HyPhy message board - Neightbor Joining.bf crash in XP

Antonio Carvajal-Rodrígue Guest	Neightbor Joining.bf crash in XP Apr 25^th, 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
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Simon

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Re: Neightbor Joining.bf crash in XP
Reply #1 - Apr 25^th, 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

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Antonio Carvajal Rodrígue

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Re: Neightbor Joining.bf crash in XP
Reply #2 - Apr 27^th, 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

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Re: Neightbor Joining.bf crash in XP
Reply #3 - Apr 27^th, 2005 at 7:26am

Dear Antonio,

Quote:

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

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Antonio Carvajal Rodrígue

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Re: Neightbor Joining.bf crash in XP
Reply #4 - Apr 28^th, 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

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Simon Ex Member	Re: Neightbor Joining.bf crash in XP Reply #5 - Apr 28^th, 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
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Antonio Carvajal Rodrígue Guest	Re: Neightbor Joining.bf crash in XP Reply #6 - Apr 28^th, 2005 at 1:17pm Dear Simon: Yes, I have tried with the p3 version and it works perfectly. Thankyou very much, antonio
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Re: Neightbor Joining.bf crash in XP
Reply #7 - May 11^th, 2005 at 11:41am

Dear Antonio,

Quote:

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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