Failure to creating the reference database and index of nr_euk

[AlexSongh]

Hi I have a problem when downloading the euk_nr database using the slurm scripts I have installed a kaiju conda environment, and run the following codes

My HPC settings were #SBATCH --ntasks-per-node=8 #SBATCH --mem-per-cpu=16GB #SBATCH --nodes=1 #SBATCH --cpus-per-task=1

my codes are as follows:

source ~/.bachrc 
conda activate kaiju 
cd /nfs/turbo/cee-raskin/hangsong
mkdir kaijudb
cd kaijudb
kaiju-makedb -s nr_euk

I have following issues, do you know what's wrong and how to solve this?

Thanks!

[pmenzel]

Hm I don't know. Maybe the file got corrupted during download.

btw, check the README to see how much memory you need for building the database.

[AlexSongh]

I have enough memory in the storage account. Which I have 3 TB storage. But when I download it, it showed broken pipe. Then I changed to a slurm scripts. Do you know how to solve this issue?

[pmenzel]

I was thinking about RAM, not storage. Maybe it's better for you to download the index from the web server, see https://kaiju.binf.ku.dk/server

[AlexSongh]

Thank you!