Running METAP SERVER Tue Sep 19 20:44:01 CEST 2017 ID=17091920432231171 /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/17091920432231171 + hostname metap + uname -a Linux metap 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 21:17:51 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 tumor sh REFERENCE=n PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin PWD=/home/metap2/public_html/users/17091920432231171 PRIVAT=0 LANG=en_US.UTF-8 SHLVL=1 HOME=/home/metap2 ID=17091920432231171 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 32598 Sep 19 20:44 .R.Rout adding: kendall.csv (deflated 75%) adding: PCA_PC1_PC3.map (deflated 65%) adding: summary.csv (deflated 45%) adding: colsToMark.x.csv (deflated 52%) adding: phenotypes.csv (deflated 43%) adding: kendall.pdf (deflated 71%) adding: data_all.csv (deflated 44%) adding: PCATreatment_PC1_PC2.png (deflated 37%) adding: pValuesForAllMetabolites__Treatment.csv (deflated 71%) adding: PCA_PC1_PC2.png (deflated 37%) adding: cv_average.csv (deflated 49%) adding: processing_log.txt (deflated 55%) adding: options (deflated 40%) adding: colsToMark.csv (deflated 18%) adding: phenotypes_numeric.csv (deflated 43%) adding: cv.pdf (deflated 82%) adding: ctrl_cv.csv (deflated 45%) adding: PCA_PC1_PC2.map (deflated 65%) adding: PCA_PC2_PC3.map (deflated 65%) adding: hypothesisTests_complete_data.pdf (deflated 87%) adding: PCATreatment_PC1_PC2.map (deflated 66%) adding: bonferroni.csv (deflated 32%) adding: rowsToMark.csv (deflated 54%) adding: metabNamesMapping.csv (deflated 49%) adding: PCA.pdf (deflated 76%) adding: out_params.txt (stored 0%) adding: input (deflated 44%) adding: data.csv (deflated 44%) adding: phenotypes.txt (deflated 45%) adding: phenotypes_for_QC.csv (deflated 45%) adding: PCATreatment_PC1_PC3.png (deflated 28%) adding: histograms.pdf (deflated 91%) adding: PCATreatment_propOfVar.png (deflated 16%) adding: barplots/1024636908_sbarplot.png (deflated 51%) adding: barplots/Ser_barplot_Treatment.png (deflated 31%) adding: barplots/Lys_barplot_Treatment.png (deflated 32%) adding: barplots/Ala_barplot.map (deflated 66%) adding: barplots/Cit_barplot_Treatment.png (deflated 32%) adding: barplots/Trp_barplot.map (deflated 67%) adding: barplots/Val_barplot.map (deflated 67%) adding: barplots/Lys_barplot.map (deflated 67%) adding: barplots/Val_barplot_Treatment.png (deflated 34%) adding: barplots/Asn_barplot.map (deflated 67%) adding: barplots/Gln_barplot.png (deflated 48%) adding: barplots/1024636723_sbarplot.map (deflated 74%) adding: barplots/Orn_barplot_Treatment.png (deflated 34%) adding: barplots/Ala_barplot.png (deflated 48%) adding: barplots/Gln_barplot_Treatment.png (deflated 33%) adding: barplots/Ile_barplot_Treatment.png (deflated 36%) adding: barplots/Gly_barplot.map (deflated 66%) adding: barplots/Arg_barplot_Treatment.png (deflated 37%) adding: barplots/Met_barplot.png (deflated 34%) adding: barplots/Leu_barplot_Treatment.png (deflated 33%) adding: barplots/Thr_barplot.map (deflated 67%) adding: barplots/Phe_barplot_Treatment.png (deflated 37%) adding: barplots/1024636912_sbarplot.png (deflated 48%) adding: barplots/Pro_barplot_Treatment.png (deflated 33%) adding: barplots/His_barplot_Treatment.png (deflated 34%) adding: barplots/Asn_barplot.png (deflated 41%) adding: barplots/1024636882_sbarplot.map (deflated 74%) adding: barplots/Ile_barplot.png (deflated 43%) adding: barplots/His_barplot.map (deflated 66%) adding: barplots/Lys_barplot.png (deflated 39%) adding: barplots/Orn_barplot.png (deflated 41%) adding: barplots/Asp_barplot_Treatment.png (deflated 31%) adding: barplots/1024636927_sbarplot.png (deflated 50%) adding: barplots/Tyr_barplot.map (deflated 66%) adding: barplots/Orn_barplot.map (deflated 67%) adding: barplots/Glu_barplot.png (deflated 44%) adding: barplots/Glu_barplot.map (deflated 66%) adding: barplots/Asn_barplot_Treatment.png (deflated 30%) adding: barplots/Tyr_barplot.png (deflated 38%) adding: barplots/Pro_barplot.png (deflated 45%) adding: barplots/Leu_barplot.map (deflated 67%) adding: barplots/Glu_barplot_Treatment.png (deflated 31%) adding: barplots/Trp_barplot.png (deflated 50%) adding: barplots/1024636912_sbarplot.map (deflated 74%) adding: barplots/1024636723_sbarplot.png (deflated 48%) adding: barplots/Ala_barplot_Treatment.png (deflated 35%) adding: barplots/Gly_barplot_Treatment.png (deflated 34%) adding: barplots/1024636897_sbarplot.png (deflated 50%) adding: barplots/Gln_barplot.map (deflated 66%) adding: barplots/1024636882_sbarplot.png (deflated 49%) adding: barplots/Gly_barplot.png (deflated 49%) adding: barplots/Cit_barplot.png (deflated 36%) adding: barplots/Met_barplot_Treatment.png (deflated 28%) adding: barplots/Phe_barplot.map (deflated 67%) adding: barplots/Leu_barplot.png (deflated 37%) adding: barplots/Val_barplot.png (deflated 45%) adding: barplots/1024636927_sbarplot.map (deflated 74%) adding: barplots/Cit_barplot.map (deflated 66%) adding: barplots/Arg_barplot.map (deflated 67%) adding: barplots/1024636908_sbarplot.map (deflated 74%) adding: barplots/Trp_barplot_Treatment.png (deflated 39%) adding: barplots/Arg_barplot.png (deflated 52%) adding: barplots/1024636897_sbarplot.map (deflated 74%) adding: barplots/Ile_barplot.map (deflated 66%) adding: barplots/Phe_barplot.png (deflated 44%) adding: barplots/His_barplot.png (deflated 43%) adding: barplots/Pro_barplot.map (deflated 66%) adding: barplots/Thr_barplot_Treatment.png (deflated 34%) adding: barplots/Ser_barplot.png (deflated 37%) adding: barplots/Met_barplot.map (deflated 67%) adding: barplots/Asp_barplot.map (deflated 67%) adding: barplots/Thr_barplot.png (deflated 42%) adding: barplots/Tyr_barplot_Treatment.png (deflated 31%) adding: barplots/Ser_barplot.map (deflated 67%) adding: barplots/Asp_barplot.png (deflated 41%) adding: data_all_beforeCheck.csv (deflated 45%) adding: PCATreatment.pdf (deflated 77%) adding: PCATreatment_PC1_PC3.map (deflated 65%) adding: data_beforeCheck.csv (deflated 45%) adding: PCA_PC1_PC3.png (deflated 31%) adding: LAT1_cv.csv (deflated 45%) adding: phenotypes_nominal.csv (deflated 43%) adding: pca.rotations.csv (deflated 50%) adding: PCATreatment_PC2_PC3.png (deflated 29%) adding: PCA_propOfVar.png (deflated 20%) adding: aux.txt (stored 0%) adding: kendall.png (deflated 77%) adding: server_log.txt (deflated 79%) adding: metabolitesForDropping.csv (deflated 6%) adding: PCATreatment_PC2_PC3.map (deflated 65%) adding: PCA_PC2_PC3.png (deflated 28%) adding: phenotypes_beforeCheck.csv (deflated 48%) 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 860 -rw-r--r-- 1 www-data www-data 1553 Sep 19 20:43 input.tmp -rw-r--r-- 1 www-data www-data 168 Sep 19 20:43 phenotypes.txt.tmp -rw-r--r-- 1 www-data www-data 1553 Sep 19 20:43 input -rw-r--r-- 1 www-data www-data 168 Sep 19 20:43 phenotypes.txt -rw-r--r-- 1 www-data www-data 0 Sep 19 20:43 aux.txt -rw-r--r-- 1 www-data www-data 237 Sep 19 20:43 options -rwxr-xr-x 1 www-data www-data 609 Sep 19 20:43 metaPjob.cmd drwxrwxrwx 2095 metap2 metap2 258048 Sep 19 20:44 .. -rw-rw-r-- 1 metap2 metap2 1 Sep 19 20:44 out_params.txt -rw-rw-r-- 1 metap2 metap2 1552 Sep 19 20:44 input_4R -rw-rw-r-- 1 metap2 metap2 200 Sep 19 20:44 metabNamesMapping.csv -rw-rw-r-- 1 metap2 metap2 1596 Sep 19 20:44 data_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 165 Sep 19 20:44 phenotypes_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 1635 Sep 19 20:44 data_all_beforeCheck.csv -rw-rw-r-- 1 metap2 metap2 635 Sep 19 20:44 ctrl_cv.csv -rw-rw-r-- 1 metap2 metap2 646 Sep 19 20:44 LAT1_cv.csv -rw-rw-r-- 1 metap2 metap2 13701 Sep 19 20:44 cv.pdf -rw-rw-r-- 1 metap2 metap2 2 Sep 19 20:44 cv.ok -rw-rw-r-- 1 metap2 metap2 48 Sep 19 20:44 metabolitesForDropping.csv -rw-rw-r-- 1 metap2 metap2 378 Sep 19 20:44 cv_average.csv -rw-rw-r-- 1 metap2 metap2 250 Sep 19 20:44 colsToMark.x.csv -rw-rw-r-- 1 metap2 metap2 44 Sep 19 20:44 colsToMark.csv -rw-rw-r-- 1 metap2 metap2 84 Sep 19 20:44 rowsToMark.csv -rw-rw-r-- 1 metap2 metap2 121 Sep 19 20:44 phenotypes_for_QC.csv -rw-rw-r-- 1 metap2 metap2 121 Sep 19 20:44 phenotypes.csv -rw-rw-r-- 1 metap2 metap2 1552 Sep 19 20:44 data.csv -rw-rw-r-- 1 metap2 metap2 1596 Sep 19 20:44 data_all.csv -rw-rw-r-- 1 metap2 metap2 121 Sep 19 20:44 phenotypes_nominal.csv -rw-rw-r-- 1 metap2 metap2 121 Sep 19 20:44 phenotypes_numeric.csv -rw-rw-r-- 1 metap2 metap2 2352 Sep 19 20:44 summary.csv -rw-rw-r-- 1 metap2 metap2 97407 Sep 19 20:44 histograms.pdf drwxrwxrwx 2 www-data www-data 4096 Sep 19 20:44 barplots -rw-rw-r-- 1 metap2 metap2 533 Sep 19 20:44 pValuesForAllMetabolites__Treatment.csv -rw-rw-r-- 1 metap2 metap2 54381 Sep 19 20:44 hypothesisTests_complete_data.pdf -rw-rw-r-- 1 metap2 metap2 114 Sep 19 20:44 bonferroni.csv -rw-rw-r-- 1 metap2 metap2 739 Sep 19 20:44 PCA_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1678 Sep 19 20:44 PCA_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 739 Sep 19 20:44 PCA_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1806 Sep 19 20:44 PCA_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 741 Sep 19 20:44 PCA_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 1874 Sep 19 20:44 PCA_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 2543 Sep 19 20:44 pca.rotations.csv -rw-rw-r-- 1 metap2 metap2 8884 Sep 19 20:44 PCA.pdf -rw-rw-r-- 1 metap2 metap2 766 Sep 19 20:44 PCATreatment_PC1_PC2.map -rw-rw-r-- 1 metap2 metap2 1703 Sep 19 20:44 PCATreatment_PC1_PC2.png -rw-rw-r-- 1 metap2 metap2 766 Sep 19 20:44 PCATreatment_PC1_PC3.map -rw-rw-r-- 1 metap2 metap2 1827 Sep 19 20:44 PCATreatment_PC1_PC3.png -rw-rw-r-- 1 metap2 metap2 768 Sep 19 20:44 PCATreatment_PC2_PC3.map -rw-rw-r-- 1 metap2 metap2 1865 Sep 19 20:44 PCATreatment_PC2_PC3.png -rw-rw-r-- 1 metap2 metap2 9969 Sep 19 20:44 PCATreatment.pdf -rw-rw-r-- 1 metap2 metap2 5181 Sep 19 20:44 kendall.pdf -rw-rw-r-- 1 metap2 metap2 896 Sep 19 20:44 kendall.csv -rw-rw-r-- 1 metap2 metap2 32598 Sep 19 20:44 .R.Rout -rw-rw-r-- 1 metap2 metap2 3563 Sep 19 20:44 kendall.png -rw-rw-r-- 1 metap2 metap2 2521 Sep 19 20:44 PCATreatment_propOfVar.png -rw-rw-r-- 1 metap2 metap2 2189 Sep 19 20:44 PCA_propOfVar.png -rw-rw-r-- 1 metap2 metap2 1373 Sep 19 20:44 processing_log.txt -rw-rw-r-- 1 metap2 metap2 8020 Sep 19 20:44 server_log.txt -rw-rw-r-- 1 metap2 metap2 169544 Sep 19 20:44 download.zip drwxrwxrwx 3 www-data www-data 4096 Sep 19 20:44 . + set - Finishing METAP SERVER