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Created by Justin van der Hooft@Hooft001Maintainer

Fasttree related error messages obtained by Glasgow co-worker

The following probably fasttree related error messages were obtained by a Glasgow co-worker, but he cannot put them here, hence, I do it on his behalf! His email is: 2332462H@student.gla.ac.uk and his name is Grimur Hjorleifsson Eldjarn

  • Obscure error message if (undocumented) fasttree dependency is not met fasttree is not on any requirements list that I could find (most notably README). When the dependency is not satisfied, the program currently crashes with an OSError when the subprocess fails, and does not report the offending command.

  • Fasttree warnings if installed via package manager (Ubuntu 17.10, 17.4) When running Big-Scape with fasttree installed via package manager on Ubuntu 17.10 and 17.4, the following error message appears very frequently:

WARNING! This alignment consists of closely-related and very-long sequences. WARNING! FastTree (or other standard maximum-likelihood tools) may not be appropriate for aligments of very closely-related sequences like this one, as FastTree does not account for recombination or gene conversion

Seems to be related to this (see bottom of page): http://darlinglab.org/blog/2015/03/23/not-so-fast-fasttree.html
so the user may actually need to build fasttree for him/herself. Is there a way to suppress the warnings if they are irrelevant (even going so far as to hijack stdout/stderr for the subprocess?), or check if the fasttree build is valid and alert the user if it isn't? (Perhaps use dummy data and check the process output for warnings?)