Unable to build db.

[abskumar]

I am getting error while running:
kraken2-build --standard --db kraken2_db

Error:
rsync: link_stat "/refseq/archaea/assembly_summary.txt" (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(1861) [Receiver=3.2.7]
Error downloading assembly summary file for archaea, exiting.

Please help.

[ideshigenomics]

code: kraken2-build --standard --threads 12 --db ~/kraken2-master/Kraken2_DB

Error:
rsync: link_stat "/all/GCF/030/643/725/GCF_030643725.1_ASM3064372v1/GCF_030643725.1_ASM3064372v1_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(1865) [generator=3.2.7]
rsync_from_ncbi.pl: rsync error, exiting: 5888

[jenniferlu717]

This happens when NCBI hasnt updated their assembly_summary.txt file to remove/change links that no longer work. The build should work after a couple days unfortunately.

You can remove the line containing that link in the assembly_summary.txt file and try to redownload or you can manually download the libraries (or use krakenuniq-download)

[abskumar]

It seems that the code is trying to download "assembly_summary.txt" files from various folders: archaea, viral, bacteria etc.
However, these files do not exist on NCBI site any more.
I believe NCBI has now a single composite file: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt
I am not sure how to process this.

[jenniferlu717]

Ah....Thanks for letting me know. We will have to update the kraken download scripts to accommodate this but this may take some time

[abskumar]

Thanks.
Will appreciate an update message when this is done.

[cement-head]

KRAKEN2 is broken:

 ./kraken2-build --standard --threads 24 --db kraken2-std-db
Downloading taxonomy tree 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

[josruirod]

Also struggling with this error, as in issue https://github.com/DerrickWood/kraken2/issues/847

jenniferlu717 has commented

This happens when NCBI hasnt updated their assembly_summary.txt file to remove/change links that no longer work. The build should work after a couple days unfortunately.

You can remove the line containing that link in the assembly_summary.txt file and try to redownload or you can manually download the libraries (or use krakenuniq-download)

Removing the line containing that genome in the assembly_summary.txt worked. I had to modify download_genomic_library.sh though, so assembly_summary is not recreated each execution of kraken2-build

[IrinaVKuznetsova]

Has the issue been fixed?
Thank you.

[Ivalize]

Hi,
@IrinaVKuznetsova you could try these two options:
#518

or (downloading and creating your own database)
https://benlangmead.github.io/aws-indexes/k2

I hope it helps you
Regards,