NCBI Will Retire rsync Support for FTP Downloads on June 1, 2026

[mruehlemann]

NCBI Will Retire rsync Support for FTP Downloads on June 1, 2026:
https://ncbiinsights.ncbi.nlm.nih.gov/2026/03/25/retire-rsync-support-ftp-downloads/

Apparently this affects MEDI download and database build already now.

In the download R script, I managed to get it running with this replacement code using wget:

ncbi_rsync <- function(url, out) {
  ret <- system2(
    "wget",
    c(
      "--retry-connrefused",
      "--waitretry=1",
      "--read-timeout=60",
      "--timeout=60",
      "-t", "1",
      "-O", out,
      url
    )
  )
  Sys.chmod(out, "0755")
  return(ret)
} 

and in the build_kraken.nf, adding the --use-ftp flag to the kraken2-build command seems to resolve additional issues

[ADGM]

Hi,

The download step of database.nf was throwing me errors, but I replaced the ncbi_rsync function in the download.R script with the code above and it now proceeds with the download_sequences step.

Previous error:

Command error:
@error: Unknown module 'genomes'
rsync error: error starting client-server protocol (code 5) at main.c(1850) [Receiver=3.4.1]
ERROR [2026-05-20 13:46:54] Failed downloading https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/051/903/755/GCA_051903755.1_Apium_graveolens_Challenger_Celery//GCA_051903755.1_Apium_graveolens_Challenger_Celery_genomic.fna.gz :(
ERROR [2026-05-20 13:46:55] Failed downloading https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/030/737/875/GCA_030737875.1_ASM3073787v1//GCA_030737875.1_ASM3073787v1_genomic.fna.gz :(
ERROR [2026-05-20 13:46:56] Failed downloading https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/038/502/295/GCA_038502295.1_RDA_Ac_1.0//GCA_038502295.1_RDA_Ac_1.0_genomic.fna.gz :(
ERROR [2026-05-20 13:46:58] Failed downloading https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/051/903/715/GCA_051903715.1_ASM5190371v1//GCA_051903715.1_ASM5190371v1_genomic.fna.gz :(
ERROR [2026-05-20 13:46:59] Failed downloading https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/047/404/395/GCA_047404395.1_ASM4740439v1//GCA_047404395.1_ASM4740439v1_genomic.fna.gz :(
ERROR [2026-05-20 13:47:00] Failed downloading https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/029/339/315/GCA_029339315.1_ASM2933931v1//GCA_029339315.1_ASM2933931v1_genomic.fna.gz :(
ERROR [2026-05-20 13:47:01] Failed downloading https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/122/585/GCA_026122585.1_DCI_ANoc_v1//GCA_026122585.1_DCI_ANoc_v1_genomic.fna.gz :(
ERROR [2026-05-20 13:47:02] Failed downloading https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/965/638/055/GCA_965638055.1_BOLBOS01.2//GCA_965638055.1_BOLBOS01.2_genomic.fna.gz :(

Thank you!

[cdiener]

Yep, we noticed the same. Great that they turned it off a month early. The next update of MEDI will use the NCBI Datasets CLI for Genome downloads, however Kraken2 will be harder to fix because it is not really maintained anymore.