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ManichanhLab / FunOMIC

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uhgg database index seems to be broken #1

Open mdhamedhussain opened 2 years ago

mdhamedhussain commented 2 years ago

Hello,

First of all, Thank you for your effort on developing a dedicated functional database for fungal metagenomics workflow. I am really looking forward to bring this into my workflow.

However, when I tried to run bowtie2 with the downloaded uhgg database (from the website), it gives bowtie2 error showing segmentation fault. I thought it might be a memory issue. I ran it on a system with higher memory but the issue remained.

Any chance we could get the uhgg fasta file used for building the index, so that we could build the index ourselves? Thanks once again!

ManichanhLab commented 1 year ago

Hi @mdhamedhussain

We have retrieved the uhgg fasta file from this site. http://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v1.0/uhgg_kraken2-db/library/

Hope my answer helps.

Best,

Zixuan