rsync error while using standard build

[jquxch1]

Hello,

I am trying to execute the standard build of the Kraken database and I recieved this error:

rsync: link_stat "/all/GCF/000/837/285/GCF_000837285.6_ASM83728v2/GCF_000837285.6_ASM83728v2_genomic.fna.gz" (in genomes) failed: No such file or directory (2)
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1518) [generator=3.0.9]
rsync_from_ncbi.pl: rsync error, exiting: 5888

I recently changed the rsync_from_ncbi.pl script due to the error that many people having on #508, so perhaps that may have to do with that?

Any help would be appreciated.

[shengxin450]

Perhaps the current network network and NCBI connection is not stable, this time, there is no other way, can only try for many times. Or you can download the taxonomic files (Taxonomy) first, and then download the sequence files of the standard database for humans, bacteria, archaea, etc. respectively, and then build the library. Like this:
(1) kraken2-build --threads 56 --db ~/kraken2_db --download-taxonomy
(2) kraken2-build --threads 56 --db ~/kraken2_db --download-library bacteria
(3) kraken2-build --threads 56 --db ~/kraken2_db --download-library viral
(4) kraken2-build --threads 56 --db ~/kraken2_db --download-library archaea
(5) kraken2-build --threads 56 --db ~/kraken2_db --download-library UniVec_Core
......
kraken2-build --build --threads 56 --db ~/kraken2_db
By the way, when I download the virus sequence file, I have the same problem as you have, maybe the standard database build error is due to the virus database problem？！祝你顺利