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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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Return of the FTP error- rsync_from_ncbi.pl: unexpected FTP path (new server?) #847

Open Madeleine-Meyer opened 3 months ago

Madeleine-Meyer commented 3 months ago

Hello everyone,

I am trying to download the standard Kraken2 database and I'm having issues with the rsync_fromncbi.pl file. Here is my terminal input and the resulting output and error:

Input: kraken2-build --standard --db Kraken2_standard_database_NCBI

Output: Downloading nucleotide gb accession to taxon map... done. Downloading nucleotide wgs accession to taxon map... done. Downloaded accession to taxon map(s) Downloading taxonomy tree data... done. Uncompressing taxonomy data... done. Untarring taxonomy tree data... done. rsync_from_ncbi.pl: unexpected FTP path (new server?) for https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/762/265/GCF_000762265.1_ASM76226v1

Obviously, I Googled the error and when I opened rsync_from_ncbi.pl I saw that the original if statement causing the problems has already accounted for NCBI's switch to https. I tired every variation I could think of swapping out ftp and https and I'm out of ideas. Is the NCBI database having issues or has something changed and does the code need updating?

For reference, I installed Kraken2 under 48 hours ago, so I am using the most up-to-date versions of the code.

Also, edited to add that I get the same error if I try the following as well: kraken2-build --download-library bacteria --db Kraken2_standard_database_NCBI

BioJM commented 2 months ago

Hello，I've encountered the same issue as well. Have you found a solution?

ChillarAnand commented 2 months ago

@Madeleine-Meyer , @BioJM How did you install kraken2? From source or using conda?

Madeleine-Meyer commented 2 months ago

@Madeleine-Meyer , @BioJM How did you install kraken2? From source or using conda?

Hello @ChillarAnand, I used the source code. I haven't found a solution yet but I've been side stepping the issue for the time being by just building my own custom library with only the species I'm interested in.

ChillarAnand commented 2 months ago

Are you using any tools to download specific species data? @Madeleine-Meyer

Madeleine-Meyer commented 2 months ago

Are you using any tools to download specific species data? @Madeleine-Meyer

No, I just downloaded what I wanted from GenBank (https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=780). My downloads weren't particularly large, so I didn't need to use NCBI's command line tools https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/. I have never used their command line tools, but will likely give them a try in the near future.

SamCT commented 2 months ago

This is still a significant issue. I am not keen to rewriting a series of interlinked perl scripts. Hoping that the Kraken2 devs can come to a quick fix so we can have an Kraken2 db that is up-to-date with a broad set of refseq species.