RAxML-HPC BlackBox ERROR

[ERIKA JULIANA OBANDO MONTOYA]

Hello everyone

I am using RAxMl via Cipres for a phylogeny project. My database have 212 protein sequences. But I havent obtained any tree in the results files. I was looking for in the stdout.txt  and I found an error message saying:

This is RAxML MPI Process Number: 5
ERROR: Sequences out of alignment
40 (instead of 52) residues read in sequence 2 ----------
Printing error context:

-------- --------MD
             AEPKRKF

In other hand, I found this message in the phylip sfu page

In PHYLIP, enter 'I' (to change to sequential), change any other options, and then 'y' to begin the analysis. 

With luck, the taxon names will scroll across the screen (with user trees you will see no progress until the program is done computing). 

Otherwise, you may get a message: sequences out of alignment, or base ratios wrong. Maximum likelihood, which is computationally intensive and 

one of the slowest programs on earth, is much faster with user trees but again the progress of the run is not indicated. 

Nevertheless I don't understand what that mean.

Someone can explain me what are happened and how I can stop the problem?

but the way, the sequences titles are some like this:

BV

1503

3922

Cw112

Cw77

Ge0

Ge3

Gloe

Gv5

Thanks,

[Alexandros Stamatakis]

RAxML uses a relaxed PHYLIP format that is specified here:

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

Apart from that you can send me your alignment to my personal email such
that I can have a look what might be wrong.

Alexis

> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> For more options, visit 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

www.exelixis-lab.org

[Mark Miller]

For CIPRES runs, you should of course try the docs Alexis suggested, but if you cant figure it out you can also send a bug report to cipres. If you have run the job in the past two weeks, and include the file _JOBINFO.TXT we should be able to help.

Best,

Mark

[ERIKA JULIANA OBANDO MONTOYA]

Thank you Professor Alexis

Could you give me your email address?

[ERIKA JULIANA OBANDO MONTOYA]

Thank you Mark 

Yes, I tried run the project this week and I have the JOBINFO.TXT file. Nevertheless I worked in a not login way. 

the Guest user was: Guest-1519745095735

date 2/27/18, 08:31

If not this is the information inside JOBINFO.TXT file

Task\ label=VV
Task\ ID=1420112
Tool=RAXMLHPC2BB
created\ on=2018-02-27 08:31:56.0
JobHandle=NGBW-JOB-RAXMLHPC2BB-D146DA163C044B44B091E52EEC100DC2
resource=comet
User\ ID=109979
User\ Name=Guest-1519745095735
email=1519745095735

Output=(raxml_outputfiles,RAXML_*,UNKNOWN,UNKNOWN,UNKNOWN),(all_outputfiles,*,UNKNOWN,UNKNOWN,UNKNOWN)
ChargeFactor=1.000000
cores=24
JOBID=14526601

Thanks in advance

[Alexis]

I had a look at your alignment file, and also tried executing it with RAxML, I was able to start an analysis of file: 

FDBRs.phy without any problems, so I don't know where the problem could be, maybe you didn't specify that it is a protein alignment? 

Alexis 

[ERIKA JULIANA OBANDO MONTOYA]

Thanks for you quickly response

not, it was not that. I specified that was a protein alignment.

thank you any way.

[Alexandros Stamatakis]

Then there's mot much more I can do from my side as I am not responsible
for maintining the CIPRES server,

Alexis

[ERIKA JULIANA OBANDO MONTOYA]

Hello

I would like ask help again. I couldnot result my problem so I decided make the aligment using nucleotid database but I have the same problem. I did not obtain the tree and the error mesages is the same. 

Problem reading alignment file 
ERROR: Sequences out of alignment
40 (instead of 52) residues read in sequence 2 ----------
Printing error context:

-----atg gacgccgagc
             ccaagag

This time I use my personal count so I was enregistered. Ny username is anailujakire

Could you help me? I attached the aligment phy file too. 

Thanks in advance

El miércoles, 28 de febrero de 2018, 10:42:09 (UTC-5), Mark Miller escribió:

[Alexandros Stamatakis]

Could you please have a look at the relaxed phylip format specification
in the RAxML manual (I sent you the link) first.

This should help you to understand why your file can't be parsed.

Alexis

[msf....@gmail.com]

Hello,

I am having a similar problem...

ERROR: Sequences out of alignment

23 (instead of 100) residues read in sequence 9 ----------------------------------------------------------------------------------------------------

Printing error context:

-------------------

Nomascus

Problem reading alignment file 

My .phy file (converted in PAUP) seems to be organized correctly? I also noticed in your manual that RAxML says that there needs to be a space between the taxon ID and sequence, which my file has...otherwise white space does not make a difference?

Do you have any suggestions on how to format my alignment file?

Thank you!

[Alexandros Stamatakis]

Can you send me the alignment file to my personal email, such that I can
have a look?

Alexis

> > an email to raxml+un...@googlegroups.com <javascript:>
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.

> > 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
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>

[raxml]

Hi Margot,

I looked at the files you sent me: 

1. They are in FASTA format and not in PHYLIP 

2. The command line version of RAxML can read them, but not the web-server 

3. So you can either use the comman dline version of RAxML or upload phylip formatted files to the web-server.

Alexis 

[Margot P]

Hi Alexis,

Thank you so much for looking at this. I had converted my .aln files to phylip, which was what I was using in the RAxML command on the command line, but I think there may have been a formatting issue. I adjusted the white space in the phylip format and I got it to run. Example:

SampleSequenceID

NucleotideSequence.......

Does RAxML prefer phylip files to be formatted a certain way? I thought I had read in the manual that it was flexible with spacing.

Thanks again for your help, I really appreciate it.

To unsubscribe from this group and stop receiving emails from it, send an email to raxml+unsubscribe@googlegroups.com.

[Alexandros Stamatakis]

> Thank you so much for looking at this. I had converted my .aln files to
> phylip, which was what I was using in the RAxML command on the command
> line, but I think there may have been a formatting issue. I adjusted the
> white space in the phylip format and I got it to run. Example:
>
> SampleSequenceID
> NucleotideSequence.......

Interesting.

> Does RAxML prefer phylip files to be formatted a certain way? I thought
> I had read in the manual that it was flexible with spacing.

Yes, it should be, if you could send me the Phylip files that didn't
work I can investigate further.

> Thanks again for your help, I really appreciate it.

:-)

Alexis