[EMBOSS] emma: problem with filename : please help

[Duhaime Johanne]

Thank you to both of you.

You were right: it depends on the clustalw version. I had installed version 2 but version 1 was also in my path. Clustalw 2.0 was the first in the path but there was a permission problem so clustalw 1 was used. Sorry!

Now it works fine for protein alignement. But I still have a problem with a nucleic acid file

mercure{duhaimj}111: emma multiplenucleic.tfa
Multiple alignment program - interface to ClustalW program
output sequence set [ai632122.aln]:
Dendrogram (tree file) from clustalw output file [ai632122.dnd]:



 CLUSTAL W 2.0 Multiple Sequence Alignments


Error: parameter required for /dnamatrix
Error: Failed to open filename '00019719B'
Problem writing out EMBOSS alignment fileSegmentation fault
mercure{duhaimj}112: more multiplenucleic.tfa
>AI632122 Description:  ts85b08.x1 NCI_CGAP_GC6 Homo sapiens cDNA clone IMAGE:2238039 3',
TTCATTAATTTGCATTTATTTTCGGGAAGTAATGTAGATAAAGAGGAGGAGGGAGACTGC
CTTACATTTCAACAAGTAATTTGTGATCTTCACATCAGACAAATCAAATTTACAAATTAC
TTTCCCACCTACTGGACGAAGCGGCCAAAGCCAAAATTGATACACAGGCGCGCGGGCTCT
CCGCAGATTTCGGAGAACGAAGGTGCACTAAAAACTCACTAGACAAAACAAGGGTGTTGA
AAGAGAGAAGCCGACAGAGGAGTTGGAACTGGGTTTGGGGCCTGGGTTTGTTTGTTTTTC
CCTAATGCTGTACTTTTACGGATTTTGTTTTGTTTTGT
>AI813505 LOCUS       AI813505      530 bp    mRNA            EST       21-DEC-1999
GCGGCCGCCACCGGGTTCCCACCTAGTCCCGCAGCCGCTGCAGCCGCTGGGTTGGCGGAA
GAGCTGGACGCCGAGCTAGAGGACGAGGCAGAGCTGGACACAGCTGGCGGCGTGAATTGG
CCACTGCTTTCGGAGCCCGAGCTCTCCCGCACTGGAGAGGACTTCTTCTTGGCTGGGCGG
CTCTTGGTTCCGCTCCCGCTCTGCTGCTGCTGGCGGCATTTGTCGCGGCGGTTCTTGAAC
CAGACCTGGACTCTAGACTCCGGCAGGTTGATCTTGAGCGCCACCTCCTCCCGCATGAAG
ATGTCAGGGTAGCGAGTCTTGGCGAAGAGCGCCTCGAGCACGTCCAGCTGTGAACGCGTG
AAGGTGGTGCGCTCCCGCCGCTGCTTCCGCGGAGTGGCCGGATAGCCCACGGATGGGTGC
AGGAGGTCCATGGCGGGCCCGGCCAGGCCCAGCCCGTTCATGCCGTATGGGGGTTGTTTG
AGGTAAGACATCATGCTAACAGCTGGGTGGAGGCGCCCCGACGGATCCAG
>AI813507 LOCUS       AI813505      530 bp    mRNA            EST       21-DEC-1999
GCGGCCGCCACCGGGTTCCCACCTAGTCCCGCAGCCGCTGCAGCCGCTGGGTTGGCGGAA
GAGCTGGACGCCGAGCTAGAGGACGAGGCAGAGCTGGACACAGCTGGCGGCGTGAATTGG
CCACTGCTTTCGGAGCCCGAGCTCTCCCGCACTGGAGAGGACTTCTTCTTGGCTGGGCGG
CTCTTGGTTCCGCTCCCGCTCTGCTGCTGCTGGCGGCATTTGTCGCGGCGGTTCTTGAAC
CAGACCTGGACTCTAGACTCCGGCAGGTTGATCTTGAGCGCCACCTCCTCCCGCATGAAG
ATGTCAGGGTAGCGAGTCTTGGCGAAGAGCGCCTCGAGCACGTCCAGCTGTGAACGCGTG
AAGGTGGTGCGCTCCCGCCGCTGCTTCCGCGGAGTGGCCGGATAGCCCACGGATGGGTGC
AGGAGGTCCATGGCGGGCCCGGCCAGGCCCAGCCCGTTCATGCCGTATGGGGGTTGTTTG
AGGTAAGACATCATGCTAACAGCTGGGTGGAGGCGCCCCGACGGATCCAG

Thank you so much...
Johanne


-----Message d'origine-----
De : Peter Rice [mailto:pmr at ebi.ac.uk]
Envoyé : Wednesday, 16 April 2008 08:58
À : Duhaime Johanne
Cc : emboss-bug at emboss.open-bio.org
Objet : Re: [EMBOSS] emma: problem with filename : please help

Duhaime Johanne wrote:

> In the old mail 2002. It was reported that the problem could be sold by changing the code in emma.c.

That was a different problem with temporary filenames on Linux.

> %emma
> Multiple alignment program - interface to ClustalW program
> Input (gapped) sequence(s): multipleprotein.tfa
> output sequence set [hs70_achkl.aln]:
> Dendrogram (tree file) from clustalw output file [hs70_achkl.dnd]:
>
> Error: Failed to open filename '00022023B'

Do you have clustalw installed? Emma needs clustalw installed as it is a
wrapper.

The 00023023A file is the input to clustalw. The missing 00023023B file
is the alignment output by clustalw.

Can you send the input file you used (multipleprotein.tfa), and if
possible the version of clustalw you have installed (running clustalw
from the command line should tell you).

regards,

Peter Rice