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Mutation analysis and trace diff in the Staden software package Version-2003.0b1

Ingrid Revet I.m.revet at amc.uva.nl
Thu Jul 10 03:11:52 EST 2003


Dear professor,

In april this year I downloaded the Staden software package 
Version-2003.0b1
Since then I have been trying to analyse sequence files for mutations.
Unfortunately I couldn't get the "mutation analysis" sub-program working.
Although I am a molecular biologist I tried to discover the problem 
(with a lot of help of people who do work with computers!)
I think that the "Mutation detection" sub-program tries to run 
"trace_diff".
I'll include the error message, why I think that, over here:

- Report from 'Mutation Detection' -
ERR: couldn't execute "trace_diff": no such file or directory

There is no "trace_diff.exe" included in the Staden package.
There is a "tracediff.exe"
So I simply tried copying that program and changing its name in 
trace_diff.exe.
Unfortunately that didn't help either.
I didn't get an error message by the "report of Mutation Detection", but 
with the "failed files".
The first part of that is included here, the rest you'll find underneath 
this message.

Failed files:
{D:/Ingrid/Sequence/MSX1 exon1/3077t51controle.exp} (EXP) 'trace_diff: 
Unknown option -S, ignoring.Unable to open experiment file 4.0, 
skipping.\nUnable to open experiment file -s, skipping.

I think that a different version of tracediff is included in the Staden 
package.
The version the Mutation detection program needs isn't included in the 
package.
The version that is included in the Staden package is: tracediff v2.00. 
MRC Laboratory of Molecular Biology, Copyright (C) 2002. All Rights 
Reserved.
But like I said, I am not an expert, so I hope you can help me with 
finding the solution of the problem.
Thanks in advance.

Sincerely,

Ingrid Revet



Failed files:
  {D:/Ingrid/Sequence/MSX1 exon1/3077t51controle.exp} (EXP) 'trace_diff: 
Unknown option -S, ignoring.Unable to open experiment file 4.0, 
skipping.\nUnable to open experiment file -s, skipping.\nUnable to open 
experiment file 50, skipping.\nUnable to open experiment file -e, 
skipping.\nUnable to open experiment file 400, skipping.\nUnable to open 
experiment file -b, skipping.\nUnable to open experiment file 50, 
skipping.\nUnable to read PR record from experiment file 
D:/Ingrid/Sequence/MSX1 exon1/3077t51controle.exp, assuming forward 
strand.'
  {D:/Ingrid/Sequence/MSX1 exon1/3078t51controle.exp} (EXP) 'trace_diff: 
Unknown option -S, ignoring.Unable to open experiment file 4.0, 
skipping.\nUnable to open experiment file -s, skipping.\nUnable to open 
experiment file 50, skipping.\nUnable to open experiment file -e, 
skipping.\nUnable to open experiment file 400, skipping.\nUnable to open 
experiment file -b, skipping.\nUnable to open experiment file 50, 
skipping.\nUnable to read PR record from experiment file 
D:/Ingrid/Sequence/MSX1 exon1/3078t51controle.exp, assuming forward 
strand.\nInsufficient sequence overlap to compute trace alignment for 
D:/Ingrid/Sequence/MSX1 exon1/3078t51controle.ztr.'
  {D:/Ingrid/Sequence/MSX1 exon1/3077c6.exp} (EXP) 'trace_diff: Unknown 
option -S, ignoring.Unable to open experiment file 4.0, 
skipping.\nUnable to open experiment file -s, skipping.\nUnable to open 
experiment file 50, skipping.\nUnable to open experiment file -e, 
skipping.\nUnable to open experiment file 400, skipping.\nUnable to open 
experiment file -b, skipping.\nUnable to open experiment file 50, 
skipping.\nUnable to read PR record from experiment file 
D:/Ingrid/Sequence/MSX1 exon1/3077c6.exp, assuming forward strand.'
  {D:/Ingrid/Sequence/MSX1 exon1/3078c6.exp} (EXP) 'trace_diff: Unknown 
option -S, ignoring.Unable to open experiment file 4.0, 
skipping.\nUnable to open experiment file -s, skipping.\nUnable to open 
experiment file 50, skipping.\nUnable to open experiment file -e, 
skipping.\nUnable to open experiment file 400, skipping.\nUnable to open 
experiment file -b, skipping.\nUnable to open experiment file 50, 
skipping.\nUnable to read PR record from experiment file 
D:/Ingrid/Sequence/MSX1 exon1/3078c6.exp, assuming forward 
strand.\nInsufficient sequence overlap to compute trace alignment for 
D:/Ingrid/Sequence/MSX1 exon1/3078c6.ztr.'
  {D:/Ingrid/Sequence/MSX1 exon1/3077c7.exp} (EXP) 'trace_diff: Unknown 
option -S, ignoring.Unable to open experiment file 4.0, 
skipping.\nUnable to open experiment file -s, skipping.\nUnable to open 
experiment file 50, skipping.\nUnable to open experiment file -e, 
skipping.\nUnable to open experiment file 400, skipping.\nUnable to open 
experiment file -b, skipping.\nUnable to open experiment file 50, 
skipping.\nUnable to read PR record from experiment file 
D:/Ingrid/Sequence/MSX1 exon1/3077c7.exp, assuming forward strand.'
  {D:/Ingrid/Sequence/MSX1 exon1/3078c7.exp} (EXP) 'trace_diff: Unknown 
option -S, ignoring.Unable to open experiment file 4.0, 
skipping.\nUnable to open experiment file -s, skipping.\nUnable to open 
experiment file 50, skipping.\nUnable to open experiment file -e, 
skipping.\nUnable to open experiment file 400, skipping.\nUnable to open 
experiment file -b, skipping.\nUnable to open experiment file 50, 
skipping.\nUnable to read PR record from experiment file 
D:/Ingrid/Sequence/MSX1 exon1/3078c7.exp, assuming forward 
strand.\nInsufficient sequence overlap to compute trace alignment for 
D:/Ingrid/Sequence/MSX1 exon1/3078c7.ztr.'

-- 
._._._._._._._._._._._._._._._._._._._._._._._._._._._. 
Ingrid Revet
Ph. D. student
Academic Medical Center - University of Amsterdam
Department of Human Genetics 
M1-159, Meibergdreef 9
P. O. Box 22660
1100 DD Amsterdam
The Netherlands
Tel (31)20-5666592
_._._._._._._._._._._._._._._._._._._._._._._ _._._._._.


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