Running METAP SERVER Tue Aug 8 13:28:01 CEST 2017 ID=1708081327223277 /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/1708081327223277 + 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 U266 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/1708081327223277 PRIVAT=0 LANG=en_US.UTF-8 SHLVL=1 HOME=/home/metap2 ID=1708081327223277 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 32586 Aug 8 13:28 .R.Rout adding: kendall.csv (deflated 74%) adding: PCA_PC1_PC3.map (deflated 66%) adding: summary.csv (deflated 53%) adding: colsToMark.x.csv (deflated 36%) adding: phenotypes.csv (deflated 45%) adding: kendall.pdf (deflated 72%) adding: data_all.csv (deflated 54%) adding: PCA_PC1_PC2.png (deflated 38%) adding: PCAtreatment_PC1_PC2.png (deflated 38%) adding: PCAtreatment_propOfVar.png (deflated 16%) adding: cv_average.csv (deflated 49%) adding: processing_log.txt (deflated 56%) adding: options (deflated 41%) adding: PCAtreatment_PC1_PC2.map (deflated 66%) adding: colsToMark.csv (deflated 13%) adding: PCAtreatment_PC1_PC3.png (deflated 41%) adding: phenotypes_numeric.csv (deflated 45%) adding: cv.pdf (deflated 83%) adding: PCA_PC1_PC2.map (deflated 65%) adding: PCA_PC2_PC3.map (deflated 65%) adding: PCAtreatment_PC2_PC3.png (deflated 40%) adding: hypothesisTests_complete_data.pdf (deflated 86%) adding: pValuesForAllMetabolites__treatment.csv (deflated 51%) adding: PCAtreatment.pdf (deflated 76%) adding: bonferroni.csv (deflated 32%) adding: rowsToMark.csv (deflated 55%) adding: metabNamesMapping.csv (deflated 49%) adding: PCA.pdf (deflated 76%) adding: out_params.txt (stored 0%) adding: input (deflated 54%) adding: data.csv (deflated 54%) adding: phenotypes.txt (deflated 45%) adding: DU_cv.csv (deflated 45%) adding: phenotypes_for_QC.csv (deflated 45%) adding: histograms.pdf (deflated 91%) adding: barplots/Cit_barplot_treatment.png (deflated 28%) adding: barplots/1022150464_sbarplot.map (deflated 74%) adding: barplots/Ala_barplot.map (deflated 67%) adding: barplots/Trp_barplot.map (deflated 67%) adding: barplots/Val_barplot.map (deflated 67%) adding: barplots/Pro_barplot_treatment.png (deflated 35%) adding: barplots/Ile_barplot_treatment.png (deflated 36%) adding: barplots/Lys_barplot.map (deflated 67%) adding: barplots/Asn_barplot.map (deflated 67%) adding: barplots/Gln_barplot.png (deflated 38%) adding: barplots/Ala_barplot.png (deflated 41%) adding: barplots/Ala_barplot_treatment.png (deflated 34%) adding: barplots/Phe_barplot_treatment.png (deflated 28%) adding: barplots/Tyr_barplot_treatment.png (deflated 32%) adding: barplots/Asp_barplot_treatment.png (deflated 33%) adding: barplots/Gly_barplot.map (deflated 67%) adding: barplots/Met_barplot.png (deflated 36%) adding: barplots/Thr_barplot.map (deflated 67%) adding: barplots/Val_barplot_treatment.png (deflated 32%) adding: barplots/Thr_barplot_treatment.png (deflated 29%) adding: barplots/Asn_barplot_treatment.png (deflated 26%) adding: barplots/Asn_barplot.png (deflated 35%) adding: barplots/1022150479_sbarplot.map (deflated 74%) adding: barplots/Ile_barplot.png (deflated 37%) adding: barplots/His_barplot.map (deflated 67%) adding: barplots/1022150450_sbarplot.png (deflated 51%) adding: barplots/Lys_barplot.png (deflated 40%) adding: barplots/Orn_barplot.png (deflated 38%) adding: barplots/1022150445_sbarplot.png (deflated 52%) adding: barplots/Tyr_barplot.map (deflated 67%) adding: barplots/Orn_barplot.map (deflated 67%) adding: barplots/Glu_barplot.png (deflated 34%) adding: barplots/Glu_barplot.map (deflated 67%) adding: barplots/Tyr_barplot.png (deflated 37%) adding: barplots/Trp_barplot_treatment.png (deflated 32%) adding: barplots/Pro_barplot.png (deflated 42%) adding: barplots/Leu_barplot.map (deflated 67%) adding: barplots/Trp_barplot.png (deflated 38%) adding: barplots/1022150479_sbarplot.png (deflated 50%) adding: barplots/1022150445_sbarplot.map (deflated 74%) adding: barplots/Lys_barplot_treatment.png (deflated 34%) adding: barplots/Orn_barplot_treatment.png (deflated 23%) adding: barplots/Gln_barplot.map (deflated 67%) adding: barplots/Leu_barplot_treatment.png (deflated 28%) adding: barplots/Arg_barplot_treatment.png (deflated 29%) adding: barplots/1022150431_sbarplot.png (deflated 51%) adding: barplots/Gly_barplot.png (deflated 35%) adding: barplots/Cit_barplot.png (deflated 30%) adding: barplots/1022150431_sbarplot.map (deflated 74%) adding: barplots/Phe_barplot.map (deflated 67%) adding: barplots/Leu_barplot.png (deflated 32%) adding: barplots/Val_barplot.png (deflated 37%) adding: barplots/Met_barplot_treatment.png (deflated 32%) adding: barplots/Gln_barplot_treatment.png (deflated 33%) adding: barplots/Cit_barplot.map (deflated 67%) adding: barplots/Arg_barplot.map (deflated 67%) adding: barplots/1022150464_sbarplot.png (deflated 52%) adding: barplots/1022150426_sbarplot.png (deflated 53%) adding: barplots/1022150426_sbarplot.map (deflated 74%) adding: barplots/Arg_barplot.png (deflated 32%) adding: barplots/Glu_barplot_treatment.png (deflated 26%) adding: barplots/Ile_barplot.map (deflated 67%) adding: barplots/Phe_barplot.png (deflated 32%) adding: barplots/His_barplot.png (deflated 33%) adding: barplots/Gly_barplot_treatment.png (deflated 29%) adding: barplots/Pro_barplot.map (deflated 67%) adding: barplots/Ser_barplot_treatment.png (deflated 32%) adding: barplots/Ser_barplot.png (deflated 36%) adding: barplots/Met_barplot.map (deflated 67%) adding: barplots/His_barplot_treatment.png (deflated 26%) adding: barplots/Asp_barplot.map (deflated 67%) adding: barplots/Thr_barplot.png (deflated 34%) adding: barplots/1022150450_sbarplot.map (deflated 74%) adding: barplots/Ser_barplot.map (deflated 67%) adding: barplots/Asp_barplot.png (deflated 41%) adding: data_all_beforeCheck.csv (deflated 54%) adding: data_beforeCheck.csv (deflated 55%) adding: PCA_PC1_PC3.png (deflated 43%) adding: phenotypes_nominal.csv (deflated 45%) adding: pca.rotations.csv (deflated 49%) adding: PCA_propOfVar.png (deflated 21%) adding: PCAtreatment_PC2_PC3.map (deflated 66%) adding: aux.txt (stored 0%) adding: PCAtreatment_PC1_PC3.map (deflated 66%) adding: kendall.png (deflated 77%) adding: server_log.txt (deflated 79%) adding: metabolitesForDropping.csv (stored 0%) adding: UL_cv.csv (deflated 46%) adding: PCA_PC2_PC3.png (deflated 40%) 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 864 -rw-r--r-- 1 www-data www-data 1661 Aug 8 13:27 input.tmp -rw-r--r-- 1 www-data www-data 189 Aug 8 13:27 phenotypes.txt.tmp -rw-r--r-- 1 www-data www-data 1661 Aug 8 13:27 input -rw-r--r-- 1 www-data www-data 189 Aug 8 13:27 phenotypes.txt -rw-r--r-- 1 www-data www-data 0 Aug 8 13:27 aux.txt -rw-r--r-- 1 www-data www-data 236 Aug 8 13:27 options -rwxr-xr-x 1 www-data www-data 603 Aug 8 13:27 metaPjob.cmd drwxrwxrwx 2078 metap2 metap2 258048 Aug 8 13:28 .. -rw-rw-r-- 1 metap2 metap2 1 Aug 8 13:28 out_params.txt -rw-rw-r-- 1 metap2 metap2 1660 Aug 8 13:28 input_4R -rw-rw-r-- 1 metap2 metap2 200 Aug 8 13:28 metabNamesMapping.csv -rw-rw-r-- 1 metap2 metap2 1704 Aug 8 13:28 data_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 1764 Aug 8 13:28 data_all_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 186 Aug 8 13:28 phenotypes_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 650 Aug 8 13:28 DU_cv.csv -rw-rw-r-- 1 metap2 metap2 646 Aug 8 13:28 UL_cv.csv -rw-rw-r-- 1 metap2 metap2 12592 Aug 8 13:28 cv.pdf -rw-rw-r-- 1 metap2 metap2 2 Aug 8 13:28 cv.ok -rw-rw-r-- 1 metap2 metap2 8 Aug 8 13:28 metabolitesForDropping.csv -rw-rw-r-- 1 metap2 metap2 388 Aug 8 13:28 cv_average.csv -rw-rw-r-- 1 metap2 metap2 180 Aug 8 13:28 colsToMark.x.csv -rw-rw-r-- 1 metap2 metap2 61 Aug 8 13:28 colsToMark.csv -rw-rw-r-- 1 metap2 metap2 84 Aug 8 13:28 rowsToMark.csv -rw-rw-r-- 1 metap2 metap2 109 Aug 8 13:28 phenotypes_for_QC.csv -rw-rw-r-- 1 metap2 metap2 114 Aug 8 13:28 phenotypes.csv -rw-rw-r-- 1 metap2 metap2 1660 Aug 8 13:28 data.csv -rw-rw-r-- 1 metap2 metap2 1697 Aug 8 13:28 data_all.csv -rw-rw-r-- 1 metap2 metap2 114 Aug 8 13:28 phenotypes_nominal.csv -rw-rw-r-- 1 metap2 metap2 114 Aug 8 13:28 phenotypes_numeric.csv -rw-rw-r-- 1 metap2 metap2 2587 Aug 8 13:28 summary.csv -rw-rw-r-- 1 metap2 metap2 97664 Aug 8 13:28 histograms.pdf drwxrwxrwx 2 www-data www-data 4096 Aug 8 13:28 barplots -rw-rw-r-- 1 metap2 metap2 114 Aug 8 13:28 bonferroni.csv -rw-rw-r-- 1 metap2 metap2 279 Aug 8 13:28 pValuesForAllMetabolites__treatment.csv -rw-rw-r-- 1 metap2 metap2 53742 Aug 8 13:28 hypothesisTests_complete_data.pdf -rw-rw-r-- 1 metap2 metap2 739 Aug 8 13:28 PCA_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1708 Aug 8 13:28 PCA_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 739 Aug 8 13:28 PCA_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1599 Aug 8 13:28 PCA_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 741 Aug 8 13:28 PCA_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 1645 Aug 8 13:28 PCA_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 2517 Aug 8 13:28 pca.rotations.csv -rw-rw-r-- 1 metap2 metap2 8383 Aug 8 13:28 PCA.pdf -rw-rw-r-- 1 metap2 metap2 766 Aug 8 13:28 PCAtreatment_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1711 Aug 8 13:28 PCAtreatment_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 766 Aug 8 13:28 PCAtreatment_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1623 Aug 8 13:28 PCAtreatment_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 768 Aug 8 13:28 PCAtreatment_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 1652 Aug 8 13:28 PCAtreatment_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 9060 Aug 8 13:28 PCAtreatment.pdf -rw-rw-r-- 1 metap2 metap2 5256 Aug 8 13:28 kendall.pdf -rw-rw-r-- 1 metap2 metap2 927 Aug 8 13:28 kendall.csv -rw-rw-r-- 1 metap2 metap2 32586 Aug 8 13:28 .R.Rout -rw-rw-r-- 1 metap2 metap2 3582 Aug 8 13:28 kendall.png -rw-rw-r-- 1 metap2 metap2 2452 Aug 8 13:28 PCAtreatment_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2127 Aug 8 13:28 PCA_propOfVar.png -rw-rw-r-- 1 metap2 metap2 1471 Aug 8 13:28 processing_log.txt -rw-rw-r-- 1 metap2 metap2 8010 Aug 8 13:28 server_log.txt -rw-rw-r-- 1 metap2 metap2 175137 Aug 8 13:28 download.zip drwxrwxrwx 3 www-data www-data 4096 Aug 8 13:28 . + set - Finishing METAP SERVER