centrifuge-download not working with "vertebrate_mammalian"

Question

[gastonviarengo]

Hello,

I'm trying to build an index on Centrifuge as detailed in https://ccb.jhu.edu/software/centrifuge/manual.shtml#database-download-and-index-building. So far I was able to download archaeal, bacterial and viral genome assemblies but when I try to download human and mouse genomes nothing happens and I get the detailed list of arguments for the "centrifuge-download" command. I'm using :

centrifuge-download -o library -d "vertebrate_mammalian" -a "Chromosome" -t 9606 -c 'reference genome' >> seqid2taxid.map

as detailed in the manual. I believe the command line is OK so I don't seem to find out where the mistake is (or maybe something else is happening). As an alternative I've downloaded all data for human genome GRCh38.p12 from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.38_GRCh38.p12/ but I am not sure that would be correctly recognized later when I have to build the index.

I would really appreciate your help since I'm stuck here and I can't continue without having the human and mouse genomes downloaded in order to build the centrifuge index.

Thank you!

Answer 1

[Bastien Hervé]

Hello, You have to input the database you want to search in (refseq, genbank, contaminants, taxonomy) :

<database>        One of refseq, genbank, contaminants or taxonomy:
                      - use refseq or genbank for genomic sequences,
                      - contaminants gets contaminant sequences from UniVec and EmVec,
                      - taxonomy for taxonomy mappings.

Something like :

centrifuge-download -o library -d 'vertebrate_mammalian' -a "Chromosome" -t 9606 -c 'reference genome' refseq > seqid2taxid.map
centrifuge-download -o library -d 'vertebrate_mammalian' -a "Chromosome" -t 9606 -c 'reference genome' taxonomy