Error Messages from RaxML Black Box

[Aja Michelle]

Hi,

I'm an undergraduate student who's new to both phylogenetics and RaxML.  I've utilized the available search option to query the group about the error messages I'm getting while attempting to utilize RaxML Black Box, without resolution.  I have a data set of 179 species, with sequences just over 1000 bps in length.  I have converted my aligned sequences from FASTA format to PHYLIP.  I've received several different error messages in return, including "could not read data: TOO FEW SPECIES."

I don't think I have too few species with 179 in total. 

How do I fix this? 

Thank you in advance!

~Aja  

[Alexandros Stamatakis]

It's probably an issue with the phylip format, please read page 6

in http://sco.h-its.org/exelixis/oldPage/RAxML-Manual.7.0.4.pdf

I assume that there is a space missing between taxon names and the
sequences.

RAxML uses relaxed PHYLIP format.

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

[Aja Michelle]

Hi Alexis! 

...seems my original reply to your post has been deleted.

Thank you so much for your response! :)
 
I went through and checked my formatting to make sure I had only one single space between my taxon and sequence, and to include a return carriage at the to signal the end of each row.  When I resubmitted to blackbox, I received a new error message stating that the alignment could not be read.  I did a group search and found a thread where you suggested to someone else that they should utilize the "-f c" algorithm to see if the alignment can be properly read by RaxML and if not, the reason for this.  I discovered that two of my sequences were misaligned because they were slightly shorter than the others.  This was an error on my part when I was checking the formatting; I accidentally deleted one of the bps.  I corrected the misalignment and then checked the formatting again.  This time the error message was that I had two identical pairs. 

"IMPORTANT WARNING: Sequences A.allisoni.40_1\ and A.allisoni.40_5\ are exactly identical

IMPORTANT WARNING: Sequences A.porcatus.51_1.2.3\ and A.porcatus.51_4\ are exactly identical

IMPORTANT WARNING
Found 2 sequences that are exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.

Just in case you might need it, an alignment file with
sequence duplicates removed is printed to file 07phylip.txt.reduced
Alignment format can be read by RAxML"

I chose the reduced file for my resubmission to BlackBox and it WORKED!!! SUCH a relief!

But please, give me your opinion.  There is not a lot of data available on these species and keeping the identical sequences seems beneficial.  The sequences are all from four different anoles respectively.  What do you think?

Thanks again!

~Aja

[Alexandros Stamatakis]

I believe that the issue of identical sequences has been discussed on
this group before. It will not add any signal or information if you have
two exactly identical sequences.

Alexis

On 07/02/2013 02:16 AM, Aja Michelle wrote:
> Hi Alexis!
>
> ...seems my original reply to your post has been deleted.
>
> Thank you so much for your response! :)
>
> I went through and checked my formatting to make sure I had only one single
> space between my taxon and sequence, and to include a return carriage at
> the to signal the end of each row. When I resubmitted to blackbox, I
> received a new error message stating that the alignment could not be read.
> I did a group search and found a thread where you suggested to someone else
> that they should utilize the "-f c" algorithm to see if the alignment can
> be properly read by RaxML and if not, the reason for this. I discovered
> that two of my sequences were misaligned because they were slightly shorter
> than the others. This was an error on my part when I was checking the
> formatting; I accidentally deleted one of the bps. I corrected the
> misalignment and then checked the formatting again. This time the error
> message was that I had two identical pairs.
>

> *"IMPORTANT WARNING: Sequences A.allisoni.40_1\ and A.allisoni.40_5\ are

> exactly identical
>
> IMPORTANT WARNING: Sequences A.porcatus.51_1.2.3\ and A.porcatus.51_4\ are
> exactly identical
>
> IMPORTANT WARNING
> Found 2 sequences that are exactly identical to other sequences in the
> alignment.
> Normally they should be excluded from the analysis.
>
> Just in case you might need it, an alignment file with
> sequence duplicates removed is printed to file 07phylip.txt.reduced

> Alignment format can be read by RAxML"*

[Danielle Wasserman]

Hello group,

I'm getting the same error message, " Could not read data: too few species". I try copy pasting and uploading file, same result. I added a partition but I couldn't get it to work before that. I went ahead and attached the sequence rich text file in case there's a mistake that's easy to spot. This is my first time using blackbox. I have only one gene in this run. 48 species. Hopefully it's an easy fix!   -Danielle

[Danielle Wasserman]

I realize any uploaded file must be phylip but i can't download the software for a few days which is why I'm trying to use blackbox (should copy-paste).

[Mark Miller]

Hi Danielle,

I can help with that. There are a couple of issues with your data set. The first issue, the one causing the problem you are seeing is that there is a carriage return that creates a blank line between the header (48 960)

and the first line of the matrix. This violates Phylip format rules, and creates the impression to raxml that your data set is null. Hence the error message too few (zero) species, since you said there were 48. 

So first remove that line break. Because of the quirks of formatting and parsing, the subsequent carriage returns after each sequence are all ok. 

Second, your first taxon contains a blank space between genus and species.

As Alexis mentioned above, relaxed format thinks blank space means "end of taxon name, now the sequence begins", so you will get an error saying the first non-allowed dna letter in

borneensis  is a bad base. In this case it will be "e".

So but an underscore between genus and species, and then life should be good.

Best,

Mark

[Olivia Zhang]

Hello

I am a master student in biology in LMU. I have 185 sequences with 2300 amino acids. They were aligned by MAFFT. The alignment was converted to PHYLIP format by EMBOSS Seqret. The phylip file worked in RaxML blackbox. But when I tried to improve the alignment in Jalview to get rid of some gaps, the modified alignment in PHYLIP format cannot be read by RaxML Blackbox. It said:" Could not read data: The file /tmp/phpzn0VMc.phylip you want to open for reading does not exist, exiting .." Yet the modified alignment in FASTA format saved in a mfa generated by Jalview can be read and the program can run. I really don't know what to do.

Thank you in advance

Olivia Zhang

 

在 2013年6月30日星期日 UTC+2上午9:23:24，Aja Michelle写道：

[Alexandros Stamatakis]

Hi Olivia,

Are you using the blackbox for this as well?

The error message you are getting indicates that the file is not there,
did you maybe forget to upload it?

Alexis

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