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Runing Checkm2 using MiDAS db #114

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Hedi65 opened this issue Sep 19, 2024 · 0 comments
Open

Runing Checkm2 using MiDAS db #114

Hedi65 opened this issue Sep 19, 2024 · 0 comments

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@Hedi65
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Hedi65 commented Sep 19, 2024

Hi

I am working with metagenomic data from waste water. it is quite common for us to use MiDAS database instead of Kraken2 for instance. i downloaded the taxonomy file from MiDAS website https://www.midasfieldguide.org/guide/downloads and created a DIAMOND db and i renamed the db to uniref100.KO.1.dmnd, and i replaced it with the checkm2 db file. i am doing this because i assume that the percentage of completeness and contamination linked directly with the db in use. However i am getting an error due to annotation.

here what i got

checkm2 predict --input /home/user/Downloads/Flye_Bins_Maxbin/*.fasta --output-directory /home/user/Downloads/Flye_Bins_Maxbin/F_MaxBin_checkm2_MiDAS --threads 12

[09/19/2024 11:31:33 AM] INFO: Running CheckM2 version 1.0.2
[09/19/2024 11:31:33 AM] INFO: Running quality prediction workflow with 12 threads.
[09/19/2024 11:31:34 AM] INFO: Calling genes in 8 bins with 12 threads:
Finished processing 8 of 8 (100.00%) bins.
[09/19/2024 11:32:00 AM] INFO: Calculating metadata for 8 bins with 12 threads:
Finished processing 8 of 8 (100.00%) bin metadata.
[09/19/2024 11:32:00 AM] INFO: Annotating input genomes with DIAMOND using 12 threads
[09/19/2024 11:32:02 AM] INFO: Processing DIAMOND output
[09/19/2024 11:32:02 AM] ERROR: No DIAMOND annotation was generated. Exiting

so i am wondering if it possible to run checkm2 using custom db (in my case) and if yes how i can solve this error.

thanks for your help

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