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"
