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