Kneaddata_database hangs halfway through download

Infrastructure and utilities KneadData
1

Hello,

I am new to processing shotgun metagenomic data and wanted to start off with KneadData (v0.12.0) to clean up my sequences. I am running into trouble with kneaddata_database installing the human genome database. It will get about 50-70% complete and then stop. For instance, the command and output would look like:

kneaddata_database --download human_genome bowtie2 /home/kneaddb
Download URL: http://huttenhower.sph.harvard.edu/kneadData_databases/Homo_sapiens_hg37_and_human_contamination_Bowtie2_v0.1.tar.gz
Downloading file of size: 3.48 GB

2.11 GB 60.52 % 7.49 MB/sec 3 min 8 sec

And freeze like this until the process is cancelled. I am currently using ubuntu through wsl which I thought maybe be causing issues so I have attempted the same install on a linux machine, but I run into the same issue of the database file not downloading. Attempting to download the database file with wget on either machine gives the same issue, stopping after about 2 GB.

Any advice would be appreciated!
-Sarah

2

For anyone having the same issue, I have found a workaround by installing the file with aria2 (https://aria2.github.io/). The command would just be:

aria2c -x 16 -s 16 http://huttenhower.sph.harvard.edu/kneadData_databases/Homo_sapiens_hg37_and_human_contamination_Bowtie2_v0.1.tar.gz

3

Hi @svancuren ,
Thank you for posting this work around for the download issue.
We are trying to resolve the download bandwidth issue on the server side. I would reccomend using the aria2 till the issue gets resolved.

Regards,
Sagun