32/64 bit error for ExaML, "Please parse the binary alignment file on the same hardware on which you intend to run ExaML."

[EB]

Hi, 

I have binary data which I am trying to run with ExAML

Here is the command I run (I did not "make the file binary" again as the documentation details, and used RAxML to create the starting tree):

-----------------

$ mpirun -np 40 ./examl-AVX -t /.../myfile_starter_tree.tree -m GAMMA -s /soure_file1.phy -n T1001

Here is the error I get:

Error: the address data type has a size of 64 bits on the current system while on the system on which you created the binary alignment file using the parser the address size is 28418464 bits!

Usually this indicates that the parser was executed on a 32-bit system while you are trying to run ExaML on a 64-bit system.

Please parse the binary alignment file on the same hardware on which you intend to run ExaML.

The binary data matrices were constructed using a Python-3.5.1 script on 64-bit machines. I don't see where anything used 32-bits....

Is there someway to maybe "overwrite" this error? As far as I can tell, I don't understand why there would be this conversion error. 

Any help? 

Thanks

[Alexey Kozlov]

Hi Evan,

you got this error because your alignment is in PHYLIP format, while for ExaML you're supposed to convert it to the
binary format first, using parse-examl command. Please refer to ExaML documentation for details:

https://github.com/stamatak/ExaML/blob/master/manual/ExaML.pdf

Best,
Alexey

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[EB]

Hi Alexey, 

Thanks for the response. 

I guess then I am confused by the documentation. My PHYLIP file is already in binary: 0, 1, or ?. This is a fundamental property of the data I am working with. 

Based on the documentation, I should use `/.parse-examl` with the `-m` flag. But my data is fundamentally binary, so there are no `-m` flag options for me. 

What should users do if the PHYLIP data is binary to get with? 

Thanks for the help, Evan

[Alexey Kozlov]

Hi Evan,

please use "-m BIN" for your data (it might be not in the manual, but you can see this option if you run
./parse-examl -h).

The was apparently a confusion about the meaning of "binary": I was referring not to the datatype with two states, but
to the internal ExaML representation of an alignment (as opposed to text-based PHYLIP format). If you use ExaML, you
must convert your PHYLIP/FASTA alignment to this format first, regardless of the data type (DNA, AA or 0/1).

Best,
Alexey

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[EB]

Hi Alexey, 

Thanks for the clarification. Yes, I was confused by the manual. On p. 4, it appears there are only two "types of data" associated with "-m": DNA and PROT

I will try this with BIN. 

Thank you for the help, Evan