No such file or directory at AOM/downloadHandler.pm line 89.

[LittleFrogHill]

Hi all,

I used the conda installed the alienomics_v0.3.2, but I can't download the third-party database. I used command line "micromamba run -n alienomics alienomics_v0.3.2 -dd -ddf BURT -ddl /home/shangao/Data/alienomics_database" and error showed likes this:
/\ | | |__ |\ | / \ |/| | / /__
/~~\ |___ | |___ | | _/ | | | _, .__/ 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

Wed, 15 May 2024 14:51:08 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 >>>

Wed, 15 May 2024 14:51:08 Checking alienomics mandatory modules
Wed, 15 May 2024 14:51:08 Installing third party databases for Alienomics
output folder: /home/shangao/Data/alienomics_database/third_party_DB/

Wed, 15 May 2024 14:51:08 NCBI taxonomic database
downloading taxdump
No such file or directory at AOM/downloadHandler.pm line 89.

Can you help me fix this? I checked the folder there is no AOM in the conda/env/alienomics_v0.3.2, it located in a cache then.

Bests,
Shan

[jnarayan81]

Hi @LittleFrogHill
The AOM/downloadHandler.pm module, available at this link, contains hardcoded links to the NCBI taxonomy database, which appear to be outdated. For the time being, please download the latest taxonomy database from NCBI's FTP server and run Alienomics with BUR instead of BURT values.

We will fix it in next version.
Thanks
Jit

[LittleFrogHill]

Thank you for reply.
The module from your link I also found from the previous version, butt not work for me. I will try when you fixed the problem.

Bests,
Shan