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  • ElMichael
    Member
    • Jun 2009
    • 31

    #1

    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:
    [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, 10:25 AM.

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