Centrifuge Database Download Error

[DanMan-09]

I'm trying to install the database, the first step,

centrifuge-download -o taxonomy taxonomy

worked fine, but when I tried

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

it gave many errors as such

Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/assembly_summary.txt ...
Downloading 471 archaea genomes at assembly level Complete Genome ... (will take a while)
ssh: Could not resolve hostname https: Name or service not known
rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
rsync error: unexplained error (code 255) at io.c(235) [Receiver=3.1.2]

Error downloading https://rsync.ncbi.nlm.nih.gov/genomes/all/GCF/000/762/265/GCF_000762265.1_ASM76226v1/GCF_000762265.1_ASM76226v1_genomic.fna.gz!
ssh: Could not resolve hostname https: Name or service not known
rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
rsync error: unexplained error (code 255) at io.c(235) [Receiver=3.1.2]

[MardahlM]

I also experience this issue. Can anyone help?

[mourisl]

Are other download programs (i.e. "curl" or "wget") available on your system?

[MardahlM]

I use a Docker container for Centrifuge 1.0.4 and use curl to download.

[sanderdebacker]

As mentioned in Issue#67, centrifuge-download now has the option to specify the download program with -g.

[beckdac]

@sanderdebacker That -g option conflicts with another -g option and therefore it doesn't always work correctly.

[Altay88]

Hi,

I faced the same problem with the download genomes from NCBI. Can anyone help?

centrifuge-download -P 32 -o library -m -d "archaea,bacteria,viral,fungi" refseq > seqid2taxid.map

Error downloading https://rsync.ncbi.nlm.nih.gov/genomes/all/GCF/029/338/215/GCF_029338215.1_ASM2933821v1/GCF_029338215.1_ASM2933821v1_genomic.fna.gz!
rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
ssh: Could not resolve hostname https: Temporary failure in name resolution
rsync error: unexplained error (code 255) at io.c(231) [Receiver=3.2.7]
rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
rsync error: unexplained error (code 255) at io.c(231) [Receiver=3.2.7]
ssh: Could not resolve hostname https: Temporary failure in name resolution