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Old 03-09-2011, 07:31 AM   #1
ElMichael
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Location: UK

Join Date: Jun 2009
Posts: 31
Default Grab bacterial genomes from NCBI

Hi! I want to download the whole batch of the bacterial genomes from NCBI. Here I found a way to do it but when I run command idfetch -c 1 -o bac_genomes -G bac.acc.lst -t 5 it gives me the following message:
Quote:
[idfetch] ERROR: GI=284047386|db=NULL|ent=0| Input
ID1server-back.gotseqentry.seq.annot.E.data.ftable.E.data.rna.<type>
8 is an invalid value for type.
[idfetch] ERROR: GI=284047386|db=NULL|ent=0| Input
ID1server-back.gotseqentry.seq.annot.E.data.ftable.E.data.rna.ext.
Unable to match element in ext.
[idfetch] ERROR: GI=284047386|db=NULL|ent=0| Input
ID1server-back.gotseqentry.seq.annot.E.data.ftable.E.data.rna.ext.
Did not AsnReadVal before AsnReadId. line 0
Could anybody, please, tell me how to retrieve genomes from NCBI using command line?

UPD: script from the mentioned post retrieved ~2500 genomes from the list of ~3500 genomes. I can't figure out what is the problem.

Last edited by ElMichael; 03-09-2011 at 09:25 AM.
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