fasta format running error..

[huku]

I have seen same question posted in January. Because I cannot find solution. I would like to post similar question again. 

I converted example file, dna.phy, to fasta format and tried to run RAXML with it. But, I got the following errors.

------(start) ---------- 

RAxML can't, parse the alignment file as phylip file 

it will now try to parse it as FASTA file

Fasta parsing error, RAxML expects an alignment.

the last sequence in the alignment seems to have a different length

-----(end)-----------

The converted fasta file is as follows. 

---(start)----

>Cow 60 bp

ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA

>Carp 60 bp

ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT

>Chicken 60 bp

ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC

>Human 60 bp

ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT

>Loach 60 bp

ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT

>Mouse 60 bp

ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA

>Rat 60 bp

ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT

>Seal 60 bp

ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA

>Whale 60 bp

ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC

>Frog 60 bp

ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA

---(end)-------

Even if I delete "60 bp", I get same error. 

I would greatly appreciate if someone gives me hint to resolve this problem. 

[huku]

I am using ver. 8.0.12 

[Alexandros Stamatakis]

can you please send me the fasta file as attachment?

thanks,

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

[Tae-Kun Seo]

Dear Dr. Alexandros Stamatakis,

Thank you for your reply. Here are my files.

Sincerely,
Tae-Kun Seo

2014-03-10 18:22 GMT+09:00 Alexandros Stamatakis
<alexandros...@gmail.com>:

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[Alexandros Stamatakis]

thanks for the data, the bug is fixed now in version 8.0.13

alexis

[Seo, Tae-Kun]

Thanks!

I will look into it.

Sincerely,
Tae-Kun

2014-03-12 오전 1:41, Alexandros Stamatakis 쓴 글:

[anirvan chatterjee]

Dear Alexis,

I am getting the same (Fasta parsing error, RAxML expects an alignment.

the last sequence in the alignment seems to have a different length) error.

I am using RAxML version 8.0.26. The fasta file is attahced herewith.

I am new to raxML and apologize for my ignorance. Your help will be greatly appreciated.

Thanks,
Anirvan

[Alexandros Stamatakis]

Dear Anirvan,

The sequences do have different lengths, so they ar enot in alignment,
check the last two seqs. in the fasta file:

>Vibrio cholerae ABC ATPase
MATVSLRKVEKKYENGFKAVHGIDLDIREGEFMVFVGPSGCAKSTTLRMIAGLESISGGEIRIGNKVVND
LPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKEEIKRRVEEAAEKLEITDLLYRKPKEMSGGQR
QRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRVKIAQLHQSLKEEGNPATMIYVTHDQTEALTLGDRI
CVLNLGKIMQVDTPANLYNYPANKFVASFIGSPAMNLIDTVIREDNGPLYIEISNGIRMFIPVEKQKALR
EYINKPVCFGIRPEHIRVAEPGDTINAFEGILTVVENMGNEKYLYFKVGGKELIARVNDQTITTADIGKP
IRFNLNTAFCHIFDFYSEKNLTNNRE
>T4 Terminase
MEQPINVLNDFHPLNEAGKILIKHPSLAERKDEDGIHWIKSQWDGKWYPEKFSDYLRLHKIVKIPNNSDK
PELFQTYKDKNNKRSRYMGLPNLKRANIKTQWTREMVEEWKKCRDDIVYFAETYCAITHIDYGVIKVQLR
DYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQAIELL
PDFLQPGIVEWNKGSIELDNGSSIGAYASSPDAVRGNSFAMIYIDECAFIPNFHDSWLAIQPVISSGRRS
KIIITTTPNGLNHFYDIWTAAVEGKSGFEPYTAIWNSVKERLYNDEDIFDDGWQWSIQTINGSSLAQFRQ
EHTAAFEGTSGTLISGMKLAVMDFIEVTPDDHGFHQFKKPEPDRKYIATLDCSEGRGQDYHALHIIDVTD
DVWEQVGVLHSNTISHLILPDIVMRYLVEYNECPVYIELNSTGVSVAKSLYMDLEYEGVICDSYTDLGMK
QTKRTKAVGCSTLKDLIEKDKLIIHHRATIQEFRTFSEKGVSWAAEEGYHDDLVMSLVIFGWLSTQSKFI

They clearly have different lengths, hence you need to fix your alignment.

Alexis

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[anirvan chatterjee]

Thanks Alexis for pointing this out.

[Adrian Allen]

Dear all, 

I'm having similar problems with raxml on my Mac.  I'm using a pipeline on a linux machine to construct a .fasta alignment, but when I try to run raxml on my Mac, I get the error message about the failure to parse and extra spaces in the final alignment.  I've checked the text file and can't see a problem.  All alignments look to have the same number of characters.  I've attached the non working alignment below.

Thanks

Adrian

[Lucas Czech]

Hi Adrian,

the file seems to work with RAxML 8.1.24 on Ubuntu. Which RAxML version are you using? Also, can you please copy the exact error message?!

One thing you can try is to add one line break after the last sequence. There is none, i.e., the file ends with the last character of a sequence. In unix-like systems (that is, also Mac), files are often expected to end with a single new line character after the last actual character.

If this also does not help, can you please zip the file and send it again. I am not sure whether the text format is changed when sending it as plain text, which makes reproducing the error problematic.

So long
Lucas

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[Alexandros Stamatakis]

Adrian,

Your file also works for the most up-to-date version of RAxML v 8.2.10.

You could also try the all new RAxML-NG and see if that works.

Alexis

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