Help with Staden: I get get_comment invalid argument error.

Mike Noren mikemikemike at my-dejanews.com
Wed Jan 23 17:07:38 EST 2002


Just downloaded Staden 2001.0 for Windows. I've used Staden under
linux some two years ago and remember a little, but much have changed.

When I try to process my ABI files (which open fine in TREV), they
seem to pass (PREGAP4 puts them in the PASSED list), but every module
complains with this error message:

<module name>::run: couldn't execute "get_comment": invalid argument

And GAP4 can't read the output - it claims it's in the wrong format,
so apparently PREGAP hasn't in fact processed the file.


What I do is this:
* I fire up PREGAP.
* Using Addfiles I enter the ABI files (in this case just one).
* I've unchecked all modules except
Estimate, Trace, Initialize, Quality (and I've tried with GAP4 and
Enter checked).  
* Then I press RUN.

============================================================
Wed 23 Jan 23:01:46 2002: Terminating modules
------------------------------------------------------------
- Report Production -
Passed files:
    {C:/Program Files/Staden Package/userdata/sp1a.ab1} (ABI)

Failed files:

                       ***   Processing finished   ***
-------------------------------------------------------------
Wed 23 Jan 23:01:46 2002 init::run: couldn't execute "get_comment":
invalid argument
Wed 23 Jan 23:01:46 2002 eba::run: couldn't execute "get_comment":
invalid argument
Wed 23 Jan 23:01:46 2002 convert_trace::run: couldn't execute
"get_comment": invalid argument
Wed 23 Jan 23:01:46 2002 init_exp::run: couldn't execute
"get_comment": invalid argument
---------------------------------------------------------------------------------------------------

I've tried the example files which came with Staden, with the exact
same result.

Presumably it's something simple; I've not dotted an i or crossed a t
somewhere, but I'll be darned if I know where.


More info: What I want to do is to read in a series of lanes from an
ABI run, do a shotgun assembly, and output a consensus. Nothing fancy.
I'm running Windows XP Pro. I've obtained a license-file for Staden
and put it in the TABLES directory. GET_COMMENT.EXE does exist in the
Windows-bin directory, and is executable (but outputs nothing when run
from a DOS prompt).


Any help appreciated. 
Also, if someone knows of a tutorial or walk-through for Staden,
something which holds my hand a bit more than the Staden help does...


PS: Don't reply in email to the From: address of this post - it is a
junk account I use wherever spam-bots can be expected to be
patrolling; it's real but I never check it. Reply to this newsgroup,
or mail me at: mike_norenAThotmail.com, where AT should be replaced
with a @



Michael Norén, Doctoral student,
Stockholm University and                      Tel: Int +46 (0)8 5195 5163
Swedish Museum of Natural History,     Fax: Int +46 (0)8 5195 5181
                        "Nihil umquam facile" 




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