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deng-lab / viroprofiler

A containerized bioinformatics pipeline for viral metagenomic data analysis
https://deng-lab.github.io/viroprofiler
MIT License
23 stars 12 forks source link

Please update the database (From NCBI) #10

Open nitinShukla1912 opened 1 year ago

nitinShukla1912 commented 1 year ago

Description of the bug

Issue : Resolving ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)... failed: Name or service not known. wget: unable to resolve host address ‘ftp.ncbi.nih.gov’

Please update to this,

https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-06-01.zip

as the database you are using is old and (.nlm is missing)

Command used and terminal output

nextflow run deng-lab/viroprofiler -r main -profile singularity --mode "setup"

Relevant files

No response

System information

No response

rujinlong commented 1 year ago

Hi @nitinShukla1912, thanks for the feedback. Could you please check your network? I can download taxdump file with no problem (wget -O taxdump.zip https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2022-08-01.zip).

For updating to the new taxdump, I also need to update the mmseqs taxonomy database, which relied on the taxdump. This will take some time. I noticed you made a pull request, could you please push it to the dev-update_ncbi_taxa branch, not the main branch? I will merge it to the main branch when everything is tested successfully.