Open sachinharle opened 2 months ago
Im in the same boat. Im trying to trouble shoot now to see if I can come up with a fix as no one has responded yet. Of course, this looks like your request was put in on Friday, so maybe they'll get back to us today.
Interesting, this unfortunately happens when NCBI includes a link in their files that does not connect to an actual file. Kraken2 just uses the data provided by NCBI to determine which filepaths to download. I do not have a solution except to suggest downloading the full standard pre-built database here: https://benlangmead.github.io/aws-indexes/k2
thank you for the reply. I used the prebuilt file as suggested from : [(https://benlangmead.github.io/aws-indexes/k2)]
When building barcken database with following command:
racken-build -d /media/fgl/Data/Databases/kraken2/k2_standard_20240112 -t 96 -k 35 -l 76
it gives error
ERROR: Database taxonomy /media/fgl/Data/Databases/kraken2/k2_standard_20240112/taxonomy/nodes.dmp does not exist
where can I get or generate nodes.dmp
file?
I found the solution for my question : get or generate nodes.dmp file?
I renamed ktaxonomy.tsv
file available with prebuilt database k2_standard_20240112 to nodes.dmp
and put it in taxonomy folder and it worked. thanks again.
I get the following error when building kraken2 database:
rsync: link_stat "/all/GCF/037/914/965/GCF_037914965.1_ASM3791496v1/GCF_037914965.1_ASM3791496v1_genomic.fna.gz" (in genomes) failed: No such file or directory (2)
'GCF_037914965.1_ASM3791496v1_genomic.fna.gz', this exact file does not exist at :
https://ftp.ncbi.nlm.nih.gov/genomes//all/GCF/037/914/965/GCF_037914965.1_ASM3791496v1/
Please help me out here