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):
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?)