[BiO BB] Error messages when running blastpgp (NCBI PSI-BLAST)
Osnat Dafni
dafniosn at post.tau.ac.il
Wed Nov 1 04:46:43 EST 2006
The database was downloaded as a fasta file, and I used NCBI's "formatdb" before
running blastpgp. Unfortunately I don't have the exact command line used with
formatdb, but I did not used any special options - everything was set to
default.
I have some hints that this is a memory issue: when I remove half the sequences
from the input file, the errors go away, and when I decrease the value of
parameters such as -e and -h (e-value cut-offs), I get less error lines.
However, it still puzzles me why would changing the output format with -m (as I
wrote in my previous message) eliminates the errors (or perhaps just reduces
them for the input file size I'm using for my debugging).
Quoting Iddo Friedberg <idoerg at burnham.org>:
> Osnat Dafni wrote:
>
> need more info.. how did you formatdb your database?
>
> Iddo
>
> > Hi,
> >
> > I'm trying to run the local version of ncbi psi-blast (blastpgp) using a
> > self-generated database and a fasta query file. I get the following error
> > messages repeatedly while the program runs:
> >
> > [NULL_Caption] ERROR: ncbiapi [000.000] BioseqFindFunc: couldn't uncache
> > [NULL_Caption] ERROR: ncbiapi [000.000] ObjMgrNextAvailEntityID failed
> with idx
> > 2048
> >
> > I'm using the following command line:
> >
> > blastpgp -d db_file -i query_file -e 1.0 -m 8 -o output_file -I T -a 2 -j 4
> -h
> > 0.001
> >
> > While experimenting I've noticed that when replacing the option "-m 8"
> (tabular
> > output format) with "-m 0" (default output format), the errors go away.
> >
> > Does any one has any information about what could be causing these errors?
> > Thanks in advance.
> >
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>
> --
>
> Iddo Friedberg, Ph.D.
> Burnham Institute for Medical Research
> 10901 N. Torrey Pines Rd.
> La Jolla, CA 92037
> Tel: (858) 646 3100 x3516
> Fax: (858) 795 5249 ** NEW **
> http://iddo-friedberg.org
> http://BioFunctionPrediction.org
>
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