Food_abundance.csv output inconsistencies

[alexvcrr]

I ran the pipeline for a set of samples using the latest versions of the pipeline and database and came across a few issues.

1. First issue is that initially I seen that 0 food reads were assigned to a particular sample (see last line in screenshot). The pipeline completed with no errors.

This was slightly surprising as the file had more reads than some of the others where food reads were assigned. I followed up by moving the two fastq files associated with the problematic sample into a new subdirectory and reran the pipeline. After rerunning I'm seeing results.

Curious why this might be. Is this a bug or should I expect the results to vary with the number of samples processed and/or some stochastic effects ?

2. I noticed that the column reporting bacterial reads displays 0 mapped reads for all the samples. Not sure why this is as there are plenty of bacterial reads assigned in S_counts.csv and G_counts.csv.

3. There is also an issue with the output in the lineage and taxis_lineage columns in D_counts.csv. The output looks like this "K__;p__;c__;o__;f__;g__;s__" and ";;;;;;" for the two columns respectively. This is not an issue for the G or S counts files.