batch processing

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chris blair

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Nov 17, 2016, 4:08:41 PM11/17/16
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Hi Alexis, 

Are there any RAxML wrappers out there that work with some of the newer versions of RAxML? Also do you know of a script to easily convert a batch of nexus files to phylip? Thanks.

Chris

Alexandros Stamatakis

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Nov 18, 2016, 6:31:02 AM11/18/16
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On 17.11.2016 22:08, chris blair wrote:
> Hi Alexis,
>
> Are there any RAxML wrappers out there that work with some of the newer
> versions of RAxML?

I am not aware of any but it also really depends on what you want to do.
The RAxML command line args should be backward compatible with most of
the existing scripts.

> Also do you know of a script to easily convert a
> batch of nexus files to phylip? Thanks.

No, sorry, but somebody else on this list might hopefully know.

Alexis

>
> Chris
>
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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

chris blair

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Nov 20, 2016, 12:33:37 PM11/20/16
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Hey Alexis, 

I am writing a computer tutorial for my systematics course and would like to use RAxML to calculate gene trees (~1000) to feed into species tree analyses. 

Chris

chris blair

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Nov 20, 2016, 3:04:33 PM11/20/16
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I am trying to write a script to loop through phylip files, but an getting errors with the -n flag. Here is the current script:

#!/bin/bash
for i in *.phy
do
echo "Processing $i"
./raxml -T 2 -f a -m GTRGAMMA -p 685387 -x 574684 -# autoMRE -s *.phy -n Test.$i;
done

I am sure that I am missing something small, but I cannot seem to figure it out. Thanks!

Chris

Alexey Kozlov

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Nov 20, 2016, 3:12:18 PM11/20/16
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Hi Chris,

try changing "-# autoMRE" into "-N autoMRE" (# is problematic since it defines a line comment in shell scripts).

Also, there is a perl script called "applyRAxML2AllFilesInDirectory.pl" in the "usefulScripts" directory of RAxML, which
should do pretty much the same.

Best,
Alexey
> > For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout>.
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> of Arizona at Tucson
>
> www.exelixis-lab.org <http://www.exelixis-lab.org>

chris blair

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Nov 20, 2016, 3:53:09 PM11/20/16
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Hi Alexey, 

Changing the flag to -N did not help.

I downloaded the perl script and it appears to run, although it gives me errors about not being able to parse the phylip files correctly. This is the command I used:

perl applyRAxML2AllFilesInDirectory.pl ./ "./raxmlHPC-PTHREADS-AVX2 -T 2 -f a -m GTRGAMMA -p 685387 -x 574684 -# autoMRE -s *.phy -n output*"


Chris

Alexey Kozlov

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Nov 20, 2016, 4:20:50 PM11/20/16
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Hi Chris,

when using applyRAxML2AllFilesInDirectory.pl script, you don't have to provide "-s" and "-n" options as they will be
added by the script, i.e.

perl applyRAxML2AllFilesInDirectory.pl ./ "./raxmlHPC-PTHREADS-AVX2 -T 2 -f a -m GTRGAMMA -p 685387 -x 574684 -# autoMRE"

This will however run raxml on ALL files in the directory (not just *.phy), so you should copy them into a separate dir
if needed.
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Alexandros Stamatakis

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Nov 21, 2016, 6:14:09 AM11/21/16
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I think Alexey's answer should solve the issue (thanks Alexey),
regarding the error you are getting, please copy and paste the error
message here, otherwise we can not help you,

Alexis

chris blair

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Dec 3, 2016, 10:08:04 AM12/3/16
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Thanks Alexey. All is well now.

Chris
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