[EMBOSS] emma

[Staffa, Nick (NIH/NIEHS)]

Our emma from Jemboss was returning the input sequences in a fasta file
without aligning them.
>From command line we discovered that we had no clustalw!

SysAdmin obtained clustalw2 and made a symbolic link set to 'clustalw'
Running clustalw goes OK and generates this identification:
******** CLUSTAL 2.0.7 Multiple Sequence Alignments  ********

Command line emma in conjunction with this program generates this error:


rpmbuild.niehs.nih.gov> emma Multiple alignment program - interface to
ClustalW program Input (gapped) sequence(s):  Lemur_align.fasta output
sequence set [lemur.aln]: Dendrogram (tree file) from clustalw output file
[lemur.dnd]:  CLUSTAL 2.0.7 Multiple Sequence Alignments Error: parameter
required for /dnamatrix Error: Failed to open filename '00003189B' Problem
writing out EMBOSS alignment fileSegmentation fault rpmbuild.niehs.nih.gov>
Y¹d think the defaults would be sufficient.
Y¹d think that Jemboss would do a better job of reporting problems.


 
Nick Staffa 
Telephone: 919-316-4569  (NIEHS: 6-4569)
Scientific Computing Support Group
NIEHS Information Technology Support Services Contract
(Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov)
National Institute of Environmental Health Sciences
National Institutes of Health
Research Triangle Park, North Carolina