output file is not written

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whitec...@gmail.com

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Nov 11, 2014, 3:48:14 AM11/11/14
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Hi,
I noticed that the raxmlHPC-PTHREADS-SSE3 exection is finished without error but the output file designated by -n was not written. Is it normal and would it have been the same as RAxML_bestTree.fileName where fileName is the output file name? could RAxML_bestTree.fileName be considered as the final tree. here is the command line

raxmlHPC-PTHREADS-SSE3 -f a -x 12345 -p 12345 -N 100 -s fileName -n fileName.tre -m PROTGAMMAJTT -T 20

Thanks

Carol

Alexandros Stamatakis

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Nov 11, 2014, 4:09:17 AM11/11/14
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Dear Carol,

Please read the manual at:

http://sco.h-its.org/exelixis/resource/download/NewManual.pdf

Alexis
--
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

whitec...@gmail.com

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Nov 11, 2014, 9:35:48 AM11/11/14
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Hi,
I reran raxml, got no error msg and still the output file was not created. according to your manual, if 2 runs are carried out in the dir, raxml generates an err msg and doesn't write in the output as it is confusing. Didn't find another case when raxml doesn't write into the output file that could explain my case. perhaps I overlooked.

thanks for your help and advices,

Alexandros Stamatakis

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Nov 13, 2014, 5:04:00 AM11/13/14
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the command line you use should generate a best ML tree that is written
to a file called RAxML_bestTree.runID did it write such a file?

Alexis

whitec...@gmail.com

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Nov 13, 2014, 5:33:29 AM11/13/14
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yes, it did and it contains the scores.is it the tree file? I thought that it should generate a file with the name given by -n

Chees,

Alexandros Stamatakis

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Nov 13, 2014, 8:52:09 AM11/13/14
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it should contain the tree, not the scores, the name passed by -n is
appended to all output files of a run,

alexis

On 13.11.2014 11:33, whitec...@gmail.com wrote:
> yes, it did and it contains the scores.is it the tree file? I thought that
> it should generate a file with the name given by -n
>
> Chees,
>
> On Thursday, November 13, 2014 11:04:00 AM UTC+1, Alexis wrote:
>>
>> the command line you use should generate a best ML tree that is written
>> to a file called RAxML_bestTree.runID did it write such a file?
>>
>> Alexis
>>

whitec...@gmail.com

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Nov 13, 2014, 9:05:47 AM11/13/14
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so the info file says

Found 1 tree in File RAxML_bestTree.myfile.tre

Best-scoring ML tree written to: RAxML_bestTree.myfile.tre

so this file contains the score and the labels.

other files are info, bipatition and bootstrap with the same name. no more files

am I missing any file?

Alexandros Stamatakis

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Nov 13, 2014, 9:34:02 AM11/13/14
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Yes, the RAxML_bestTree.myfile.tre contains the tree topology in Newick
format with branch lengths.

On 13.11.2014 15:05, whitec...@gmail.com wrote:
> so the info file says
>
> Found 1 tree in File RAxML_bestTree.myfile.tre
>
> Best-scoring ML tree written to: RAxML_bestTree.myfile.tre
>
> so this file contains the score and the labels.
>
> other files are info, bipatition and bootstrap with the same name. no more
> files
>
> am I missing any file?
>
> On Thursday, November 13, 2014 2:52:09 PM UTC+1, Alexis wrote:
>>
>> it should contain the tree, not the scores, the name passed by -n is
>> appended to all output files of a run,
>>
>> alexis
>>

Lu Santo

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Oct 19, 2016, 8:49:07 AM10/19/16
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Hi,

The RAxML_bestTree.runID is not being written at the end of my run.

I am using this command line:
raxmlHPC-MPI -m GTRGAMMA -p 12345 -d -N 200 -s input.phylip -n runID

The run proceeds with no errors, but at the end I only get the following outputs: RAxML_log.runID.RUN.N, RaxML_randomTree.runID.RUN.N, RAxML_result.runID.RUN.N (with N = 0-200 for the three file types), and RAxML_info.runID. 

I have successfully obtained the RAxML_bestTree.runID for several other runs, but it is not working for this particular one (run twice with the same result). In this problematic case, I noticed that the RAxML_info.runID lacks any further information after the 200 inferences (attached).

Any ideas on what the problem is?

Thanks,

Lu


RAxML_info.runID

Alexandros Stamatakis

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Oct 21, 2016, 3:27:28 AM10/21/16
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1. You should use the most up to date RAxML version 8.2.9
2. Probably you will need to wait a bit for the final tree, is the
process still running? The final optimizations do take some time.

alexis
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