bias correction for help

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Sithions Brand

Feb 29, 2024, 5:44:05 AMFeb 29
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Hi everyone,

I encountered a problem while performing bias correction for SNP sequences generated by GBS-SNP-CROP. When I ran RAxML, I received the following error message: 'For partition No Name Provided, you specified that the likelihood score should be corrected for invariant sites via an ascertainment bias correction. However, some sites in this partition are already invariant. This is not allowed, please remove all invariant sites and try again, exiting...' I cannot understand why this error is occurring. My command was: ./raxmlHPC-SSE3 -s 1.phy -f a -x 1234 -p 1234 -# 1000 -m ASC_GTRCAT -V --K80 --asc-corr=lewis -n 3.phy -o S19,S20,S21,S18.

Thank you!

Xu Jun

Alexandros Stamatakis

Mar 4, 2024, 12:06:30 AMMar 4
Dear Xu,

Which part of the error message which I believe is rather verbose don't
you understand?

It tells you that your MSA already contains some invariant columns which
should be removed prior to doing an analysis under the ascertainment
bias correction.

The reason for this is that the maths do not work and break down if you
are trying to correct for asc. bias in a MSA that contains some
invariant sites already.

I believe that somebody wrote a script to remove such sites for exactly
this purpose (using asc. bias correction) a couple of years ago.

Please also consider switching to the new version of RAxML:

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Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology (Crete lab) (Heidelberg lab)

Sithions Brand

Mar 4, 2024, 12:31:31 AMMar 4
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Dear Alexandros Stamatakis,

I found a script for deleting invariant sites (, but it doesn't seem to achieve my goal because when I run it again, I encounter the same error, and it appears that the invariant sites are still present. 

I also need to remove invariant sites as input for raxml-ng, and my input file consists of concatenated SNPs.

Thank you!

Xu Jun


Mar 4, 2024, 4:41:14 AMMar 4
to raxml
Maybe the script is not removing sites containing a single character but also some gaps and undetermined characters, such sites are also considered as being invariable. 
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