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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