Question: Where can I find the effective median coverage in the Supernova logs?
Answer: When debugging Supernova crashes it may be helpful to know the effective median coverage. This can be estimated a priori based on expected genome size and number of reads input, but it is wise to double-check (for example if your genome size estimation was off). This metric is estimated during the ASSEMBLER_TR stage of Supernova, so this article is only helpful if the run progressed that far:
Within the _stdout for the ASSEMBLER_TR stage, search for "effective_coverage_median" e.g.:
$ grep effective_coverage_median ASSEMBLER_CS/_ASSEMBLER/ASSEMBLER_TR/fork0/chnk0/_stdout
Wed May 16 22:53:28 2018: logging effective_coverage_median=56.2