Road Map

graceful exiting in case star, bowtie2, or trinity crash (lack of memory for example)
count gene features in the host map bam file for pathway quantification - e.g., innate immunity, hypoxia. this requires a custom GTF file be added to resources/ and a software dependency for the featureCounts program
open question of how to later analyze orfs_noblastp.fasta (perhaps k-mer composition)
improve logging and graceful exits: write error to stderr (not stdout), and echo step in the error message (so know where error occurred); determine how to deal with w constituent programs that echo a lot of verbiage to stdout or stderr (do we want this stuff in the main logs, sub-logs, etc.?)
make a testing framework with sample files, so code can be changed w/o fear of error
get the machine learning part working: design a panel of RNA (transcriptome) pathogen dilutions (and then calibrate sensitivity etc)
make SGE mem flags options or configurable via the config file

"pandora aggregate" will condense the information from individual runs into a single table with a fixed set of features:
total reads
number of non-human reads
summary stats of the contig distribution
viral load, # viral taxa
bacterial load, # bacterial taxa
breakdown of aerobic / facultative / anaerobic bacteria
breakdown of gram positive / negative bacteria
recurrent AA motifs from discovery orfs_noblastp.fasta (comma separated list of motif_id's)
explore correlations between host expression and microbial summary features

design a 2D calibration panel to promote intuition about sensitivity vs. load vs. genome size etc.
how to give a probabilistic assignment of taxa present?

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