[Bioclusters] weird errors from formatdb

[Wim Glassee]

Hi Jeremy,

I noticed the same errors and reported them to the NCBI, apparently the
problem has been fixed in version 2.2.5

Wim

Wim Glassee - BioInformatics Unit - Molecular Genetics Group - =
Department of
BioChemistry - University of Antwerp - BELGIUM - email: =
wim.glassee@ua.ac.be


> -----Original Message-----
> From: bioclusters-admin@bioinformatics.org [mailto:bioclusters-
> admin@bioinformatics.org] On Behalf Of Jeremy Mann
> Sent: donderdag 5 december 2002 17:02
> To: Bioclusters
> Subject: [Bioclusters] weird errors from formatdb
>=20
> After ryncing the BLAST databases from bio-mirror.net, I am now in the
> process of formatting. I am encountering stdout errors when formatting
> the nr database. Here is snip:
>=20
> <snip>
>=20
> formatdb] ERROR: nr.phrOutput
> Blast-def-line-set.E.<title>
> Invalid value(s) [1] in VisibleString
> [AIG1#gi|12324508|gb|AAG52213.1|AC022288_12 AIG1; 4264-2635 =
[Arabidopsis
> thaliana] ...]
> [formatdb] ERROR: nr.phrOutput
> Blast-def-line-set.E.<title>
> Invalid value(s) [1] in VisibleString [CsmE#gi|21648095|gb|AAM73279.1|
> chlorosome envelope protein E [Chlorobium tepidum TLS] ...]
> [formatdb] ERROR: nr.phrOutput
> Blast-def-line-set.E.<title>
> Invalid value(s) [1] in VisibleString [DppC#gi|1574113|gb|AAC22839.1|
> dipeptide ABC transporter, permease protein (dppC) [Haemophilus
> influenzae Rd] ...]
> [formatdb] ERROR: nr.phrOutput
> Blast-def-line-set.E.<title>
> Invalid value(s) [1] in VisibleString [K3R#gi|347484|gb|AAC37869.1| =
ORF
> C2L ...]
> [formatdb] ERROR: nr.phrOutput
> Blast-def-line-set.E.<title>
>=20
> </snip>
>=20
>=20
> I am using:
>=20
> uncompress -c nr.Z | formatdb -i stdin -o T -n nr
>=20
> Should I worry about these errors?
>=20
> Thanks.
>=20
>=20
> --
> Jeremy Mann
> jeremy@biochem.uthscsa.edu
>=20
> University of Texas Health Science Center
> Bioinformatics Core Facility
> Phone: (210) 567-2672