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HYPHY Package >> HyPhy bugs >> Neightbor Joining.bf crash in XP
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Message started by Antonio Carvajal-Rodrígue on Apr 25th, 2005 at 2:31am

Title: Neightbor Joining.bf crash in XP
Post by Antonio Carvajal-Rodrígue on Apr 25th, 2005 at 2:31am
Hello, I am using a pentium 4 machine on XP. When running the Neightbor Joining.bf  script I get a crash. I think is due to some illegal address access in TreeMatrix2TreeString function or other related with the treenodes matrix but I am not sure.

Regards,
Antonio

Title: Re: Neightbor Joining.bf crash in XP
Post by Simon on Apr 25th, 2005 at 10:25pm
Dear Antonio,

Firstly, thanks for letting us know about this, we really appreciate bug reports. Could you provide a little more information on your error? Your error probably stems from one of two sources:

1. On Windows, I have found that if you run certain analyses in a particular order, one can crash HyPhy. Does it crash when the neighbor joining is the first analysis you run?

2. Are the sequences names in your alignment 'clean'? HyPhy has some nice features that allow you to attach different models to different branches, at the cost of having a convention for sequence names. The easy way to check this is to load the data into HyPhy (File>Open>Open Data File), go into the Data>Name Display > Clean up sequence names, and then see if any sequences are renamed. Any usual characters ('.', '-') in the sequence names will be converted.

Best
Simon

Title: Re: Neightbor Joining.bf crash in XP
Post by Antonio Carvajal Rodrígue on Apr 27th, 2005 at 2:14am
Dear Simon: to your first question the answer is yes, is the first analysis I run. To the second the answer is  again yes, the sequences names are clean indeed the bf crashes with example data you provide vg p51.nex and also with my data.

I hope this help and thank you very much for the program hyphy.

sincerely,
antonio

Title: Re: Neightbor Joining.bf crash in XP
Post by Sergei on Apr 27th, 2005 at 7:26am
Dear Antonio,


wrote on Apr 27th, 2005 at 2:14am:
Dear Simon: to your first question the answer is yes, is the first analysis I run. To the second the answer is  again yes, the sequences names are clean indeed the bf crashes with example data you provide vg p51.nex and also with my data.


Would you be kind enough to provide me with all analysis options (e.g. the distance measure) which lead to a crash on p51.nex?

It is very embarassing indeed to have the program crash on our own example data, so I would like to fix this ASAP.

Cheers,
Sergei

Title: Re: Neightbor Joining.bf crash in XP
Post by Antonio Carvajal Rodrígue on Apr 28th, 2005 at 1:23am
Dear Sergei:
I just execute NeighborJoining.bf -> Distance formulae (but also crashes with full likelihood) -> nucleotide -> get the data (p51.nex) -> negative branches (also crashes with branch forced to 0) -> JC69

when execute fulllikelihood I make JC69 and fixed ratios and again crashes both with negative or forced0 branches.

I hope this help, if you want any other information please don't hesitate on ask it to me.

thankyou,
antonio

Title: Re: Neightbor Joining.bf crash in XP
Post by Simon on Apr 28th, 2005 at 11:55am
Dear Antonio,

I've managed to reproduce the bug; it appears to be specific to the Pentium 4 build. While this is being followed up, you should be able to use HYPHY-P3.EXE.

Best wishes
Simon

Title: Re: Neightbor Joining.bf crash in XP
Post by Antonio Carvajal Rodrígue on Apr 28th, 2005 at 1:17pm
Dear Simon:
Yes, I have tried with the p3 version and it works perfectly.
Thankyou very much,
antonio

Title: Re: Neightbor Joining.bf crash in XP
Post by Sergei on May 11th, 2005 at 11:41am
Dear Antonio,


wrote on Apr 28th, 2005 at 1:17pm:
Yes, I have tried with the p3 version and it works perfectly.


I have removed the P4 optimized binary from the distribution for the time-being. The crashes are probably due to some obscure bug that becomes fatal when the compiler optimizes for P4. I'll keep investigating...

Cheers,
Sergei

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