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floating exception on trying to read data file (Read 4952 times)

konrad

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floating exception on trying to read data file
Nov 10^th, 2005 at 3:27am

Hi Sergei,

I'm trying to get Hyphy (single processor version) to work on a cluster with OS/architecture details as follows:

Linux deepthought 2.6.11-gentoo-r3 #4 SMP Thu Jul 21 08:41:05 SAST 2005 i686 Intel(R) Xeon(TM) CPU 2.80GHz GenuineIntel GNU/Linux

It compiles and runs fine using the p51.nex example file. However, on calling ReadDataFile for my .nex file (which works fine on my local machine), the program crashes with the message "Floating exception".

The start of my .nex file is as given below (the most obvious difference between this and p51.nex is the absence of a list of taxlabels).

regards,
Konrad

---------
#NEXUS

BEGIN TAXA;
DIMENSIONS NTAX = 10;
END;

BEGIN CHARACTERS;
DIMENSIONS NCHAR = 1500;
FORMAT
DATATYPE = DNA
GAP=-
MISSING=?
;

MATRIX

seq1 ACTGTG...

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: floating exception on trying to read data file Reply #1 - Nov 10^th, 2005 at 3:47am Dear Konrad, I haven't seen this bug before; would you mind compiling HyPhy with the DEBUG flag ([code]sh build.sh DEBUG[/code]), then running it from within GDB [code] gdb ./HYPHYDebug run myFile.bf [/code] so that you can pinpoint the line of code where the exception is raised? Cheers, Sergei
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konrad

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Re: floating exception on trying to read data file
Reply #2 - Nov 10^th, 2005 at 4:29am

Unfortunately gdb is not installed on this cluster, and I don't have access to install things.

I've just noticed this in messages.log:
Expected 1500 sites, but found 15000

Since there are 10 sequences with 1500 nucs each, this must mean it is reading all of the data but missing the sequence names. A problem with sequence names, spacing, line breaks or something similar? What are the formal requirements for these?

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Sergei

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Re: floating exception on trying to read data file
Reply #3 - Nov 10^th, 2005 at 4:53am

Dear Konrad,

Quote:

Expected 1500 sites, but found 15000

This suggests that all of the sequences are lumped into a single sequence; probably due to new line issues in the matrix part of the NEXUS file. Make sure that in the data matrix, each sequence is on a new line.

Still, the floating point exception is odd.

Cheers,
Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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konrad Junior Member Offline I love YaBB 1G - SP1! Posts: 53	Re: floating exception on trying to read data file Reply #4 - Nov 10^th, 2005 at 5:04am Yes, everything is on a new line. I got it working by inserting a taxlabels line, though. Strange.
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Sergei

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Re: floating exception on trying to read data file
Reply #5 - Nov 10^th, 2005 at 5:06am

Dear Konrad,

[quote author=konrad link=1131622021/0#4 date=1131627846]Yes, everything is on a new line. I got it working by inserting a taxlabels line, though. Strange.
[/quote]

This could indicate a problem with my NEXUS reader. Could you send me the file which was breaking the reader by e-mail?

Cheers,
Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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