adding: pValuesForAllMetabolites__treatment.csv (deflated 49%) adding: PCAtreatment.pdf (deflated 77%) adding: bonferroni.csv (deflated 32%) adding: rowsToMark.csv (deflated 56%) adding: metabNamesMapping.csv (deflated 49%) adding: PCA.pdf (deflated 77%) adding: out_params.txt (stored 0%) adding: input (deflated 54%) adding: data.csv (deflated 54%) adding: phenotypes.txt (deflated 45%) adding: phenotypes_for_QC.csv (deflated 46%) adding: histograms.pdf (deflated 91%) adding: AD_cv.csv (deflated 47%) adding: barplots/1022150590_sbarplot.map (deflated 74%) adding: barplots/Cit_barplot_treatment.png (deflated 34%) adding: barplots/Ala_barplot.map (deflated 67%) adding: barplots/Trp_barplot.map (deflated 67%) adding: barplots/1022150551_sbarplot.png (deflated 52%) adding: barplots/Val_barplot.map (deflated 67%) adding: barplots/Pro_barplot_treatment.png (deflated 31%) adding: barplots/Ile_barplot_treatment.png (deflated 31%) adding: barplots/Lys_barplot.map (deflated 67%) adding: barplots/Asn_barplot.map (deflated 67%) adding: barplots/1022150547_sbarplot.png (deflated 51%) adding: barplots/Gln_barplot.png (deflated 35%) adding: barplots/Ala_barplot.png (deflated 28%) adding: barplots/Ala_barplot_treatment.png (deflated 26%) adding: barplots/Phe_barplot_treatment.png (deflated 30%) adding: barplots/Tyr_barplot_treatment.png (deflated 32%) adding: barplots/Asp_barplot_treatment.png (deflated 28%) adding: barplots/Gly_barplot.map (deflated 67%) adding: barplots/Met_barplot.png (deflated 40%) adding: barplots/Thr_barplot.map (deflated 66%) adding: barplots/Val_barplot_treatment.png (deflated 30%) adding: barplots/Thr_barplot_treatment.png (deflated 28%) adding: barplots/1022150566_sbarplot.map (deflated 74%) adding: barplots/Asn_barplot_treatment.png (deflated 31%) adding: barplots/Asn_barplot.png (deflated 39%) adding: barplots/Ile_barplot.png (deflated 42%) adding: barplots/1022150551_sbarplot.map (deflated 74%) adding: barplots/His_barplot.map (deflated 67%) adding: barplots/Lys_barplot.png (deflated 34%) adding: barplots/Orn_barplot.png (deflated 37%) adding: barplots/Tyr_barplot.map (deflated 67%) adding: barplots/Orn_barplot.map (deflated 67%) adding: barplots/Glu_barplot.png (deflated 36%) adding: barplots/Glu_barplot.map (deflated 67%) adding: barplots/1022150571_sbarplot.png (deflated 51%) adding: barplots/Tyr_barplot.png (deflated 38%) adding: barplots/Trp_barplot_treatment.png (deflated 27%) adding: barplots/Pro_barplot.png (deflated 35%) adding: barplots/Leu_barplot.map (deflated 67%) adding: barplots/Trp_barplot.png (deflated 31%) adding: barplots/Lys_barplot_treatment.png (deflated 30%) adding: barplots/Orn_barplot_treatment.png (deflated 30%) adding: barplots/Gln_barplot.map (deflated 67%) adding: barplots/Leu_barplot_treatment.png (deflated 28%) adding: barplots/Arg_barplot_treatment.png (deflated 32%) adding: barplots/Gly_barplot.png (deflated 35%) adding: barplots/Cit_barplot.png (deflated 44%) adding: barplots/1022150585_sbarplot.png (deflated 51%) adding: barplots/1022150585_sbarplot.map (deflated 74%) adding: barplots/Phe_barplot.map (deflated 67%) adding: barplots/Leu_barplot.png (deflated 32%) adding: barplots/Val_barplot.png (deflated 35%) adding: barplots/1022150590_sbarplot.png (deflated 51%) adding: barplots/Met_barplot_treatment.png (deflated 27%) adding: barplots/Gln_barplot_treatment.png (deflated 30%) adding: barplots/Cit_barplot.map (deflated 67%) adding: barplots/Arg_barplot.map (deflated 67%) adding: barplots/Arg_barplot.png (deflated 41%) adding: barplots/Glu_barplot_treatment.png (deflated 31%) adding: barplots/1022150566_sbarplot.png (deflated 50%) adding: barplots/Ile_barplot.map (deflated 67%) adding: barplots/Phe_barplot.png (deflated 41%) adding: barplots/His_barplot.png (deflated 37%) adding: barplots/Gly_barplot_treatment.png (deflated 28%) adding: barplots/Pro_barplot.map (deflated 67%) adding: barplots/Ser_barplot_treatment.png (deflated 28%) adding: barplots/Ser_barplot.png (deflated 32%) adding: barplots/Met_barplot.map (deflated 67%) adding: barplots/His_barplot_treatment.png (deflated 33%) adding: barplots/Asp_barplot.map (deflated 67%) adding: barplots/Thr_barplot.png (deflated 37%) adding: barplots/1022150571_sbarplot.map (deflated 74%) adding: barplots/1022150547_sbarplot.map (deflated 74%) adding: barplots/Ser_barplot.map (deflated 67%) adding: barplots/Asp_barplot.png (deflated 32%) adding: data_all_beforeCheck.csv (deflated 54%) adding: data_beforeCheck.csv (deflated 55%) adding: PCA_PC1_PC3.png (deflated 36%) adding: phenotypes_nominal.csv (deflated 45%) adding: pca.rotations.csv (deflated 49%) adding: PCA_propOfVar.png (deflated 19%) adding: PCAtreatment_PC2_PC3.map (deflated 66%) adding: aux.txt (stored 0%) adding: AL_cv.csv (deflated 46%) adding: PCAtreatment_PC1_PC3.map (deflated 66%) adding: kendall.png (deflated 76%) adding: server_log.txt (deflated 79%) adding: PCA_PC2_PC3.png (deflated 34%) adding: phenotypes_beforeCheck.csv (deflated 49%) 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 856 -rw-r--r-- 1 www-data www-data 1663 Aug 8 13:30 input.tmp -rw-r--r-- 1 www-data www-data 189 Aug 8 13:30 phenotypes.txt.tmp -rw-r--r-- 1 www-data www-data 1663 Aug 8 13:30 input -rw-r--r-- 1 www-data www-data 189 Aug 8 13:30 phenotypes.txt -rw-r--r-- 1 www-data www-data 0 Aug 8 13:30 aux.txt -rw-r--r-- 1 www-data www-data 233 Aug 8 13:30 options -rwxr-xr-x 1 www-data www-data 603 Aug 8 13:30 metaPjob.cmd drwxrwxrwx 2079 metap2 metap2 258048 Aug 8 13:31 .. -rw-rw-r-- 1 metap2 metap2 1 Aug 8 13:31 out_params.txt -rw-rw-r-- 1 metap2 metap2 1662 Aug 8 13:31 input_4R -rw-rw-r-- 1 metap2 metap2 200 Aug 8 13:31 metabNamesMapping.csv -rw-rw-r-- 1 metap2 metap2 1706 Aug 8 13:31 data_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 1766 Aug 8 13:31 data_all_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 186 Aug 8 13:31 phenotypes_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 651 Aug 8 13:31 AD_cv.csv -rw-rw-r-- 1 metap2 metap2 651 Aug 8 13:31 AL_cv.csv -rw-rw-r-- 1 metap2 metap2 12283 Aug 8 13:31 cv.pdf -rw-rw-r-- 1 metap2 metap2 2 Aug 8 13:31 cv.ok -rw-rw-r-- 1 metap2 metap2 392 Aug 8 13:31 cv_average.csv -rw-rw-r-- 1 metap2 metap2 166 Aug 8 13:31 colsToMark.x.csv -rw-rw-r-- 1 metap2 metap2 84 Aug 8 13:31 rowsToMark.csv -rw-rw-r-- 1 metap2 metap2 1662 Aug 8 13:31 data.csv -rw-rw-r-- 1 metap2 metap2 61 Aug 8 13:31 colsToMark.csv -rw-rw-r-- 1 metap2 metap2 109 Aug 8 13:31 phenotypes_for_QC.csv -rw-rw-r-- 1 metap2 metap2 114 Aug 8 13:31 phenotypes.csv -rw-rw-r-- 1 metap2 metap2 1699 Aug 8 13:31 data_all.csv -rw-rw-r-- 1 metap2 metap2 114 Aug 8 13:31 phenotypes_numeric.csv -rw-rw-r-- 1 metap2 metap2 114 Aug 8 13:31 phenotypes_nominal.csv -rw-rw-r-- 1 metap2 metap2 2574 Aug 8 13:31 summary.csv -rw-rw-r-- 1 metap2 metap2 97099 Aug 8 13:31 histograms.pdf drwxrwxrwx 2 www-data www-data 4096 Aug 8 13:31 barplots -rw-rw-r-- 1 metap2 metap2 114 Aug 8 13:31 bonferroni.csv -rw-rw-r-- 1 metap2 metap2 275 Aug 8 13:31 pValuesForAllMetabolites__treatment.csv -rw-rw-r-- 1 metap2 metap2 52971 Aug 8 13:31 hypothesisTests_complete_data.pdf -rw-rw-r-- 1 metap2 metap2 739 Aug 8 13:31 PCA_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1811 Aug 8 13:31 PCA_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 739 Aug 8 13:31 PCA_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1719 Aug 8 13:31 PCA_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 739 Aug 8 13:31 PCA_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 1774 Aug 8 13:31 PCA_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 2520 Aug 8 13:31 pca.rotations.csv -rw-rw-r-- 1 metap2 metap2 9528 Aug 8 13:31 PCA.pdf -rw-rw-r-- 1 metap2 metap2 766 Aug 8 13:31 PCAtreatment_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1819 Aug 8 13:31 PCAtreatment_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 766 Aug 8 13:31 PCAtreatment_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1741 Aug 8 13:31 PCAtreatment_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 766 Aug 8 13:31 PCAtreatment_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 1780 Aug 8 13:31 PCAtreatment_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 10205 Aug 8 13:31 PCAtreatment.pdf -rw-rw-r-- 1 metap2 metap2 5319 Aug 8 13:31 kendall.pdf -rw-rw-r-- 1 metap2 metap2 929 Aug 8 13:31 kendall.csv -rw-rw-r-- 1 metap2 metap2 32526 Aug 8 13:31 .R.Rout -rw-rw-r-- 1 metap2 metap2 3599 Aug 8 13:31 kendall.png -rw-rw-r-- 1 metap2 metap2 2585 Aug 8 13:31 PCAtreatment_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2250 Aug 8 13:31 PCA_propOfVar.png -rw-rw-r-- 1 metap2 metap2 1419 Aug 8 13:31 processing_log.txt -rw-rw-r-- 1 metap2 metap2 7958 Aug 8 13:31 server_log.txt -rw-rw-r-- 1 metap2 metap2 177053 Aug 8 13:31 download.zip drwxrwxrwx 3 www-data www-data 4096 Aug 8 13:31 . + set - Finishing METAP SERVER