Hello again, Vadim.

I just ran the tool on main using known good data and it runs as
expected - ploteig is clearly being found correctly - so it looks like
your data is the source of your problem - it definitely has some
issues. You can find the data I used (the sample data supplied with
plink) and import it for testing from the 'medium' folder in the
'GenotypeSamples' shared data library at
http://main.g2.bx.psu.edu/library

In the MDLD data,

1) affection status (col 6 in the .fam file) is set to missing for all
subjects - that's normally used to set the plot symbol and legend so
may be a source for the eigensoft error.

2) The family id (first column) of the pedigree in your MDLD.fam file
contains the population group as a text field. While that seems like a
logical thing to do, it's not the way pedigrees with all unrelateds
are normally specified and eigensoft may be getting confused - the
normal convention is that every independent family has the same family
id - you have dozens of unrelated (no father/mother id) subjects in
the same 'family'

Now that I see how you are using the tool, I think we need a better
and more flexible way to specify the nominal population group for the
plot - not just case/control as I'd originally conceived the tool.
Thanks for bringing up this more general use case. I'll take a look at
adding an optional plink style phenotype text file to provide those
indicators and let you know when I have something to test.

FYI the GRR plot is interesting - two 'unrelated' subjects HGDP00794
and HGDP00801 are almost certainly siblings or a parent/child pair -
not enough data to tell - you would have to remove one of that pair to
get strictly valid eigenvectors.

Once again, thanks for using Galaxy and thanks again for helping us
make it even better...


On Mon, May 16, 2011 at 11:13 PM, Ross <ross.laza...@gmail.com> wrote:
> 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-b...@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 'vadimveren...@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;
>



-- 
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;

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