Re: Error reading pedigree file

From: Arthur <asremlforum_at_VSNI.CO.UK>
Date: Sat, 3 Oct 2009 00:09:37 +0100

Dear Matt,
Thanks for enclosing your code.
I ran the job on the latest code and it read the pedigree fine reporting

finalflyped.txt !ALPHA !MAKE !SKIP 1
 Reading pedigree file finalflyped.txt: skipping 1 lines
   37154 identities in the pedigree over 14 generations.
       Assuming first parent is Sire,
       Sires SiresofSire DamsofSire Dams SiresofDam DamsofDam
        4127 1089 1161 4712 1080 1159
 Using an adapted version of Meuwissen & Luo GSE 1992 305-313:
 PEDIGREE [finalflyped.txt ] has 37154 identities, 102186 Non zero elements
 GIV0 Ainverse 37154 7 -20260.88
So there is nothing fundamentally wrong with the pedigree.

Further more, the message you report indicates that the pedigree
contains 37154 individuals which is correct, so your version did manage
to read the whole file and identify the correct bumber of individuals.

If there are pedigree ordering problems, ASReml reports a (cryptic) message announcing them. Apparently your run did not report any such messages.

That leaves the possability that it is a memory problem and you need to
increase the workspace. My version defaults to 32Mbyte but earlier versions
defaulted to 8 or 16 Mbyte workspace.

If increasing workspace (e.g. -S5 option in ASReml 1 or 2)
does not resolve the issue, get back to me.

There is another problem; my run of your job reported

 Univariate analysis of tars
 Error at field 1 [2000638] of record 3400 [line 3400]
 Increase the number of levels DECLARED for factor nest
nest 1013 1983217 -1
year 13 1983 2000
foster 939 1983229 2000127
 Fault: Increase declared levels for factor nest
  Last line read was: 2000638 2000 BR99580 2000138 17.80 9.20 1.762 -0.989

Since it has read about 60% of the data, I suggest changing the
declaration part of the .as file to
        nest !I 1500 # 1413

        year !I

        ring !P

        foster !I 1400 #1333

Well 1500 and 1400 were my guesses, but 1413 and 1333 turn out to be the
correct numbers.

I trust this helps.

I have not looked at the model to consider whether I think it is reasonable.

Arthur Gilmour

Retired Principal Research Scientist (Biometrics)

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Received on Sun Oct 03 2009 - 00:09:37 EST

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