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DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
GNU General Public License v3.0
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Error when downloading only bacteria version #260

Open dafin678 opened 1 year ago

dafin678 commented 1 year ago

Hi,

I always encounter this issue " Download failed! have a look at valid domains at ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq . ", when I run this script

# download all bacterial genomes from RefSeq to folder "library"

centrifuge-download -o library -m -d "bacteria" refseq > seqid2taxid.map

Help me please, I must finish it for my undergraduate thesis :(

Thank you, Regards

Dafin

mourisl commented 1 year ago

Which version of Centrifuge are you using? Do you have the intermediate file assembly_summary.txt from centrifuge-download command?

dafin678 commented 1 year ago

i use v1.0.4 which is the latest version, how to get the intermediate file assembly_summary.txt sir ? or i think, how to check the file was exist ?

mourisl commented 1 year ago

After a second thought, I think your issue might be different.

  1. Can you try to remove the quotes on the bacteria in your command?
  2. Do you have wget or curl on your system?
  3. If so, can you run wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt on your system?