[EMBOSS] Error in EMMA

[George Magklaras]

Hi,

I am under the impression that the version of emboss you are using (4) 
is designed to interface to version 1.8x of clustalw and hence there 
could be difficulties. I think the interface to clustal 2.0.x series was 
addressed in a latter version of EMBOSS (5 or perhaps 6).

On my EMBOSS version 6.0.1 server, I ran this against clustalw 2.0.10 
flawlessly (files attached). So, I suggest that you either:

i)Upgrade to EMBOSS 6.0.1
ii)try to run emboss 4.0.0 emma with clustalw 1.8x .

Obviously i) is better than ii).

GM

-- 
--
George Magklaras BSc Hons MPhil
RHCE:805008309135525

Senior Computer Systems Engineer/UNIX-Linux Systems Administrator
EMBnet Technical Management Board
The Biotechnology Centre of Oslo,
University of Oslo
http://www.no.embnet.org


jean mao wrote:
> Hi,
> The version of EMBOSS I am using is 4.0.0. I received an error from 
> 'EMMA'. I will appreciate if someone can help me with this:
> 
> Error: Failed to open filename '00028079B'
> Problem writing out EMBOSS alignment file
> 
>  CLUSTAL 2.0.9 Multiple Sequence Alignments
> Error: parameter required for /dnamatrix
> 
> Under our .../htdocs/emboss/output/955836
> are files:
> 
> total 8
> -rw-r--r-- 1 webcpu webcpu 2121 Mar  2 09:18 00028079A
> -rw-r--r-- 1 webcpu webcpu    0 Mar  2 09:18 dendoutfile
> -rw-r--r-- 1 webcpu webcpu 3999 Mar  2 09:18 index.html
> -rw-r--r-- 1 webcpu webcpu    0 Mar  2 09:18 outseq
> 
> The sequences I used  is at the bottom of this message.
> 
> I did some googling on this and found someone suggested to modify emma.c 
> file to :
>      dna_matrix = ajAcdGetListSingle( "dnamatrix");
>      m2c = ajStrGetCharFirst(dna_matrix);
> 
>      if(m2c=='i')
>          ajStrAssignC(&m2str,"iub");
>      else if(m2c=='c')
>          ajStrAssignC(&m2str,"clustalw");
>      else if(m2c=='o')
>          ajStrAssignC(&m2str,"own");
> 
> I did that but still got the same error.
> 
> Could someone help me with this? Thank you very much.
> 
> Jean Mao
> 
>> gyrAprobe
> ttccgcagtttacgacaccatcgtccgtat
>> gyrA
> atgaccgacgcaaccatccgccacgaccacaaattcgccctcgaaaccctgcccgtcagc
> cttgaagacgaaatgcgcaaaagctatctcgactacgccatgagcgtcattgtcgggcgc
> gcgctgccggacgttcgcgacggcctaaagccggtgcaccggcgcgtactgtacgcgatg
> cacgagctgaaaaataactggaatgccgcctacaaaaaatcggcgcgcatcgtcggcgac
> gtcatcggtaaataccacccccacggcgattccgcagtttacgacaccatcgtccgtatg
> gcgcaaaatttcgctatgcgttatgtgctgatagacggacagggcaacttcggatcggtg
> gacgggcttgccgccgcagccatgcgctataccgaaatccgcatggcgaaaatctcacat
> gaaatgctggcagacattgaggaagaaaccgttaatttcggcccgaactacgacggtagc
> gaacacgagccgcttgtactgccgacccgtttccccacactgctcgtcaacggctcgtcc
> ggtatcgccgtcggtatggcgaccaacatcccgccgcacaacctcaccgacaccatcaac
> gcctgtctgcgtcttttggacgaacccaaaaccgaaatcgacgaactgatcgacattatc
> caagcccccgacttcccgaccggggcaaccatctacggcttgggcggcgtgcgcgaaggc
> tataaaacaggccgcggccgcgttgttatgcgcggtaagacccatatcgaacccataggc
> aaaaacggcgaacgcgaacgcatcgttatcgacgaaatcccctatcaggtcaacaaagcc
>> gyrANM
> atgaccgacgcaaccatccgccacgaccacaaattcgccctcgaaaccctgccggtaagc
> cttgaagacgaaatgcgcaaaagctatctcgactacgccatgagcgtcattgtcgggcgc
> gcgctgccggacgttcgcgacggtctcaagccggtacaccgccgcgtactgtacgcgatg
> cacgagctgaaaaacaactggaatgccgcctacaaaaaatcggcgcgcattgtcggcgac
> gtcatcggtaaataccacccccacggcgataccgccgtatacgacaccatcgtccgtatg
> gcgcaaaatttcgctatgcgttatgtgctgatagacggacagggcaacttcggatcggtg
> gacgggcttgccgccgcagccatgcgctacaccgaaatccgcatggcgaaaatttcccac
> gaaatgctggcagacattgaggaagaaaccgtcaatttcggcccgaactacgacggtagc
> gaacacgagccgcttgtactgccgacccgtttccccacactgctcgtcaacggctcgtcc
> ggcatcgccgtcggcatggcgaccaatatcccgccgcacaacctttctgataccgtcaat
> gcctgcctgcgcctgctcgatgcacccgacaccgaaatcgacgaactgatcgacattatc
> caagcccccgacttcccgaccggggcaaccatctacggcttgagcggcgtgcgcgaaggc
> tataaaacaggccgcggccgcgtcgttatgcgcggtaagacccatatcgaacccataggc
> agaaacggcgaacgcgaagccatcgttatcgacgaaatcccctatcaggtcaacaaagcc
>> gyrA338rt
> gccctcgaaaccctgccggtaagccttgaagacgaaatgcgcaaaagctatctcgactac
> gccatgagcgtcattgtcgggcgcgcgctgccggacgttcgcgacggtctcaagccggta
> caccgccgcgtactgtacgcgatgcacgaattgaaaaacaactggaatgccgcctacaaa
> aaatcggcacgcatcgtcggcgacgtcatcggtaaataccacccccacggcgataccgcc
> gtatacgacaccatcgtccgtatggcacaaaatttcgctatgcgttatgtgctgatagac
> ggacagggcaacttcggatcggtggacgggctgccgccgc
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> 




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