ASC_FELS giving error

[pnatsi]

Hi,

I am trying to run an analysis for binary data including an ascertainment bias. This is the command I run:

raxml-ng --model BIN+G+ASC_FELS{4295} --msa binary_alingment.aln

and this is the error I get:

ERROR: You enabled ascertainment bias correction for partition noname, but it contains 4295 invariant sites. This is not allowed! Please either remove invariant sites or disable ascertainment bias correction.

I would excpect it to work since I used the correct number in the curly brackets. Am I doing something wrong? Any ideas?

Paschalis

[stamatak]

Paschali, check similar discussions on the raxml google group, I hope those will answer your question.

Alexis

On 24.06.20 12:14, Paschalis Natsidis wrote:

Hi,

I am trying to run an analysis for binary data including an ascertainment bias. This is the command I run:

raxml-ng --model BIN+G+ASC_FELS{4295} --msa binary_alingment.aln

and this is the error I get:

ERROR: You enabled ascertainment bias correction for partition noname, but it contains 4295 invariant sites. This is not allowed! Please either remove invariant sites or disable ascertainment bias correction.

I would excpect it to work since I used the correct number in the curly brackets. Am I doing something wrong? Any ideas?

Paschalis

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-- Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[pnatsi]

Thank you Alexi, it was useful indeed.

[amkozlov]

@pnatsi so can we close this issue then?

[pnatsi]

From my side yes, but maybe you want to fix that BIN+G+ASC_FELS{4295} reports an error that there are 4295 invariable sites.

People may get confused because you also say to include the number of invariable sites in curly brackets, and when you do it you still get the same error. It must be somehow clear that you need to remove the sites and then put their number in the curly brackets, in my opinion.

[amkozlov]

Do you have a suggestion how we can make it even more clear?

I guess the error message is quite straightforward:

Please either remove invariant sites or disable ascertainment bias correction

and I also added a note into +ASC model description:

https://github.com/amkozlov/raxml-ng/wiki/Input-data#single-model

[pnatsi]

OK the note is helpful. Leave it like this and you can deal with it case by case, if any. Thank you

[amkozlov]

Great, thanks for your feedback!