Staffa, Nick (NIH/NIEHS) wrote:
******** CLUSTAL 2.0.7 Multiple Sequence Alignments ********
Command line emma in conjunction with this program generates this error:
CLUSTAL 2.0.7 Multiple Sequence Alignments Error: parameter
required for /dnamatrix Error: Failed to open filename '00003189B'
There is a bug in emma, not noticed before because Clustalw 1.x
tolerated the command line.
In emboss/emma.c the code for option dnamatrix should be:
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");
(the characters tested for m2c were from another command line option so
the dnamatrix option was not being passed to clustalw).
Clustalw 1.8.x ignored the empty /dnamatrix string on the commmand line.
Y'd think the defaults would be sufficient.
They are now :-)
Y'd think that Jemboss would do a better job of reporting problems.
It is always tricky when the error is reported by another application
invoked through EMBOSS.
My favourite emma error was a Taverna workflow that failed when
executing an emma webservice. Clustalw crashed. The cause turned out to
be a user-generated FASTA file with bad end of line characters in the
sequence so the sequences became part of the first ID and emma launched
clustalw with a set of zero length sequences. We "fixed" it by requiring
all EMBOSS sequences to have at least one valid character so we can now
issue an EMBOSS error.
regards,
Peter
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