partition file on BlackBox

[RobinvanVelzen]

Dear Alexandros et al.,

I am running some preliminary ML analyses on the RAxML Blackbox (DNA
sequences for 261 taxa). I would like divide the data into three
partitions with separate model parameter estimates (I am using GTR
+CAT), and I am therefore uploading the following text in a partition
file:

cpDNA = 1-5116
mtDNA = 5117-11920
nDNA = 11921-15524

However, whenever I specify this partition file RAxML finishes within
seconds and returns empty results and logfiles.

Does anyone know what may be going wrong?

Thanks in advance for any help or suggestions.

Best wishes,

Robin

[Andre J. Aberer]

Hi Robin,

your partition file does not match the format required by RAxML.
Have a look at this example:

http://sco.h-its.org/exelixis/hands-on/dna12_3.partition.txt

RobinvanVelzen <robinv...@gmail.com> writes:

--
Best regards,
Andre J. Aberer

M.Sc. (Bioinformatics)
Scientific Computing Group

Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Schloss-Wolfsbrunnenweg 35
D-69118 Heidelberg

Tel.: +49 6221 533 264
Fax: +49 6221 533 298
Email: andre....@h-its.org
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Amtgericht Mannheim / HRB 337446
Managing Directors: Dr. h.c. Dr.-Ing. E.h. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter

[RobinvanVelzen]

Hi Andre,

Many thanks for the quick reply and for the suggestion. Apparently,
the documentation on the RAxML website is incorrect / outdated, see
http://phylobench.vital-it.ch/raxml-bb/index.php?help=model

Anyway I will correct my partition file and see if it works.

Thanks again and with best wishes,

Robin

On Apr 20, 2:46 pm, andre.abe...@googlemail.com (Andre J. Aberer)
wrote:

> Email:  andre.abe...@h-its.org

[Dr. Vinita Gowda]

Hi Andre:

Can you please give me the link for the partition file format that needs to be used on blackbox. My format has some issue and I have read the manual already and I am not able to figure it out. The model outputs are from protest.

Thanks,

Vinita

[Alexey Kozlov]

Hi Vinita,

RAxML partition file format is fairly simple, it contains lines in the following format:

<model>, <partition_name> = <start>-<end> [, <start>-<end>,...]

e.g.

LG4X, Subset1 = 1-257
LG, Subset2 = 258-937
WAG, Subset3 = 938-1864

and so on.

If you still have problems with your partition file, please post it here along with the error message that you got.

Best,
Alexey

> > http://www.h-its.org/english/research/sco/index.php <http://www.h-its.org/english/research/sco/index.php>

> >
> > Amtgericht Mannheim / HRB 337446
> > Managing Directors: Dr. h.c. Dr.-Ing. E.h. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter
>

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[Dr. Vinita Gowda]

Dear Alexey:

Thanks much. I appreciate this very much.

Best,

Vinita

------------------------------------------------------------------------------------------------------------------
Dr. Vinita Gowda         
Asst. Professor                                                  Research Associate 
IISER Bhopal                                                     MRC 166, PO Box 37012

Dept. of Biological Sciences                              National Museum of Natural History  
ITI Campus Gas Rahat Building                        Washington, DC - 20013-7012
Govindpura, Bhopal -462 023                            USA
Madhya Pradesh, India                                      E-mail: gow...@si.edu

Phone: +91-755-4092314
Lab: +91-755-4092319                  

Fax: +91-755-4092392

Web: http://www.iiserbhopal.ac.in/profile.php?empid=MjAx&page=Biological%20Sciences&pid=42&id=43 
Web: http://botany.si.edu/staff/staffPage.cfm?ThisName=104&homepage=no                

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[Dr. Vinita Gowda]

Dear Alexey:

One more big query: I am not computer literate in any form however we have few workstations and a very good HPC cluster on campus:  http://atlas.iiserb.ac.in/. I would like to run RAxML on our cluster since it is not advisable right now to run it on our local computers (and CIPRES is still down).

I have sent the RAxML installation details to one of my colleague who is in charge of the bioinformatics lab and I am hoping that we will figure this out soon. Is there a simpler manual on how to go about streamlining job submission to RAxML on a cluster?

Thanks,

Vinita

------------------------------------------------------------------------------------------------------------------
Dr. Vinita Gowda         
Asst. Professor                                                  Research Associate 
IISER Bhopal                                                     MRC 166, PO Box 37012

Dept. of Biological Sciences                              National Museum of Natural History  
ITI Campus Gas Rahat Building                        Washington, DC - 20013-7012
Govindpura, Bhopal -462 023                            USA
Madhya Pradesh, India                                      E-mail: gow...@si.edu

Phone: +91-755-4092314
Lab: +91-755-4092319                  

Fax: +91-755-4092392

Web: http://www.iiserbhopal.ac.in/profile.php?empid=MjAx&page=Biological%20Sciences&pid=42&id=43 
Web: http://botany.si.edu/staff/staffPage.cfm?ThisName=104&homepage=no                

Support: http://emailcharter.org/

On Thu, Aug 18, 2016 at 6:04 PM, Alexey Kozlov <alexei...@gmail.com> wrote:

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[Mark Miller]

Hi Vinita,

It is true CIPRES went down for a few hours a couple of days ago, but it has been back up and running within 12 hours, and is currently running fine..

Can you please let me know if you are having trouble accessing it?

Best,

Mark

[Alexey Kozlov]

Dear Vinita,

> One more big query: I am not computer literate in any form however we have few workstations and a very good HPC cluster
> on campus: http://atlas.iiserb.ac.in/. I would like to run RAxML on our cluster since it is not advisable right now to
> run it on our local computers (and CIPRES is still down).
>
> I have sent the RAxML installation details to one of my colleague who is in charge of the bioinformatics lab and I am
> hoping that we will figure this out soon. Is there a simpler manual on how to go about streamlining job submission to
> RAxML on a cluster?

Nothing I'm aware of. However, job submission scripts are cluster-specific, and that's something usually explained in
your cluster documentation. Running RAxML must be no different from running any other PTHREADS/MPI program.

There are a couple of important things you should keep in mind when running parallel version of RAxML (PTHREADS vs. MPI,
no. of threads/CPUs), but they are described in the regular RAxML manual here:

http://sco.h-its.org/exelixis/php/countManualNew.php

Also, if your alignment is large (>50K-100K sites), you might consider using ExaML instead:

http://sco.h-its.org/exelixis/web/software/examl/index.html


Cheers,
Alexey

[Dr. Vinita Gowda]

Dear Alexey:

Thanks, I will share this information with our cluster in-charge and will read-up on this myself.

One of my student is using the ETE3 server from genome.jp This is a very small protein data set and we found it to be easier to access than CIPRES. The only issue is that I cannot tell which version of RAxML they are using.

Regards,

Vinita

------------------------------------------------------------------------------------------------------------------
Dr. Vinita Gowda         
Asst. Professor                                                  Research Associate 
IISER Bhopal                                                     MRC 166, PO Box 37012

Dept. of Biological Sciences                              National Museum of Natural History  
ITI Campus Gas Rahat Building                        Washington, DC - 20013-7012
Govindpura, Bhopal -462 023                            USA
Madhya Pradesh, India                                      E-mail: gow...@si.edu

Phone: +91-755-4092314
Lab: +91-755-4092319                  

Fax: +91-755-4092392

Web: http://www.iiserbhopal.ac.in/profile.php?empid=MjAx&page=Biological%20Sciences&pid=42&id=43 
Web: http://botany.si.edu/staff/staffPage.cfm?ThisName=104&homepage=no                

Support: http://emailcharter.org/

[Alexey Kozlov]

Hi Vinita,

if they give you back RAxML_info* files, then you can find RAxML version in there. Otherwise, just contact the website
maintainers...

Best,
Alexey

On 23.08.2016 06:58, Dr. Vinita Gowda wrote:
> Dear Alexey:
>
> Thanks, I will share this information with our cluster in-charge and will read-up on this myself.

> One of my student is using the ETE3 server from genome.jp <http://genome.jp> This is a very small protein data set and

> we found it to be easier to access than CIPRES. The only issue is that I cannot tell which version of RAxML they are using.
>
> Regards,
>
> Vinita
>
> ------------------------------------------------------------------------------------------------------------------
> Dr. Vinita Gowda
> Asst. Professor Research Associate
> IISER Bhopal MRC 166, PO Box 37012
> Dept. of Biological Sciences National Museum of Natural History
> ITI Campus Gas Rahat Building Washington, DC - 20013-7012
> Govindpura, Bhopal -462 023 USA

> Madhya Pradesh, India E-mail: gow...@si.edu <mailto:gow...@si.edu>

> Phone: +91-755-4092314
> Lab: +91-755-4092319
> Fax: +91-755-4092392
>
> Web: http://www.iiserbhopal.ac.in/profile.php?empid=MjAx&page=Biological%20Sciences&pid=42&id=43
> Web: http://botany.si.edu/staff/staffPage.cfm?ThisName=104&homepage=no
> Support: http://emailcharter.org/
>

> On Mon, Aug 22, 2016 at 2:03 AM, Alexey Kozlov <alexei...@gmail.com <mailto:alexei...@gmail.com>> wrote:
>
> Dear Vinita,
>
> One more big query: I am not computer literate in any form however we have few workstations and a very good HPC
> cluster
> on campus: http://atlas.iiserb.ac.in/. I would like to run RAxML on our cluster since it is not advisable right
> now to
> run it on our local computers (and CIPRES is still down).
>
> I have sent the RAxML installation details to one of my colleague who is in charge of the bioinformatics lab and
> I am
> hoping that we will figure this out soon. Is there a simpler manual on how to go about streamlining job
> submission to
> RAxML on a cluster?
>
>
> Nothing I'm aware of. However, job submission scripts are cluster-specific, and that's something usually explained
> in your cluster documentation. Running RAxML must be no different from running any other PTHREADS/MPI program.
>
> There are a couple of important things you should keep in mind when running parallel version of RAxML (PTHREADS vs.
> MPI, no. of threads/CPUs), but they are described in the regular RAxML manual here:
>

> http://sco.h-its.org/exelixis/php/countManualNew.php <http://sco.h-its.org/exelixis/php/countManualNew.php>

>
> Also, if your alignment is large (>50K-100K sites), you might consider using ExaML instead:
>
> http://sco.h-its.org/exelixis/web/software/examl/index.html
> <http://sco.h-its.org/exelixis/web/software/examl/index.html>
>
>
> Cheers,
> Alexey
>
>
> --
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[Dr. Vinita Gowda]

Hi Alexey:

I did contact the website managers and am yet to hear from them. However, the results are the same from Blackbox which we finally managed to use so I am assuming the algorithm is comparable. + our data set is so small that chance is the version might not matter to us - only about 6 genes (over 2KB) and 50 taxa, protein data.

Thanks again ! You have been very kind in helping me out, I truly appreciate you taking time.

Cheers,

Vinita

------------------------------------------------------------------------------------------------------------------
Dr. Vinita Gowda         
Asst. Professor                                                  Research Associate 
IISER Bhopal                                                     MRC 166, PO Box 37012

Dept. of Biological Sciences                              National Museum of Natural History  
ITI Campus Gas Rahat Building                        Washington, DC - 20013-7012
Govindpura, Bhopal -462 023                            USA
Madhya Pradesh, India                                      E-mail: gow...@si.edu

Phone: +91-755-4092314
Lab: +91-755-4092319                  

Fax: +91-755-4092392

Web: http://www.iiserbhopal.ac.in/profile.php?empid=MjAx&page=Biological%20Sciences&pid=42&id=43 
Web: http://botany.si.edu/staff/staffPage.cfm?ThisName=104&homepage=no                

Support: http://emailcharter.org/

    To unsubscribe from this group and all its topics, send an email to raxml+unsubscribe@googlegroups.com
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[Alexey Kozlov]

you're welcome :)

On 24.08.2016 07:21, Dr. Vinita Gowda wrote:
> Hi Alexey:
>
> I did contact the website managers and am yet to hear from them. However, the results are the same from Blackbox which
> we finally managed to use so I am assuming the algorithm is comparable. + our data set is so small that chance is the
> version might not matter to us - only about 6 genes (over 2KB) and 50 taxa, protein data.
>
> Thanks again ! You have been very kind in helping me out, I truly appreciate you taking time.
>
> Cheers,
>
> Vinita
>
> ------------------------------------------------------------------------------------------------------------------
> Dr. Vinita Gowda
> Asst. Professor Research Associate
> IISER Bhopal MRC 166, PO Box 37012
> Dept. of Biological Sciences National Museum of Natural History
> ITI Campus Gas Rahat Building Washington, DC - 20013-7012
> Govindpura, Bhopal -462 023 USA

> Madhya Pradesh, India E-mail: gow...@si.edu <mailto:gow...@si.edu>

> Phone: +91-755-4092314
> Lab: +91-755-4092319
> Fax: +91-755-4092392
>
> Web: http://www.iiserbhopal.ac.in/profile.php?empid=MjAx&page=Biological%20Sciences&pid=42&id=43
> Web: http://botany.si.edu/staff/staffPage.cfm?ThisName=104&homepage=no
> Support: http://emailcharter.org/
>

> On Wed, Aug 24, 2016 at 4:07 AM, Alexey Kozlov <alexei...@gmail.com <mailto:alexei...@gmail.com>> wrote:
>
> Hi Vinita,
>
> if they give you back RAxML_info* files, then you can find RAxML version in there. Otherwise, just contact the
> website maintainers...
>
> Best,
> Alexey
>
> On 23.08.2016 06:58, Dr. Vinita Gowda wrote:
>
> Dear Alexey:
>
> Thanks, I will share this information with our cluster in-charge and will read-up on this myself.

> One of my student is using the ETE3 server from genome.jp <http://genome.jp> <http://genome.jp> This is a very

> small protein data set and
> we found it to be easier to access than CIPRES. The only issue is that I cannot tell which version of RAxML they
> are using.
>
> Regards,
>
> Vinita
>
> ------------------------------------------------------------------------------------------------------------------
> Dr. Vinita Gowda
> Asst. Professor Research Associate
> IISER Bhopal MRC 166, PO Box 37012
> Dept. of Biological Sciences National Museum of Natural History
> ITI Campus Gas Rahat Building Washington, DC - 20013-7012
> Govindpura, Bhopal -462 023 USA
> Madhya Pradesh, India E-mail: gow...@si.edu <mailto:gow...@si.edu>

> <mailto:gow...@si.edu <mailto:gow...@si.edu>>

> Phone: +91-755-4092314
> Lab: +91-755-4092319
> Fax: +91-755-4092392
>
> Web: http://www.iiserbhopal.ac.in/profile.php?empid=MjAx&page=Biological%20Sciences&pid=42&id=43

> <http://www.iiserbhopal.ac.in/profile.php?empid=MjAx&page=Biological%20Sciences&pid=42&id=43>
> Web: http://botany.si.edu/staff/staffPage.cfm?ThisName=104&homepage=no

> To unsubscribe from this group and all its topics, send an email to raxml+un...@googlegroups.com
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