Re: [GUSDEV] Out of Memory while loading Taxonomy data

[<ju...@cs...>]

"Kumar, Sanjeev" <San...@ng...> writes:
>
>    I am getting 'out of memory' error while loading the Taxonomy data.
>    I remember Jian Lu got this error earlier, but I couldn't find any
> solution in the archive.
>    Pl. suggest me to resolve the issue.

I recently ran into this issue as well. I got the same error that was
mentioned in the list archives, which looks something like
this:

Out of memory!
Issuing rollback() for database handle being DESTROY'd without explicit disconnect(), <MERGED> line xxx.
Issuing rollback() for database handle being DESTROY'd without explicit disconnect(), <MERGED> line xxx.

and the line number will vary depending on what *.dmp files you use.

What was happening was that in the merged.dmp file at line xxx was the
entry:

  88745	|	87265	|

and this entry would cause LoadTaxon to run endlessly until
the memory on my machine ran out.  I deleted the line
from merged.dmp and LoadTaxon would run successfully.

Without investigating "why" this line in merged.dmp would cause
this problem, I can think of two possible reasons:

  This line is an error/bug on NCBI's part.

  This line illustrates a case that the author(s) of LoadTaxon
  never considered.

I look forward to other peoples comments.


Josef



Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

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