Hi Dr. Debelius @jwdebelius
You answered my queries-thanks a lot! Also, putting multiple columns on the metadata for both numeric and categorical is a clever hack-thanks!
There's one other thing that's been bugging me ever since the day I started work on QIIME2, if you would please help me out here: It's about writing the scripts in the command prompt:
So, here's how I write my commands (example command):
PS: You will notice how I give a space after the end of a command, followed by a \ - - (spaces added for visual clarity)
output: pairwise-distances-2.qzv (left box plot)
If I copy-and-paste the same command from the tutorial, here's how it looks in the command prompt:
output: pairwise-distances-qiime.qzv (right box plot)
Comparing both outputs, they are different:
Why is this so? Am I:
a. writing the scripts in a wrong format (although they seem to work fine and output the artefacts/visualizations!)
b. It is statistical error?
I am using Qiime2 Ver 2019.10
Thank you for your time,
What you’re seeing is, likely, in part an artifact of rarefaction. Rarefaction is a random process and so, depending on how you re-sample the data, you may see slightly variations in your results. Both are correct answers.
Hi Dr. Debelius,
Thanks for your quick reply!
So, the way I am writing the scripts is correct even though it is not how tutorial scripts seem to visually appear in the command prompt?
Am I correct in saying that if my scripts were written in an incorrect format, QIIME2 would give an error instead of a visualization?
Commands can be written horizontally or with line breaks (
'\) and the command line reads them the same way. Most people who do a lot of programming tend to do line wrapping because it makes it easier to read/check steps, but you can totally write them on a single line with no breaks. And, yes, there’s a fairly robust error system that lets you know if the command is entered incorrectly. It will even prompt you to fix the spelling, for example, if that’s an issue.
Ah, I get it. That explains things. Just a last add-on (I realize it’s very late in Sweden, I am very apologetic), this is what you refer as ‘on a single line with no breaks’:
qiime gneiss balance-taxonomy '\–i-table my-table.qza '\–i-tree my-tree.qza
(please ignore all the ’ characters. They are to highlight the formatting.
There is a space between taxonomy and the backslash character without any ')
Thanks a ton, I am really grateful for your quick replies,
The default way to write a single line command is something like this, where the arguments are seperated by spaces and there are no
\ characters included.
qiime diversity pcoa --i-distance-matrix dm.qza --o-pcoa pcoa.qza
If you want to do line-wrapping so each argument is on its own line - whcih can make it easier to read - you can use the
\ character in bash to indicate a continuation:
qiime diversity pcoa \
--i-distance-matrix dm.qza \
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