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Old 07-15-2013, 11:55 AM   #1
akjones
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Location: North America

Join Date: Jun 2013
Posts: 24
Question "uninitialized value" in ABACAS

Hello all,

I've recently starting working with ABACAS as part of the PAGIT suite of programs. After one run with altered parameters for identity, word size etc. in nucmer I got this printed in my terminal window:

Use of uninitialized value $g in addition (+) at /home/pagit/bin/PAGIT/ABACAS/abacas.pl line 1124.
Use of uninitialized value $g in print at /home/pagit/bin/PAGIT/ABACAS/abacas.pl line 1231.
Use of uninitialized value $g in print at /home/pagit/bin/PAGIT/ABACAS/abacas.pl line 1236.
Use of uninitialized value $n in numeric lt (<) at /home/pagit/bin/PAGIT/ABACAS/abacas.pl line 740.

Should I be concerned? I did some searching of "uninitialized value" and "uninitialized value perl" and the results did not make it clear as to whether or not I should be concerned or make a change, it seemed to vary with the program/script in question. Any experienced ABACAS users feel free to put in their 2 cents...as a matter of fact feel ENCOURAGED to put in your 2 cents! As an fyi I have been running PAGIT/ABACAS in a linux virtual machine (ubuntu) on MacOSX. As another fyi I'm not terribly experienced with computers, and am prone to asking basic questions (trying to avoid dropping the "S" bomb).

Thanks for any help,
~Ana
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Old 07-29-2013, 04:27 AM   #2
ThomasDOtto
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Location: Cambrdige, UK

Join Date: Mar 2012
Posts: 12
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Hi,

does this post resolves the issue?
http://seqanswers.com/forums/showthr...933#post111933

Cheers,
Thomas
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