Create a run summary output

[spacocha]

Make something that outputs a summary of how many reads were removed from the analysis at each step (maybe as a log during otu_caller.py or on the intermediate files if they are saved), how many are left, how many dereplicated sequences, how many otus called etc.

[spacocha]

Here are some of the summary things I think should be included:
1.) The specific command-line input (may be useful to repeat analysis or just remember what you put)
2.) Parameters that are different from default for the analysis
3.) Record the stage in the analysis so if the it exits with an error, it is easy to open this file at any time after analysis and find out what was happening before exiting
4.) How many total reads/sequences are present at each step (maybe with a % lost at each step, or as a % of total that was input from the raw file- although that gets weird with dereplicated sequences)
5.) With demultiplexing, how many counts for each library/barcode
6.) How many were found to be chimeric for chimera checking. This is printed out during analysis, but lost if the output is not looged.
7.) How many total OTUs result