HumanN3 MGX gene families products

Data resource IBDMDB
1

Hello,
I’m interested in working with HumanN3’s gene families output from the metagenomics (MGX) HMP2.
Since the merged gene families tsv file is not available for metagenomics data and I cannot download the functional profile via http, I accessed the ftp server and navigated to the MGX subdirectory, but I found that the products from the most recent date (2018-05-04) are from HumanN2.
Is there any way I can download the merged genefamilies.tsv file from HumanN3 or at least the individual functional profiles so I can merge the gene families myself?
Thank you very much,
Gerard

2

Hi @gsergom ,

You will be able to find the Humann3 gene families output here : https://ibdmdb.org/tunnel/public/HMP2/WGS/1818/products. Please navigate to “Functional profile 3.0” and “Taxonomic profile 3.0” tabs.

Regards,
Sagun

3

Hi @sagunmaharjann ,
Thank you for your response, but the problem is that I can’t download the 1638 files via the website because I get an error: Request URI too large.
Is there any way I can download them all at the same time?

Thank you again,

Gerard

4

Hello,

I am having the same issue as @gsergom except I am trying to access HMP2 metatranscriptomic data (MTX) files. I can see all HumanN3 Metatranscriptome files under Metatranscriptomes Products | IBDMDB “ Functional profile 3.0 ”, but I cannot find these HumanN3 files using the ftp server. Any advice on batch downloading for HumanN3 would be appreciated !

Best,
Izzy

5

Hi~

I currently have the same issue as @izzymgm and would like to follow up on it. Could you please give some suggestions regarding batch downloading for HumanN3 or where to find the merged genefamily file? I’d greatly appreciate it!

6

Hello @izzymgm and @gsergom ,
Thank you for reaching out to bioBakery lab and pointing out the ftp issue in ibdmdb site. We will look into it and fix it asap. Please use the web downloads till the ftp option is fixed. Apologies for the inconvenience.

Regards,
Sagun