Question: Error, (in OrthologousMatrix) values cannot be ordered
0
gravatar for lizsel_3
14 months ago by
lizsel_30
lizsel_30 wrote:

Hi,

I have had some problems with run OMA standalone, because of each time that I finished my first or second run, I always obtain the same error message, like this: Error, (in OrthologousMatrix) values cannot be ordered. In consequence, I never obtain the Output file.
Previously, I downloaded coding genomes of caviomorph and fiomorph rodents from Ensembl and then I translated them to peptides using the Geneious program (Standar translation). In order to get orthologous groups, I modified some commands line from the Parameters, therefore, I disabled Inparalog and Paralog because I don't need these:

#InparalogTol := 3.00;
#ParalogTol := -2.5*StablePairTol;

And in Output parameters I Enabled:

StableIdsForGroups := true;
GuessIdType := false;
WriteOutput_PairwiseOrthologs := true;
WriteOutput_OrthologousPairs_orthoxml := true;
WriteOutput_OrthologousGroupsFasta := true;
WriteOutput_HOGFasta := true;
WriteOutput_Paralogs := false; 
WriteOutput_PhyleticProfileHOG := true;
WriteOutput_PhyleticProfileOG := true;

Also, I gave a tree in Newick format:

#SpeciesTree := 'estimate';
SpeciesTree := '(((Octodon,Chinchilla),Cavia),(Heterocephalus,Fukomys));';

Further, I disabled the Function prediction:

DoGroupFunctionPrediction := false;

Finally, all other parameters were left by default. However, When finishing my first and second run, I obtain the next:

Reading the all-against-all files...
 Cavia vs Cavia done, (8687/8687)
 Cavia vs Chinchilla done, (58803/58803)
 Cavia vs Octodon done, (50455/50455)
 Chinchilla vs Chinchilla done, (97919/97919)
 Chinchilla vs Octodon done, (162796/162796)
 Octodon vs Octodon done, (62701/62701)
 Matches loaded. Mem: 0.699GB
 No data collected for matches of removed splice variants
 No data collected for matches of kept splice variants
 Cavia/Cavia: remove 0 BestMatches, keep 8687
Cavia/Chinchilla: remove 0 BestMatches, keep 58803
Cavia/Octodon: remove 0 BestMatches, keep 50455
Chinchilla/Cavia: remove 0 BestMatches, keep 58803
Chinchilla/Chinchilla: remove 0 BestMatches, keep 97919
Chinchilla/Octodon: remove 0 BestMatches, keep 162796
Octodon/Cavia: remove 0 BestMatches, keep 50455
Octodon/Chinchilla: remove 0 BestMatches, keep 162796
Octodon/Octodon: remove 0 BestMatches, keep 62701

Identification of Stable-Pairs (Putative Orthologs)
Error, (in OrthologousMatrix) values cannot be ordered
/usr/local/OMA/bin/OMA: line 196: kill: (8482) - No such process

So, I don't know if my parameters are wrong with the modifications that I did; I don't know why I obtain these errors. Thanks [1]: https://www.dropbox.com/s/d5dt1srzgkt0x2p/parameters.drw?dl=0

genome • 321 views
ADD COMMENTlink modified 13 months ago by adrian.altenhoff620 • written 14 months ago by lizsel_30

You used four spaces probably to denote paragraphs, but this site uses markdown to format text, and four spaces translates into block of code in markdown-speak. Hence, your post is format as one big code block. Could you please correct this? Pay attention because > and # are also formatting marks when at the beginning of lines, to use them you have to escape them, e.g.: \>

ADD REPLYlink modified 14 months ago • written 14 months ago by h.mon26k

Tagging: adrian.altenhoff

ADD REPLYlink written 14 months ago by genomax68k
0
gravatar for adrian.altenhoff
13 months ago by
Switzerland
adrian.altenhoff620 wrote:

By commenting out the InparalogTol and ParalogTol parameters the two variables are undefined and numeric comparisons of expressions involving these two variables are no longer possible. You need to assign values to them, this should fix your problem.

ADD COMMENTlink written 13 months ago by adrian.altenhoff620
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