felsenstein's ascertainment bias correction in CIPRES

[Santiago Ceballos]

Hi,

I'm trying to run the felsenstein's ascertainment bias correction in CIPRES but I get this error:

"custom protein substitution or ascertainment bias file [p0.txt] you want to use does not exist! you need to specify the full path
 the file name shall not contain blanks!"

Mi corresponding files are:

part.txt:
[asc~p0.txt], ASC_DNA, p0=1-8527

p0.txt:
273400

Thanks,

Santiago

[Mark Miller]

Hi Santiago,

 

For CIPRES, the name of the ascertainment bias file will be set by the interface, and you have no control over it.

In your case, I believe asc~p1.txt  will work.

Check your output, and look for the bias file. It will be named p1.txt or something like that. Make sure your partition file calls for that file name.

 

You can contact me here, or directly if that doesn’t make sense.

 

Mark

[Santiago Ceballos]

Hi Mark,

thanks a lot for your quick reply. Unfortunately it didn't work, I still have the same problem. I used:

part.txt:
[asc~p1.txt], ASC_DNA, p1=1-8527

p1.txt:
273400

Santiago

[Mark Miller]

Hi Santiago,
After we looked at this together, I figured out the issue.

You have to use the newer raxml interface, raxmlhpc8_xsede

Look for this prompt:

Choose Ascertainment bias correction file 1 (will be named p1.txt)

The earlier interface does not have the option to upload the required file.

Mark

[Mark Miller]

Just to be clear, I mean "there is no option to select the required file from your data area", not "the interface does not have the option to upload the required file"

On Tuesday, January 2, 2018 at 12:13:50 PM UTC-8, Mark Miller wrote:

Hi Santiago,
After we looked at this together, I figured out the issue.

You have to use the newer raxml interface, raxmlhpc8_xsede

Look for this prompt:

Choose Ascertainment bias correction file 1 (will be named p1.txt)

The earlier interface does not have the option to upload the required file.

Mark

On Friday, December 29, 2017 at 9:52:12 AM UTC-8, Santiago Ceballos wrote:

Hi Mark,

thanks a lot for your quick reply. Unfortunately it didn't work, I still have the same problem. I used:

part.txt:
[asc~p1.txt], ASC_DNA, p1=1-8527

p1.txt:
273400

Santiago
 

El viernes, 29 de diciembre de 2017, 11:04:15 (UTC-6), Mark Miller escribió:

Hi Santiago,

 

For CIPRES, the name of the ascertainment bias file will be set by the interface, and you have no control over it.

In your case, I believe asc~p1.txt  will work.

Check your output, and look for the bias file. It will be named p1.txt or something like that. Make sure your partition file calls for that file name.

 

You can contact me here, or directly if that doesn’t make sense.

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