Unable to download and install Kneaddata database

Infrastructure and utilities KneadData
1

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

2

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

1 Like
3

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

1 Like
4

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

Thanks

7

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

8

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

9

I faced the same issue.
Posted in another thread, hoping to get some assistance.
https://forum.biobakery.org/t/difficulty-downloading-databases-in-humann3/1343/20

10

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
11

Hi, I’m also having this problem. I keep getting this error :

 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
Unable to install database. Error running command: kneaddata_database --download human_genome bowtie2 /home/ec2-user/biobakery_workflows_databases/kneaddata_db_human_genome

I’ve been trying to get this installed for the past 4 days.
Help please! Thank you

12

I have installed Kneaddata via pip install yesterday and am unable to download the database.

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

Is this issue related to a server issue?

Thanks,
Shrez

13

I have installed Kneaddata via pip install yesterday and am unable to download the database.

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

Is this problem related to a server issue?

Thanks,
Shrez

14

Hi, I am bumping this thread since I also can’t download the database,

I just installed the conda version (kneaddata v0.12.0) with mamba and did the following

kneaddata_database --download human_genome bowtie2 KNEADDB

I got this critical 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

I even tried aria2c as a workaround as suggested here…

I also tried to manually downloading this this wget… and got

ERROR: El certificado de «huttenhower.sph.harvard.edu» no es confiable.
ERROR: El certificado de «huttenhower.sph.harvard.edu» no tiene un emisor conocido.

so I guess it is a server issue…

Thanks for your help

A

15

I get a sample issue. the command “wget http://huttenhower.sph.harvard.edu/kneadData_databases/Homo_sapiens_hg37_and_human_contamination_Bowtie2_v0.1.tar.gz --no-check-certificate”should work fine. However, I don’t know if there will be any differences between this method and using kneaddata_database --download

1 Like
16

the issue from the in the download_db.py :

url_handle = urlretrieve(url, filename, reporthook=ReportHook().report)

I replace it

import subprocess
command = ['wget', url, '-O', filename, '--no-check-certificate']
subprocess.check_call(command)

All work

17

Thanks for the fix, it worked :handshake:

Best

A

18

Hi @drelo , @Dragon_Black @bmtalbot @shrez28 @DEEPCHANDA7 @SeulaPark ,

Thank you for reaching out to the bioBakery Lab and apologies for the inconvenience. The certificate issue has now been resolved. You should be able to download the databases without any issues now. Please let us know if any other issues.

Regards,
Sagun

19

Thanks Sagun!

Best

A

20

Thanks, Sagun.

I could download the database.