Running METAP SERVER Wed Aug 2 22:47:01 CEST 2017 ID=1708022246439767 /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/1708022246439767 + 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 AMO1 REFERENCE=n PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/home/metap2/public_html/users/1708022246439767 PRIVAT=0 LANG=en_US.UTF-8 SHLVL=1 HOME=/home/metap2 ID=1708022246439767 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 32601 Aug 2 22:47 .R.Rout adding: kendall.csv (deflated 73%) adding: PCA_PC1_PC3.map (deflated 65%) adding: summary.csv (deflated 48%) adding: colsToMark.x.csv (deflated 36%) adding: phenotypes.csv (deflated 45%) adding: kendall.pdf (deflated 72%) adding: data_all.csv (deflated 45%) adding: PCA_PC1_PC2.png (deflated 36%) adding: PCAtreatment_PC1_PC2.png (deflated 35%) adding: PCAtreatment_propOfVar.png (deflated 16%) adding: cv_average.csv (deflated 50%) adding: processing_log.txt (deflated 55%) adding: options (deflated 40%) adding: PCAtreatment_PC1_PC2.map (deflated 66%) adding: colsToMark.csv (deflated 13%) adding: PCAtreatment_PC1_PC3.png (deflated 25%) adding: phenotypes_numeric.csv (deflated 45%) adding: cv.pdf (deflated 82%) adding: PCA_PC1_PC2.map (deflated 65%) adding: PCA_PC2_PC3.map (deflated 66%) adding: PCAtreatment_PC2_PC3.png (deflated 24%) 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 44%) adding: data.csv (deflated 45%) adding: phenotypes.txt (deflated 45%) adding: phenotypes_for_QC.csv (deflated 46%) adding: histograms.pdf (deflated 91%) adding: AD_cv.csv (deflated 45%) adding: upperOutliers.csv (deflated 32%) adding: barplots/1022150590_sbarplot.map (deflated 74%) adding: barplots/Cit_barplot_treatment.png (deflated 30%) adding: barplots/Ala_barplot.map (deflated 66%) adding: barplots/Trp_barplot.map (deflated 67%) adding: barplots/1022150551_sbarplot.png (deflated 54%) adding: barplots/Val_barplot.map (deflated 67%) adding: barplots/Pro_barplot_treatment.png (deflated 28%) adding: barplots/Ile_barplot_treatment.png (deflated 28%) adding: barplots/Lys_barplot.map (deflated 67%) adding: barplots/Asn_barplot.map (deflated 67%) adding: barplots/1022150547_sbarplot.png (deflated 48%) adding: barplots/Gln_barplot.png (deflated 36%) adding: barplots/Ala_barplot.png (deflated 35%) adding: barplots/Ala_barplot_treatment.png (deflated 29%) adding: barplots/Phe_barplot_treatment.png (deflated 30%) adding: barplots/Tyr_barplot_treatment.png (deflated 30%) adding: barplots/Asp_barplot_treatment.png (deflated 32%) adding: barplots/Gly_barplot.map (deflated 67%) adding: barplots/Met_barplot.png (deflated 27%) adding: barplots/Thr_barplot.map (deflated 67%) adding: barplots/Val_barplot_treatment.png (deflated 28%) adding: barplots/Thr_barplot_treatment.png (deflated 28%) adding: barplots/1022150566_sbarplot.map (deflated 74%) adding: barplots/Asn_barplot_treatment.png (deflated 33%) adding: barplots/Asn_barplot.png (deflated 43%) adding: barplots/Ile_barplot.png (deflated 37%) adding: barplots/1022150551_sbarplot.map (deflated 75%) 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 66%) adding: barplots/Orn_barplot.map (deflated 67%) adding: barplots/Glu_barplot.png (deflated 35%) adding: barplots/Glu_barplot.map (deflated 67%) adding: barplots/1022150571_sbarplot.png (deflated 50%) adding: barplots/Tyr_barplot.png (deflated 39%) adding: barplots/Trp_barplot_treatment.png (deflated 26%) adding: barplots/Pro_barplot.png (deflated 32%) adding: barplots/Leu_barplot.map (deflated 67%) adding: barplots/Trp_barplot.png (deflated 30%) adding: barplots/Lys_barplot_treatment.png (deflated 31%) adding: barplots/Orn_barplot_treatment.png (deflated 29%) adding: barplots/Gln_barplot.map (deflated 67%) adding: barplots/Leu_barplot_treatment.png (deflated 30%) adding: barplots/Arg_barplot_treatment.png (deflated 29%) adding: barplots/Gly_barplot.png (deflated 33%) adding: barplots/Cit_barplot.png (deflated 42%) adding: barplots/1022150585_sbarplot.png (deflated 53%) 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 30%) adding: barplots/1022150590_sbarplot.png (deflated 51%) adding: barplots/Met_barplot_treatment.png (deflated 24%) adding: barplots/Gln_barplot_treatment.png (deflated 29%) adding: barplots/Cit_barplot.map (deflated 67%) adding: barplots/Arg_barplot.map (deflated 67%) adding: barplots/Arg_barplot.png (deflated 43%) adding: barplots/Glu_barplot_treatment.png (deflated 30%) adding: barplots/1022150566_sbarplot.png (deflated 49%) adding: barplots/Ile_barplot.map (deflated 67%) adding: barplots/Phe_barplot.png (deflated 35%) adding: barplots/His_barplot.png (deflated 34%) adding: barplots/Gly_barplot_treatment.png (deflated 26%) adding: barplots/Pro_barplot.map (deflated 67%) adding: barplots/Ser_barplot_treatment.png (deflated 28%) adding: barplots/Ser_barplot.png (deflated 34%) adding: barplots/Met_barplot.map (deflated 67%) adding: barplots/His_barplot_treatment.png (deflated 30%) adding: barplots/Asp_barplot.map (deflated 67%) adding: barplots/Thr_barplot.png (deflated 34%) 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 34%) adding: data_all_beforeCheck.csv (deflated 46%) adding: data_beforeCheck.csv (deflated 46%) adding: PCA_PC1_PC3.png (deflated 25%) 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: AL_cv.csv (deflated 45%) adding: PCAtreatment_PC1_PC3.map (deflated 66%) adding: kendall.png (deflated 77%) adding: server_log.txt (deflated 79%) adding: metabolitesForDropping.csv (stored 0%) adding: PCA_PC2_PC3.png (deflated 27%) 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 894 Aug 2 22:46 input.tmp -rw-r--r-- 1 www-data www-data 894 Aug 2 22:46 input -rw-r--r-- 1 www-data www-data 189 Aug 2 22:46 phenotypes.txt.tmp -rw-r--r-- 1 www-data www-data 189 Aug 2 22:46 phenotypes.txt -rw-r--r-- 1 www-data www-data 0 Aug 2 22:46 aux.txt -rw-r--r-- 1 www-data www-data 235 Aug 2 22:46 options -rwxr-xr-x 1 www-data www-data 603 Aug 2 22:46 metaPjob.cmd drwxrwxrwx 2317 metap2 metap2 258048 Aug 2 22:47 .. -rw-rw-r-- 1 metap2 metap2 1 Aug 2 22:47 out_params.txt -rw-rw-r-- 1 metap2 metap2 893 Aug 2 22:47 input_4R -rw-rw-r-- 1 metap2 metap2 200 Aug 2 22:47 metabNamesMapping.csv -rw-rw-r-- 1 metap2 metap2 937 Aug 2 22:47 data_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 186 Aug 2 22:47 phenotypes_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 997 Aug 2 22:47 data_all_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 646 Aug 2 22:47 AD_cv.csv -rw-rw-r-- 1 metap2 metap2 638 Aug 2 22:47 AL_cv.csv -rw-rw-r-- 1 metap2 metap2 12672 Aug 2 22:47 cv.pdf -rw-rw-r-- 1 metap2 metap2 2 Aug 2 22:47 cv.ok -rw-rw-r-- 1 metap2 metap2 4 Aug 2 22:47 metabolitesForDropping.csv -rw-rw-r-- 1 metap2 metap2 379 Aug 2 22:47 cv_average.csv -rw-rw-r-- 1 metap2 metap2 280 Aug 2 22:47 upperOutliers.csv -rw-rw-r-- 1 metap2 metap2 173 Aug 2 22:47 colsToMark.x.csv -rw-rw-r-- 1 metap2 metap2 84 Aug 2 22:47 rowsToMark.csv -rw-rw-r-- 1 metap2 metap2 114 Aug 2 22:47 phenotypes.csv -rw-rw-r-- 1 metap2 metap2 893 Aug 2 22:47 data.csv -rw-rw-r-- 1 metap2 metap2 61 Aug 2 22:47 colsToMark.csv -rw-rw-r-- 1 metap2 metap2 109 Aug 2 22:47 phenotypes_for_QC.csv -rw-rw-r-- 1 metap2 metap2 930 Aug 2 22:47 data_all.csv -rw-rw-r-- 1 metap2 metap2 114 Aug 2 22:47 phenotypes_numeric.csv -rw-rw-r-- 1 metap2 metap2 114 Aug 2 22:47 phenotypes_nominal.csv -rw-rw-r-- 1 metap2 metap2 1797 Aug 2 22:47 summary.csv -rw-rw-r-- 1 metap2 metap2 96364 Aug 2 22:47 histograms.pdf drwxrwxrwx 2 www-data www-data 4096 Aug 2 22:47 barplots -rw-rw-r-- 1 metap2 metap2 277 Aug 2 22:47 pValuesForAllMetabolites__treatment.csv -rw-rw-r-- 1 metap2 metap2 53001 Aug 2 22:47 hypothesisTests_complete_data.pdf -rw-rw-r-- 1 metap2 metap2 114 Aug 2 22:47 bonferroni.csv -rw-rw-r-- 1 metap2 metap2 741 Aug 2 22:47 PCA_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1722 Aug 2 22:47 PCA_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 741 Aug 2 22:47 PCA_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1965 Aug 2 22:47 PCA_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 741 Aug 2 22:47 PCA_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 1891 Aug 2 22:47 PCA_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 9263 Aug 2 22:47 PCA.pdf -rw-rw-r-- 1 metap2 metap2 2511 Aug 2 22:47 pca.rotations.csv -rw-rw-r-- 1 metap2 metap2 768 Aug 2 22:47 PCAtreatment_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1743 Aug 2 22:47 PCAtreatment_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 768 Aug 2 22:47 PCAtreatment_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1978 Aug 2 22:47 PCAtreatment_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 768 Aug 2 22:47 PCAtreatment_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 1920 Aug 2 22:47 PCAtreatment_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 9940 Aug 2 22:47 PCAtreatment.pdf -rw-rw-r-- 1 metap2 metap2 5298 Aug 2 22:47 kendall.pdf -rw-rw-r-- 1 metap2 metap2 923 Aug 2 22:47 kendall.csv -rw-rw-r-- 1 metap2 metap2 32601 Aug 2 22:47 .R.Rout -rw-rw-r-- 1 metap2 metap2 3585 Aug 2 22:47 kendall.png -rw-rw-r-- 1 metap2 metap2 2500 Aug 2 22:47 PCAtreatment_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2170 Aug 2 22:47 PCA_propOfVar.png -rw-rw-r-- 1 metap2 metap2 1488 Aug 2 22:47 processing_log.txt -rw-rw-r-- 1 metap2 metap2 8051 Aug 2 22:47 server_log.txt -rw-rw-r-- 1 metap2 metap2 167279 Aug 2 22:47 download.zip drwxrwxrwx 3 www-data www-data 4096 Aug 2 22:47 . + set - Finishing METAP SERVER