Hi, thanks for reporting this error. Ploteig is a perl script that is part of the eigensoft package and it seems to be inaccessible while eigensoft is executing judging from the error message. We'll fix this as soon as we can. Meanwhile, in case you didn't check, I noticed that if you click on the eye icon of items 2 and 4 in your history, the eigenplot is there - even though the history items are in an error state...I'm not sure I understand exactly how this has happened but it did. The way the samples are labelled (all are 'sample') on the plot is not very informative - I need to look more closely at the data to see how we can make the plot more useful. On Mon, May 16, 2011 at 9:48 PM, <galaxy-bugs@bx.psu.edu> wrote:
GALAXY TOOL ERROR REPORT ------------------------
This error report was sent from the Galaxy instance hosted on the server "main.g2.bx.psu.edu" ----------------------------------------------------------------------------- This is in reference to dataset id 2452824 from history id 554342 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item
3: Ancestry PCA_rgEig.txt
by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link.
main.g2.bx.psu.edu/history/view?id=1f6151421eac94f6 ----------------------------------------------------------------------------- The user 'vadimverenich@gmail.com' provided the following information:
sh: ploteig: not found
----------------------------------------------------------------------------- job id: 2167094 tool id: rgEigPCA1 ----------------------------------------------------------------------------- job command line: python /galaxy/home/g2main/galaxy_main/tools/rgenetics/rgEigPCA.py "/galaxy/main_database/files/002/452/dataset_2452822_files/MDLD" "Ancestry PCA" "/galaxy/main_pool/pool5/tmp/job_working_directory/2167094/galaxy_dataset_2452823.dat" "/galaxy/main_pool/pool5/tmp/job_working_directory/2167094/dataset_2452823_files" "4" "5" "5" "6" "/galaxy/main_pool/pool5/tmp/job_working_directory/2167094/galaxy_dataset_2452824.dat" ----------------------------------------------------------------------------- job stderr: sh: ploteig: not found
----------------------------------------------------------------------------- job stdout: smartpca -p Ancestry_PCA_pca.xls.par >Ancestry_PCA_log.txt ploteig -i Ancestry_PCA_pca.xls.evec -c 1:2 -p ??? -x -y -o Ancestry_PCA_eigensoftplot.pdf.xtxt evec2pca.perl 4 Ancestry_PCA_pca.xls.evec /galaxy/main_database/files/002/452/dataset_2452822_files/MDLD.fam Ancestry_PCA_pca.xls rgEigPCA.py got /galaxy/home/g2main/galaxy_main/tools/rgenetics/rgEigPCA.py /galaxy/main_database/files/002/452/dataset_2452822_files/MDLD Ancestry PCA /galaxy/main_pool/pool5/tmp/job_working_directory/2167094/galaxy_dataset_2452823.dat /galaxy/main_pool/pool5/tmp/job_working_directory/2167094/dataset_2452823_files 4 5 5 6 /galaxy/main_pool/pool5/tmp/job_working_directory/2167094/galaxy_dataset_2452824.dat llist=c("???") glist=c(2) par(lab=c(10,10,10)) par(mai=c(1,1,1,0.5)) pdf("Ancestry_PCA_PCAPlot.pdf",h=8,w=10) par(lab=c(10,10,10)) pca1 = c(0.076000,0.083300,0.072000,0.077100,0.079000,0.070600,0.082900,0.077600,0.077900,0.075400,0.076500,0.071000,0.070000,0.070600,0.072800,0.073100,0.068000,0.066700,0.073700,0.073400,0.074000,0.078700,0.077000,0.080100,0.063700,0.081400,0.077000,0.082500,0.083500,0.064900,0.072500,0.075200,0.078200,0.064600,0.051800,0.076600,0.059900,0.062800,0.058200,0.052800,0.060600,0.064300,0.049700,0.054000,0.058300,0.051700,0.057700,0.042700,0.046800,0.038700,0.048200,0.058600,0.035800,0.039700,0.043700,0.041300,0.033800,0.038400,0.042000,0.030600,0.042200,0.046200,0.039500,0.036500,0.039400,0.045200,0.085400,0.085600,0.084800,0.098500,0.093700,0.071400,0.088400,0.090300,0.096300,0.096900,-0.109500,-0.107400,-0.098500,-0.102900,-0.108700,-0.102900,-0.102000,-0.103400,-0.104600,-0.105300,-0.105100,-0.072000,-0.111300,-0.070000,-0.112000,-0.100200,-0.114700,-0.103900,-0.005000,-0.068300,0.018600,0.002600,0.012400,-0.000600,0.014100,0.012000,0.018300,0.011800,0.003600,0.022300,0.008! 900,0.012900,0.023900,0.084100,0.077700,0.075600,0.070000,0.077800,0.064400,0.082800,0.067100,0.064200,0.075200,0.064400,0.057500,0.056000,0.052400,0.058800,0.052600,-0.061100,-0.014800,0.047700,-0.056900,0.053200,-0.070900,0.060200,-0.070600,-0.075800,0.059800,-0.049500,0.056200,-0.073500,-0.037000,-0.055400,-0.074600,-0.068600,0.067800,0.055900,-0.072600,-0.069500,-0.077800,-0.068600,-0.070900,0.043300,0.070400,0.068000,-0.014200,-0.024000,-0.020600,-0.020400,-0.012500,-0.010300,-0.020700,-0.025500,-0.034300,-0.018900,-0.018200,-0.017100,-0.012900,-0.032600,-0.040300,-0.058900,-0.061900,-0.067100,-0.062300,-0.062800,-0.070300,-0.063700,-0.065000,-0.078900,-0.068800,-0.053300,-0.050400,-0.067800,-0.055600,-0.065300,-0.052000,-0.054400,-0.065400,-0.069000,-0.080300,-0.089400,-0.087900,-0.090100,-0.007800,-0.084000,-0.087500,-0.095700,-0.087700,-0.099300,-0.062100,-0.006700,-0.084200,-0.086400,-0.087500,-0.101600,0.033600,-0.096300,-0.090500,-0.044900,-0.055000,-0.049300,-0.! 054800,-0.059400,-0.061200,-0.055100,-0.052100,-0.055900,-0.050800,-0. 063800,-0.055800,-0.061500,-0.057900,-0.065100,-0.056400,-0.057900,-0.044500) pca2 = c(0.007500,0.001300,0.012400,0.000100,-0.001100,0.004400,0.013100,0.015700,0.015300,0.016800,0.000100,0.008200,0.008700,0.006900,0.004600,0.018400,0.003400,0.007400,0.004600,0.023700,-0.001200,-0.008500,0.015300,0.003300,-0.034300,-0.030100,-0.052700,-0.040700,-0.035400,-0.027100,-0.030700,-0.037700,-0.035500,0.117400,0.112900,-0.012000,0.118600,0.126200,0.118500,0.115200,0.118300,0.087600,0.105900,0.111500,0.118000,0.090500,0.111500,-0.026600,-0.034800,-0.047100,-0.036100,-0.040500,-0.042900,-0.036300,-0.044200,-0.041100,-0.038500,-0.042800,-0.033700,-0.042300,-0.034400,-0.033900,-0.051700,-0.040500,-0.036900,-0.048600,-0.041800,-0.041400,-0.040700,-0.045200,-0.040400,-0.046000,-0.043900,-0.055300,-0.045300,-0.035400,-0.042800,-0.039800,-0.030700,-0.032400,-0.028200,-0.039600,-0.039000,-0.035900,-0.025800,-0.030100,-0.036700,-0.014100,-0.031900,-0.026600,-0.041800,-0.031900,-0.035900,-0.011100,-0.014900,-0.027700,-0.049200,-0.027400,-0.040600,-0.032000,-0.040800,-0.0! 42800,-0.033100,-0.044500,-0.034900,-0.048500,-0.039900,-0.035900,-0.034500,-0.032300,-0.036800,-0.044800,-0.036200,-0.020200,0.005500,-0.018100,-0.029200,-0.004300,-0.027700,-0.068300,-0.057600,-0.055700,-0.049800,-0.048900,-0.058700,0.001000,0.008700,-0.048600,0.004700,-0.049600,-0.030500,-0.059400,-0.012300,-0.013800,-0.045800,0.018700,-0.048800,-0.011000,-0.001700,0.008400,-0.023000,-0.009500,-0.059300,-0.065300,-0.008000,-0.007800,-0.018700,-0.028000,0.016300,-0.051000,-0.019800,-0.031500,0.238200,0.249400,0.216100,0.235900,0.226100,0.236800,0.209900,0.149000,0.106500,0.222100,0.197900,0.210100,0.264400,0.137800,0.134200,0.019800,-0.010000,-0.010400,0.015100,0.009800,-0.002700,0.002500,-0.005600,-0.007600,-0.016600,-0.001800,-0.005400,-0.011200,-0.002700,0.016600,0.004000,0.010300,0.003800,-0.003100,-0.027700,-0.026600,-0.040400,-0.045900,-0.017100,-0.032800,-0.030000,-0.025500,-0.045500,-0.039500,-0.037300,-0.039100,-0.029200,-0.040500,-0.027500,-0.041000,-0.041900,-0! .046800,-0.038000,0.000400,-0.008000,-0.004200,-0.010300,-0.007400,-0. 014600,-0.015600,-0.016800,-0.007100,-0.012600,-0.009900,-0.012400,-0.011300,-0.018300,-0.015600,-0.014800,-0.001700,-0.006000) pgvec = c(2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2) plot(pca1,pca2,type='p',main='Ancestry_PCA', ylab='Second ancestry eigenvector',xlab='First ancestry eigenvector',col=pgvec,cex=0.8,pch=pgvec) legend("top",legend=llist,pch=glist,col=glist,title="Sample") grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted") dev.off() png("Ancestry_PCA_PCAPlot.pdf.png",h=8,w=10,units="in",res=72) plot(pca1,pca2,type='p',main='Ancestry_PCA', ylab='Second ancestry eigenvector',xlab='First ancestry eigenvector',col=pgvec,cex=0.8,pch=pgvec) legend("top",legend=llist,pch=glist,col=glist,title="Sample") grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted") dev.off() ['pdf \n', ' 2 \n', 'pdf \n', ' 2 \n']
----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;