found what I think is a bug in the win10 version of mothur 1.39.5. dist.shared kills the executable. Both win10 computers had the same failure.
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Windows version Running 64Bit Version mothur v.1.39.5 Last updated: 3/20/2017 by Patrick D. Schloss Department of Microbiology & Immunology University of Michigan http://www.mothur.org When using, please cite: Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. Distributed under the GNU General Public License Type 'help()' for information on the commands that are available For questions and analysis support, please visit our forum at https://www.mothur.org/forum Type 'quit()' to exit program Interactive Mode mothur > dist.shared(shared=fastq/workshop.trim.contigs.good.unique.good.filter.precluster.pick.pick.opti_mcc.shared, calc=braycurtis-jest-thetayc, subsample=10000) Using 1 processors. deep.sed.wp1.NA0004270319 contains 8283. Eliminating. deep.water.wm2.Blitz.H2O.51 contains 10. Eliminating. 0.03