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HyPhy: Hypothesis testing using Phylogenies
http://www.hyphy.org
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Issues Generating the right nexus file for FADE analysis in Datamonkey #1452

Closed ArfBAD2021 closed 2 years ago

ArfBAD2021 commented 2 years ago

Hi all I am trying to run the FADE Program on Datamonkey, however, a failling to righly format the Nexus file combining both the Protein alignment and the tree data. I always get the following standard error message: /var/spool/torque/mom_priv/jobs/1921107.new-silverback.SC: line 43: [: Variational-Bayes: integer expression expected /var/spool/torque/mom_priv/jobs/1921107.new-silverback.SC: line 54: [: missing `]' Check errors.log for execution error details.

Could anyone guide me, maybe by providing a template or giving hints on have to do that? I know, I need to root the tree, but all have tried has failed even using Phylotree (http://phylotree.hyphy.org) and IcyTree (https://icytree.org/). I must be doing something wrong, but I can't figure it out. Thank you

spond commented 2 years ago

Dear @ArfBAD2021,

Do you have a job ID/URL for where this is happening?

Best, Sergei

ArfBAD2021 commented 2 years ago

Dear Sergei Please, see the links below:

http://datamonkey.org/fade/61eec9275e56f71949c05015

http://datamonkey.org/fade/61eec4295e56f71949c04edd

http://datamonkey.org/fade/61eec30b5e56f71949c04e96 Thank you and Best regards Arfang BADJI Post-doctoral fellow, NaCRRI (National Crop Resources Research Institute, Namulonge, Uganda) - Makerere University, Kampala, Uganda.

Ph.D. Plant Breeding and Biotechnology/MSc: Plant and Microbial Biotechnologies Mobile: +256756736561

On Tue, Jan 25, 2022 at 4:43 PM Sergei Pond @.***> wrote:

Dear @ArfBAD2021 https://github.com/ArfBAD2021,

Do you have a job ID/URL for where this is happening?

Best, Sergei

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github-actions[bot] commented 2 years ago

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