Updating to new Greengenes

[Paul R.]

Hello,

I am having some issues updating Greengenes in a QIIME Virtual Box.  Is there a tutorial or list of instructions somewhere that I can use to replace the old version of Greengenes with the new one, and have QIIME automatically use it whenever it assigns taxonomy?

Thanks for any help in advance!

[Daniel McDonald]

Hey Paul,

I don't believe a tutorial was put together... so lets do that now :)

1) open a terminal, and change to your home directory (cd ~) or to a
directory of your choosing
2) download the gg_12_10_otus.tar.gz (curl -O
ftp://greengenes.microbio.me/greengenes_release/gg_12_10/gg_12_10_otus.tar.gz)
3) unpack the file (tar xzf gg_12_10_otus.tar.gz)
4) if you're using QIIME 1.5.0, patch the taxonomy for RDP support
(see https://groups.google.com/d/msg/qiime-forum/t74u1H4Y-Ns/vV05O0SBOEcJ)
5) open your QIIME config file located at ~/.qiime_config
6) update the "assign_taxonomy_id_to_taxonomy_fp" key to point to the
patched RDP taxonomy file
7) update the "assign_taxonomy_reference_seqs_fp" key to point to the
corresponding rep_set file

Let me know if you have any issues!
Daniel

> --
>
>
>

[Paul R.]

Hi Daniel,

Thank you for your help and creating the tutorial!  I am having an issue running step 4.  I get an error back that says "couldn't connect to host" when I run the curl -O command for the patch.  I also tried to download the file outside of the virtual box, and I am having the same issue.  Is this link down, or is it something to do with my internet connection or computer?

Thanks again!

[Paul R.]

Update:  I was able to get it downloaded using your command from later on that thread:  curl -O ftp://thebeast.colorado.edu/pub/gg_12_10_otus.rdp22_patch.tar.gz 

Thanks again for your help!

[Paul R.]

Hi Daniel,

I am having another issue with the patch.  I have it downloaded and unzipped, and I'm trying to re-train the RDP.  I run the following command:

assign_taxonomy.py -i otus/rep_set/seqs_rep_set.fasta -t /home/qiime/gg_12_10_otus/taxonomy/97_otu_taxonomy.rdp22_train.txt -r /home/qiime/gg_12_10_otus/rep_set/97_otus.fasta -o otus/rdp_assigned_taxonomy_gg/

However, I get an error message back that says:

assign_taxonomy.py: error: option -i: file does not exist: 'otus/rep_set/seqs_rep_set.fasta'

How would I go about updating this command so that it will re-train correctly?

Thank you!

[Daniel McDonald]

Hey Paul,

That error indicates it cannot find your representative sequences from
your study on the file system. You'll need to switch back to your
analysis directory for that command to work.
-Daniel

> --
>
>
>

[Paul Rosenthal]

Thanks again for your help, Daniel.  I don't currently have any data for my study, I anticipate that in the next few months.  Is there a way I can proceed with updating the Greengenes database if I don't have data for the study yet?

--

--

Paul Rosenthal
Senior Computer and Technical Specialist
PHR Technologies, SP.

 

If urgent technical assistance is needed: Please send a short description of the issue and your name to paulro...@vtext.com.  I will respond as soon as possible.

[Daniel McDonald]

Simply obtaining and unpacking the gg_12_10_otus.tar.gz is sufficient
-Daniel

> --
>
>
>

[Paul Rosenthal]

Great, thank you for your help.  When I do have study data (I am currently using sample data we have), will I need to change any of the commands when processing the data?

[Daniel McDonald]

I suggest updating your qiime_config to have the
"assign_taxonomy_id_to_taxonomy_fp" key and the
"assign_taxonomy_reference_seqs_fp" key to point to the gg_12_10 RDP
patch and the gg_12_10 rep seqs respectively
-Daniel

On Thu, Nov 1, 2012 at 12:46 PM, Paul Rosenthal

> --
>
>
>

[Paul Rosenthal]

How do I go about modifying the qiime_config file?  Do I need to replace the keys already in it, or just add yours?  I also see this when I open the file: 

# WARNING: DO NOT EDIT OR DELETE Qiime/qiime_config

# To overwrite defaults, copy this file to $HOME/.qiime_config or a full path

[Daniel McDonald]

Copy the file:

cp path/to/original/qiime_config $HOME/.qiime_config

Then open the file in an editor. I don't recall what graphical editors
are available within the VM, but I suspect kedit is:

kedit $HOME/.qiime_config

The paths you place into the qiime_config need to be correct for your
environment. The paths in the step-by-step instructions should be
correct AFAIK
-Daniel

> --
>
>
>