in augustus run how to provide mt_mode 1 to tblastn
Blast toolkit version 2.12 from July 2021 introduced the mt_mode option to use threads per query instead of alotting to portions of the db. This is a more efficient use of multiple threads for smaller databases. The tblastn program would benefit most from this (that is more than blastn or blastp, which also benefit)
I can see where it can can go in the configure() function of the TBLASTNRunner class based on a get_version check but did not know if you had other places more appropriate.
Also the TBLASTNRunner check_tool_dependencies() function does a self.version != "2.10.1+" check which is brittle and does not account for being up to version 2.13 these days.
best, Jim Henderson
p.s. would love an option to run augustus after metaeuk over the missing and fragmented orthos not found in the 2 metaeuk runs. I still run both and add augustus finds not in metaeuk and not overlapping others and that does materially reduce the Missing count in many situations. Would be much faster to only look for Missing/Fragmented with the tblastn/augustus technique but currently I'm having to run twice and then merge into the metaeuk full_table.tsv