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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(
(
gyrAprobe:0.02810,
gyrA:-0.02810)
:0.06455,
gyrANM:0.00867,
gyrA338rt:0.00604);
>gyrANM
ATGACCGACGCAACCATCCGCCACGACCACAAATTCGCCCTCGAAACCCTGCCGGTAAGC
CTTGAAGACGAAATGCGCAAAAGCTATCTCGACTACGCCATGAGCGTCATTGTCGGGCGC
GCGCTGCCGGACGTTCGCGACGGTCTCAAGCCGGTACACCGCCGCGTACTGTACGCGATG
CACGAGCTGAAAAACAACTGGAATGCCGCCTACAAAAAATCGGCGCGCATTGTCGGCGAC
GTCATCGGTAAATACCACCCCCACGGCGATACCGCCGTATACGACACCATCGTCCGTATG
GCGCAAAATTTCGCTATGCGTTATGTGCTGATAGACGGACAGGGCAACTTCGGATCGGTG
GACGGGCTTGCCGCCGCAGCCATGCGCTACACCGAAATCCGCATGGCGAAAATTTCCCAC
GAAATGCTGGCAGACATTGAGGAAGAAACCGTCAATTTCGGCCCGAACTACGACGGTAGC
GAACACGAGCCGCTTGTACTGCCGACCCGTTTCCCCACACTGCTCGTCAACGGCTCGTCC
GGCATCGCCGTCGGCATGGCGACCAATATCCCGCCGCACAACCTTTCTGATACCGTCAAT
GCCTGCCTGCGCCTGCTCGATGCACCCGACACCGAAATCGACGAACTGATCGACATTATC
CAAGCCCCCGACTTCCCGACCGGGGCAACCATCTACGGCTTGAGCGGCGTGCGCGAAGGC
TATAAAACAGGCCGCGGCCGCGTCGTTATGCGCGGTAAGACCCATATCGAACCCATAGGC
AGAAACGGCGAACGCGAAGCCATCGTTATCGACGAAATCCCCTATCAGGTCAACAAAGCC
>gyrA338rt
------------------------------------GCCCTCGAAACCCTGCCGGTAAGC
CTTGAAGACGAAATGCGCAAAAGCTATCTCGACTACGCCATGAGCGTCATTGTCGGGCGC
GCGCTGCCGGACGTTCGCGACGGTCTCAAGCCGGTACACCGCCGCGTACTGTACGCGATG
CACGAATTGAAAAACAACTGGAATGCCGCCTACAAAAAATCGGCACGCATCGTCGGCGAC
GTCATCGGTAAATACCACCCCCACGGCGATACCGCCGTATACGACACCATCGTCCGTATG
GCACAAAATTTCGCTATGCGTTATGTGCTGATAGACGGACAGGGCAACTTCGGATCGGTG
GACGGGCT-GCCGCCGC-------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
>gyrAprobe
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-----------------------------TTCCGCAGTTTACGACACCATCGTCCGTAT-
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
>gyrA
ATGACCGACGCAACCATCCGCCACGACCACAAATTCGCCCTCGAAACCCTGCCCGTCAGC
CTTGAAGACGAAATGCGCAAAAGCTATCTCGACTACGCCATGAGCGTCATTGTCGGGCGC
GCGCTGCCGGACGTTCGCGACGGCCTAAAGCCGGTGCACCGGCGCGTACTGTACGCGATG
CACGAGCTGAAAAATAACTGGAATGCCGCCTACAAAAAATCGGCGCGCATCGTCGGCGAC
GTCATCGGTAAATACCACCCCCACGGCGATTCCGCAGTTTACGACACCATCGTCCGTATG
GCGCAAAATTTCGCTATGCGTTATGTGCTGATAGACGGACAGGGCAACTTCGGATCGGTG
GACGGGCTTGCCGCCGCAGCCATGCGCTATACCGAAATCCGCATGGCGAAAATCTCACAT
GAAATGCTGGCAGACATTGAGGAAGAAACCGTTAATTTCGGCCCGAACTACGACGGTAGC
GAACACGAGCCGCTTGTACTGCCGACCCGTTTCCCCACACTGCTCGTCAACGGCTCGTCC
GGTATCGCCGTCGGTATGGCGACCAACATCCCGCCGCACAACCTCACCGACACCATCAAC
GCCTGTCTGCGTCTTTTGGACGAACCCAAAACCGAAATCGACGAACTGATCGACATTATC
CAAGCCCCCGACTTCCCGACCGGGGCAACCATCTACGGCTTGGGCGGCGTGCGCGAAGGC
TATAAAACAGGCCGCGGCCGCGTTGTTATGCGCGGTAAGACCCATATCGAACCCATAGGC
AAAAACGGCGAACGCGAACGCATCGTTATCGACGAAATCCCCTATCAGGTCAACAAAGCC
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