new user - error message

[Rebecca Buckley]

SATe User,

I am trying to do an alignment with the following settings:

MAFFT
MUSCLE
RAXML
PROTCATWAGF
Protein

And I keep getting the error message:

SATe 2.0.3, 2009-2011

Running Log (2012-04-24 10:31:32 Central Standard Time)

SATe INFO: Reading input sequences from 'C:\Users\Becky\TyrKc_seq
delete checked split replace.FASTA'...
SATe INFO: Directory for temporary files created at C:\Documents and
Settings\Administrator\.sate\kinasesatesplit1\tempfhz4zi
SATe INFO: Performing initial tree search to get starting tree...
SATe INFO: Performing initial alignment of the entire data matrix...
SATe INFO: Performing initial tree search to get starting tree...
SATe is exiting because of an error:
SATe failed because one of the programs it tried to run failed.
The invocation that failed was:
"C:\Documents and Settings\Administrator\My Documents\Downloads
\SATe v2.0.3\satewin-v2.0.3-2011Nov07\satewin-v2.0.3-2011Nov07\bin
\raxml.exe" "-m" "PROTCATWAGF" "-n" "default" "-q" "C:\Documents and
Settings\Administrator\.sate\kinasesatesplit1\tempfhz4zi\init_tree
\tempraxml6bk28d\partition.txt" "-s" "C:\Documents and Settings
\Administrator\.sate\kinasesatesplit1\tempfhz4zi\init_tree
\tempraxml6bk28d\input.phy"

Assertion failed: 0, file axml.c, line 433

This application has requested the Runtime to terminate it in an
unusual way.
Please contact the application's support team for more information.

Worker dying. Error in job.get_results = Traceback (most recent call
last):
File "sate\scheduler.pyo", line 53, in worker
File "sate\scheduler.pyo", line 250, in get_results
File "sate\scheduler.pyo", line 193, in wait
Exception: SATe failed because one of the programs it tried to run
failed.
The invocation that failed was:
"C:\Documents and Settings\Administrator\My Documents\Downloads
\SATe v2.0.3\satewin-v2.0.3-2011Nov07\satewin-v2.0.3-2011Nov07\bin
\raxml.exe" "-m" "PROTCATWAGF" "-n" "default" "-q" "C:\Documents and
Settings\Administrator\.sate\kinasesatesplit1\tempfhz4zi\init_tree
\tempraxml6bk28d\partition.txt" "-s" "C:\Documents and Settings
\Administrator\.sate\kinasesatesplit1\tempfhz4zi\init_tree
\tempraxml6bk28d\input.phy"

Assertion failed: 0, file axml.c, line 433

This application has requested the Runtime to terminate it in an
unusual way.
Please contact the application's support team for more information.


Any help would be much appreciated. Thanks.

Becky

[Tandy Warnow]

Thanks, Rebecca -- We'll get back to you quickly.

Tandy

Tandy Warnow, Professor
Department of Computer Sciences
The University of Texas at Austin

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[Mark Holder]

Hi Rebecca,
That is a crash in RAxML, probably because it did not understand the input data. Would you mind emailing your data set to my private email: mtho...@ku.edu ?

That will keep your data off this public list (and I won't use your data set for anything other than diagnosing the problem), but I might be able to figure out how to workaround this error.

If you could email the file:

> "C:\Documents and Settings\Administrator\.sate\kinasesatesplit1\tempfhz4zi\init_tree\tempraxml6bk28d\input.phy"

that would also help.


We are in the process of testing the next release of SATé, and one of the features will be stricter parsing of the input data. Hopefully that will help us generate informative error messages (unlike the one that you saw). We've found a few minor glitches with the new version, but they'll be easy to fix today. I'm still optimistic that we'll have the the next release posted by tomorrow.


all the best,
Mark

[Mark Holder]

Hi Rebecca,
This appears to be a case in which RAxML is running out of memory.

The alignment at this iteration in SATe ends up being 9502 positions and there are 751 leaves in the tree. For amino acid sequences, RAxML has to allocate a partial likelihood array for each node in the tree. Each of these arrays has to store a partial likelihood term for each combination of amino acid and rate category. When RAxML requests that much memory, the operating system says "no" which triggers the crash.

We'll look into adding support for RAxML-Light to SATé, which has lower memory requirements. Unfortunately, it is less portable and not as feature rich, and SATé relies on some of the features that were dropped. We can also see if there are other ways of compiling the general RAxML so that it will use less memory.

I have a few specific thoughts about using your data in SATé, but I'll email those to you off-list because they are not general.

Thanks for reporting the issue, and hopefully we'll be able to work out a strategy for this dataset.

all the best,
Mark

Mark Holder

mtho...@ku.edu
http://phylo.bio.ku.edu/mark-holder

==============================================
Department of Ecology and Evolutionary Biology
University of Kansas
6031 Haworth Hall
1200 Sunnyside Avenue
Lawrence, Kansas 66045

lab phone: 785.864.5789

fax (shared): 785.864.5860
==============================================