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problem reading large phylip files (Read 2622 times)
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problem reading large phylip files
Jun 15th, 2005 at 10:57pm
Hi all,

I bumped some weeks ago with an error in hyphy, after the modification you did so that large seqs are readed more efficiently, that some phylip files are not readed appropriately:

Internal Error: _DataSet::Compact called with compact represntation
Current BL Command:Read Data Set bigDataSet from file PROMPT_FOR_FILE

Check errors.log for details on execution errors.

Now I found out that this only happens with interleaved phylip files, not with the sequential phylip or the fasta files of the same data.

An example (simulation result from hyphy):
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Datamonkeys are forever...

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Re: problem reading large phylip files
Reply #1 - Jun 16th, 2005 at 6:08pm
Dear Albert,

Thanks for bringing this bug to my attention - your bug reports are invaluable! I fixed the problem, but it'll probably be another day before I put up a new distro, since I am in the middle of some code streamlining.

In the meantime, please use a sequential format for sequences over 100,000 bp long.

Also, it appears that you sample file has 4 identical sequences; may I suggest that you look at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login for an issue which results in zero branch lengths and identical sequences being simulated.


P.S. June 18th, 2005 (and later) builds should have this fixed.
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« Last Edit: Jun 17th, 2005 at 11:53pm by Sergei »  

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
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