[EMBOSS] Error in EMMA

[jean mao]

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