ignore_missing_samples flag in core_diversity_analyses.py

[Jose]

Hi,

I am trying to pass the following parameter (ignore_missing_samples) to core_diversity_analyses.py using the attached parameters file.

This is what I wrote in QIIME 1.8.

core_diversity_analyses.py -p example_parameter_file -i otu_table.biom -m mapping.txt -e 940 -o otuput -t rep_set.tre

I have tried different things but QIIME keeps telling me that I should pass the flag, thanks for your help on this!

- Jose

[Colin Brislawn]

Hello Jose,

This may be a silly question, but are you listing the name of your parameter file correctly?

-p example_parameter_file

but you file is called -p example_parameter_file.txt

Colin

[Jose]

Not silly at all! Sorry for not writing it correctly...I used -p example_parameter_file.txt.

[Colin Brislawn]

Hello Jose,

make.emperor:ignore_missing_samples True

Should that be make_emperor?

I'm still looking for any tiny thing which could throw off this script.

Colin

[Jose]

My QIIME is busy working on something else and therefore I cannot just now provide you with the exact error message...but I am 100% certain that the error was related to make.emperor.

[Colin Brislawn]

make.emperor.py or 

make_emperor.py?

My script has an underscore in it, but I'm not sure what your script looks like. It's possible they are different in different versions of qiime.

Colin

[Jose]

Sorry I did not notice you wrote underscore, could you please give me some time so I can take a closer look at this?

I am sure this should be something tiny and dumb on my side! Will let you know updates.

[Jose]

You were right! It was make_emperor. Thanks a lot!!

[Colin Brislawn]

Good catch Jose! Computers are demanding about stuff like that.

Let us know if you have any other questions. The qiime scripts page lists all the scripts, and how to use them.

http://qiime.org/scripts/ 

Colin