Beginner struggling to get started with Qiime Illumina tutorial

[Cat Pashley]

This is my first post and I am unsure how much information to give. I apologise for my ignorance but I wish to learn to use Qiime for analysing fungal ITS data. I have been on a linux course and now I wish to first do the 16S tutorial then do the ITS tutorial. 

I am using an HP Envy (16 GB ram) with windows 8.1. I have installed Qiime via a virtualBox, downloaded via the Qiime website (Virtual box 4.3.20 r96977). 

I tried to download the tutorial data by copying and pasting the text from the first box in the tutorial into the terminal but I got an error 

bash: !: event not found

by removing the ! I was able to download and unzip the files and I can see them in my folder home. 

I was talking to someone who told me that the ! relates to ipython, and that I only have python installed and that to follow the tutorials I should install ipython. I was directed to 

http://ipython.org/install.html

From where I got the commands:

pip install ipython

pip install "ipython[notebook]"

Both before and since trying to install ipython I have had other problems. I made the assumption I need to copy any text in a blue box into the terminal, but I get errors with each line I try.

If I try any of the "From" commands I get an error, for example

from: can't read /var/mail/Ipython.display

If I tried the chdir command line I get the error

bash: syntax error near unexpected token `'moving_pictures_tutorial-1.9.0/illumina''

I thought I had misunderstood the tutorial and I needed to do more than copy and paste commands. I spoke to a colleague who has used Qiime for 454 work and he tried to help me. He could see the files were there but also got errors copying the text from the blue boxes, so after moving into the illumina folder (cd into moving pictures, then cd into illumina) he skipped to trying to validate mapping command and got the error(s)

Command without ! resulted in

validate_mapping_file.py: command not found

Command wth ! resulted in 

validate_mapping_file.py -o vmf-map/ -m map.tsv -o vmf-map/ -m map.tsv

validate_mapping_file.py: command not found

He then tried some of the From commands and after getting the same error messages looked in File System / var / mail and found it to be empty. 

He suggested I post in this forum. 

As an aside, just now when I tried to find out which version of qiime I had installed before posting in this forum by typing 

print_qiime_config.py -tf

Instead of what I expected to see (information on what version I had) I had the following message:

qiime@qiime-VirtualBox:~$ print_qiime_config.py -tf

Usage: print_qiime_config.py [options] {}

[] indicates optional input (order unimportant)

{} indicates required input (order unimportant)

A simple scripts that prints out the qiime config settings and does some sanity checks.

Example usage: 

Print help message and exit

 print_qiime_config.py -h

Example 1: Print qiime config settings

 print_qiime_config.py

Example 2: Print and check qiime config settings for sanity

 print_qiime_config.py -t

print_qiime_config.py: error: no such option: -f 

It may not read as such, but I have spent many many hours on several days trying to get info by googling error messages, reading websites on linux, or looking at posts in this forum, and I'm getting nowhere and would really appreciate some guidance. Thanks. 

[Adam robbins-pianka]

Hi Cat,

If you are following the Illumina Overview Tutorial presented as an IPython notebook (here), then you'll probably want to download the notebook to your virtualbox rather than copying and pasting everything. The notebook is actually interactive, so that the explanations and code are interleaved, and you can execute the code directly from the notebook. When you are viewing the notebook online (e.g., using the link I provided above), you are using a non-interactive version of the notebook.

The IPython notebook consists of markdown cells (that's all the explanatory text and "plain english" you see when you see the notebook) and code cells (that's all the python code and QIIME script calls). By default, the code cells just execute Python code that you type into them. However, if a line is prefixed with an exclamation point, it means that the command will be executed in the shell. That's why when you copy and paste commands from the notebook, you have to remove the exclamation point (because you are executing them directly in the shell, rather than in the notebook).

I recommend running

pip install ipython[all]

Then going to the link above. In the upper-right hand corner of the page, there is a link to download the notebook. Put it on your computer in a place that is accessible by the virtual machine.

Then, from within the virtual machine, navigate to that directory and run

ipython notebook

A web browser should launch, and you should see the notebook. Click it.

This will open the notebook in an interactive session, and you can execute the code in a given cell by clicking it and hitting shift-Enter.

Hope this helps!

Best,

Adam

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[Cat Pashley]

Hi Adam,

Your reply was very helpful, and I can now open the notebook both within the virtual environment on my PC and via my uni HPC system. However, regardless of where I view it I seem to come up with error messages very early on.

I tried continuing beyond the point where I got an error, but I just run into further errors, presumably linked to the original error where I couldn't move into the correct directory.

OSError: [Errno 2] No such file or directory: 'moving_pictures_tutorial-1.9.0/illumina '

The download and unzip stage worked, I can see the moving pictures directory and ditto the illumina directory. As I am not typing my own commands but clicking in a box and hitting shift-Enter, what can I be doing wrong?

Many thanks,
Cat

[Cat Pashley]

One other thing. When I use Qiime via my university HPC system (which is not a virtual box version) when I close and reopen an IPython notebook, it remembers where I got to. On my home PC with the virtual box qiime it does not. In the terminal there is a message

IPython History requires SQLite, your history will not be saved.

When I went to the SQLite download page http://www.sqlite.org/download.html there are a lot of different options. I'm assuming there is likely to be a version in the qiime virtual box to enable people to run the tutorials in section? If so is there a simple command I need to type before opening the notebook?

Thanks again, Cat