RaxMl error "non-whitespace characters!" at end

[Hiren Ghosh]

MY error are listed bellow
I used mugsy for alignment after all i used bioperl to convert the file


use Bio::AlignIO;
 
$in  = Bio::AlignIO->new(-file => "mygenome_test.maf" ,
                         -format => 'maf');
$out = Bio::AlignIO->new(-file => ">mygenome_test_out.phy",
                         -format => 'phylip');
 
while ( my $aln = $in->next_aln ) {
  $out->write_aln($aln);
}
 

Now could not mangae the error
Can anyone please help me out...
Thanks


Oups, there is garbage at the end of your file:

10 651877
H3_chromos   TAGTTCACCA GAAAGGCCAC CGCTGAATGT TTGTCGATTA GTCCAGGTAT TCGCTGTACT
EC958_chro   TAGTTCACCA GAAAGGCCAC CGCTGAATGT TTGTCGATTA GTCCAGGTAT TCGCTGTACT
Ecoli_jj18   TAGTTCACCA GAAAGGCCAC CGCTGAATGT TTGTCGATTA GTCCAGGTAT TCGCTGTACT
H51_chromo   TAGTTCACCA GAAAGGCCAC CGCTGAATGT TTGTCGATTA GTCCAGGTAT TCGCTGTACT
H53_chromo   CAGTTCCCCA GAAAGGCCAC CGCTGAATGT TTGTCGATTG GTCCAGGTAT TCGCTGTACT
H63_chromo   CAGTTCCCCA GAAAGGCCAC CGCTGAATGT TTGTCGATTG GTCCAGGTAT TCGCTGTACT
V260_chrom   TAGTTCACCA GAAAGGCCAC CGCTGAATGT TTGTCGATTA GTCCAGGTAT TCGCTGTACT
V282_chrom   TAGTTCACCA GAAAGGCCAC CGCTGAATGT TTGTCGATTA GTCCAGGTAT TCGCTGTACT
V291_chrom   TAGTTCACCA GAAAGGCCAC CGCTGAATGT TTGTCGATTA GTCCAGGTAT TCGCTGTACT
V295_chrom   TAGTTCACCA GAAAGGCCAC CGCTGAATGT TTGTCGATTA GTCCAGGTAT TCGCTGTACT

             GAGTAACGGT ATTTTCTCCC CGCTTGTGCC GAGTTCTCGT AAACCGAGGT T-TAAATAAT
             GAGTAACGGT ATTTTCTCCC CGCTTGTGCC GAGTTCTCGT AAACCGAGGT TTTAAATAAT
             GAGTAACGGT ATTTTCTCCC CGCTTGTGCC GAGTTCTCGT AAACCGAGGT TTTAAATAAT
             GAGTAACGGT ATTTTCTCCC CGCTTGTGCC GAGTTCTCGT AAACCGAGGT TTTAAATAAT
             GAGTAACGGT ATTTTCTCCC CGCTTGTGCC GAGTTCTCGT AAACCGAGGT T
 .... and so on


RAxML correctly finished parsing your PHYLIP file,
but there seems to be garbage at the end of the file, i.e., non-whitespace characters!
RAxML will exit now

[Alexandros Stamatakis]

Hi Hiren,

Could it be that your sequences are longer than indicated?

In any case, please send me the alignment and I will check.

Alexis

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[Gloria Wang]

Hi,

I ran into the same problem. is there any solution for this problem?

[Alexandros Stamatakis]

Hi Gloria,

Check if there is garbage at the end of the file and delete it.

If that doesn't work please send us the alignment file that is
generating the error.

Alexis

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> Alexandros (Alexis) Stamatakis
>
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> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> University
> of Arizona at Tucson
>

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www.exelixis-lab.org

[Stefany Solano Gonzalez]

Hello!

I had the same problem. In my case my pipeline was the following (maybe that's the root of my problem):

1) Ran progressiveMauve and produced an alignment with *.xmfa extension

2) Used Lee Katz perl script to convert the .xmfa to phy extension

3) Used that Phylip file as input to run RaxML (raxmlHPC-PTHREADS-SSE3)

4) Got the following message from RaxML: "RAxML correctly finished parsing your PHYLIP file, but there seems to be garbage at the end of the file, i.e., non-whitespace characters! RAxML will exit now"

5) Double check the alignment but seems normal to me

Can you spot the issue? 

Best wishes,

Stefany

[Alexandros Stamatakis]

Hi Stefany,

First of all please use the new version of RAxML-NG
(https://github.com/amkozlov/raxml-ng), as standard RAxML is not
supported any more.

Regarding spotting the issue you would need to send me the alignment file.

Alexis

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas

www.exelixis-lab.org