The bioBakery help forum

Unable to download and install Kneaddata database

HI, I have insttalled kneaddata via pip install. Now, I am trying to download and install kneaddata database by the following command:
kneaddata_database --download human_genome bowtie2 ~/Desktop/
But, it reverts following error:

 Download URL: http://huttenhower.sph.harvard.edu/kneadData_databases/Homo_sapiens_hg37_and_human_contamination_Bowtie2_v0.1.tar.gz
CRITICAL ERROR: Unable to download and extract from URL: http://huttenhower.sph.harvard.edu/kneadData_databases/Homo_sapiens_hg37_and_human_contamination_Bowtie2_v0.1.tar.gz

The download link is also not working when I tried to open the link from my browser.

Thanks,
DC7

Hi user,

Apologies for the inconvenience. We had a server outage last week due to which kneaddata_database --download human_genome bowtie2 ~/Desktop/ was failing.

It should work now.

Regards,
Sagun

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Hello!
I am experiencing the same error today as DC7 had reported regarding downloading the human_genome database that you provided. I installed kneaddata using conda, and used the following code in a ssh:

kneaddata_database --download human_genome bowtie2 ./human_genome

Would you be able to assist please?
Thanks!
Brooke

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I think may be due to server problem…
Please try after sometime… my problem was solved when I tried again after few hours…

Thanks

Hello.
I also have the same error when downloading the database you provided. I am trying to download the database with the following code.

kneaddata_database --download human_genome bowtie2 ./genome/

DownloadURL:http://huttenhower.sph.harvard.edu/kneadData_databases/Homo_sapiens_hg37_and_human_contamination_Bowtie2_v0.1.tar.gz 
CRITICAL ERROR: Unable to download and extract from URL:http://huttenhower.sph.harvard.edu/kneadData_databases/Homo_sapiens_hg37_and_human_contamination_Bowtie2_v0.1.tar.gz

I’ve been experiencing errors since yesterday. It is confirmed that the download link no longer works, what should I do?

Thanks,
Seula

I receiving the same error when I try to download the database. Past posts suggest waiting an hour or two, then trying again.

I faced the same issue.
Posted in another thread, hoping to get some assistance.

Hi user,

Apologies for the inconvenience. We had a server outage over the weekend due to which downloads were failing.

It should work now.

Regards,
Sagun

1 Like