HyPhy message board - Incompatible Matrix Dimensions Exiting...

Gabriel

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Incompatible Matrix Dimensions Exiting...
Feb 14^th, 2010 at 8:02am

Hi,
I'm trying to make a Phylogeny Reconstruction. The options I used are put down below. The problem is that I get the following error ...

(9) Phylogeny Reconstruction
(3) Perform a phylogeny reconstuction for nucleotide, protein or codon data with user-selectable models using the method of neighbor joining.
(1):[Distance formulae] Use one of the predefined distance measures based on data comparisons. Fast.
(2):[Codon] Codon (several available genetic codes).
(1):[Universal] Universal code. (Genebank transl_table=1).
Please choose a codon data file:: genealig0.fasta
(2):[Force Zero] Negative Branch Lengths are Forced to 0.
(1):[Nei_Gojobori] Nei and Gojobori (1986) method.
(1):[Joint p-distance(Default)] Observed N/E[N]+Observed S/E[S]

Error:
Incompatible Matrix Dimensions Exiting...
Call stack
3 : _SITE_OS_COUNT=matrixTrick2*(_OBSERVED_S_$siteDifferenceCount)*Transpose(matrixT
rick2)
2 : distanceMatrix[i][j]=ComputeDistanceFormula(i,j)
1 : p=InferTreeTopology(1.0)
Segmentation fault

with the same file, also got the following error ...

Error:
Invalid distance matrix passed to NeighborJoin. Matrices written onto messages.log
Call stack
2 : njm=(distanceMatrix>methodIndex)>=ds.species
1 : p=InferTreeTopology(1.0)
Segmentation fault

Someone could help me?
Greetings

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Incompatible Matrix Dimensions Exiting... Reply #1 - Feb 14^th, 2010 at 8:04am Dear Gabriel, This could happen if you input an amino-acid alignment to a codon analysis. If this is not the case, please attach your input file so that I can diagnose the problem. Sergei
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Gabriel YaBB Newbies Offline Feed your monkey! Posts: 11	Re: Incompatible Matrix Dimensions Exiting... Reply #2 - Feb 14^th, 2010 at 8:32am Dear Sergei, Thank you very much for your reply. I attached my input file to see if you can spot the problem. Thanks Gabriel
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Sergei

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Re: Incompatible Matrix Dimensions Exiting...
Reply #3 - Feb 14^th, 2010 at 9:40pm

Dear Gabriel,

Gabriel wrote on Feb 14^th, 2010 at 8:32am:

Dear Sergei,
Thank you very much for your reply. I attached my input file to see if you can spot the problem.
Thanks
Gabriel

HyPhy tries to guess (for FASTA and PHYLIP files) if the content is DNA/RNA or amino-acid data.
If DNA alignments have too many N's (which yours does), then the algorithm will assume (that because N is a valid amino-acid residue) that the alignment contains aminoacid data.

Because of this, the analysis breaks. The easiest way to fix this is to replace 'N' with '?' in your FASTA file, or to save the alignment in the NEXUS format (which includes the type of the alignment).

I'll make a note to modify the heuristics for DNA/amino-acid data auto-detection for a future release.

Cheers,
Sergei

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Gabriel YaBB Newbies Offline Feed your monkey! Posts: 11	Re: Incompatible Matrix Dimensions Exiting... Reply #4 - Feb 15^th, 2010 at 5:08am Dear Sergei, Thank you very much for your help. Now, i am going to try to solve it in the way that you said me. I will write if other problem appear or if I can't solve this Cheers, Gabriel
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Gabriel

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Re: Incompatible Matrix Dimensions Exiting...
Reply #5 - Feb 16^th, 2010 at 3:20pm

Dear Sergei,
I tried both ways that you tell me (replace 'N' with '?' in my FASTA file and saving the alignment in the NEXUS format), but in both cases appeared the following error ...

Error:
Invalid distance matrix passed to NeighborJoin. Matrices written onto messages.log
Call stack
2 : njm=(distanceMatrix>methodIndex)>=ds.species
1 : p=InferTreeTopology(1.0)
Segmentation fault

Any idea why this might happen?

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Incompatible Matrix Dimensions Exiting... Reply #6 - Feb 16^th, 2010 at 3:23pm Dear Gabriel, Could you attach the NEXUS file that causes the error message to be generated? Sergei
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Incompatible Matrix Dimensions Exiting... Reply #7 - Feb 17^th, 2010 at 9:42am Dear Gabriel, Here's the converted NEXUS version of your file that should work. The trick is to set 'DATATYPE = DNA' in the FORMAT block. Cheers, Sergei
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Gabriel

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Re: Incompatible Matrix Dimensions Exiting...
Reply #8 - Feb 17^th, 2010 at 12:37pm

Dear Sergei,
I think there was an error uploading your file (the converted NEXUS version of my file that you send me), because he doesn't appear for download.
Now I attached the two files (FASTA and NEXUS). With neither can do the Phylogeny Reconstruction. I have also tried replacing the "N" with "?" (in both types of files) without good news.
Greetings
Gabriel

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Incompatible Matrix Dimensions Exiting... Reply #9 - Feb 17^th, 2010 at 1:43pm Dear Gabriel, I was able to run a phylogeny reconstruction on the NEXUS file that you attach. Could you be more specific about which analysis options you selected prior to seeing the error message? Sergei
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Gabriel

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Re: Incompatible Matrix Dimensions Exiting...
Reply #10 - Feb 17^th, 2010 at 3:47pm

Dear Sergei,
Thank you very much for your help. I found that the problem was my mistake. I'm running HYPHY from a script and the problem was in the script. I apologize for the inconvenience occasions. The transformation to the NEXUS format served me as the FASTA did not run.
Again, thank you very much and surely I will be engaging more often in this forum.
Greetings
Gabriel

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