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jnarayan81 / Alienomics

Automated pipeline for HGT and contaminant detection in an assembled, annotated genome
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Problem database download #2

Open qhelleu opened 1 year ago

qhelleu commented 1 year ago

Hi jnarayan81,

I installed alienomics with conda (as described in the wiki), and I tried to download the databases, but it doesn't work:

$ alienomics_v0.3.2 -dd -ddf BURT -ddl ./alien_DB/

/\ | | | |\ | / \ |\/| | / ` /` /~~\ | | | | | _/ | | | _, .__/ v0.3

Automated pipeline for HGT and contaminant detection in an assembled, annotated genome Contact: jnarayan81@gmail.com and polo.simion@gmail.com for support

lun., 20 mars 2023 13:42:35 Starting database download

| \ _ | | _ _ | |
| |) | / \ \ V V | ' \ | | / \ / | / _ | / -) | '| |_/ _/ _/_/|||| || \/ _,| _,| __| ||
|"""""|"""""|"""""|"""""|"""""|"""""|"""""|"""""|"""""|"""""| "-0-0-"-0-0-"-0-0-"-0-0-"-0-0-"-0-0-"-0-0-"-0-0-"-0-0-"-0-0-' v0.0.1

Automated alienomics dependencies downloader >>>

lun., 20 mars 2023 13:42:35 Checking alienomics mandatory modules lun., 20 mars 2023 13:42:35 Installing third party databases for Alienomics output folder: ./alien_DB//third_party_DB/

lun., 20 mars 2023 13:42:35 NCBI taxonomic database downloading taxdump No such file or directory at AOM/downloadHandler.pm line 89.

####################################################################### I think, the link for taxdump has changed since the latest version of alienomics. Can you confirm? Thanks.

jnarayan81 commented 1 year ago

Thank you for reporting this; it appears that there are some dependencies with the configuration file over here. The link appears to be operational. I'll update it in the next release. Please do it manually for the time being :(