These are chat archives for dereneaton/ipyrad

26th
Oct 2017
toczydlowski
@toczydlowski
Oct 26 2017 16:46
@isaacovercast Ahhh. Yup. Forgot max_alleles_consens was at the individual level. Thanks for the reminder. Carry on.
Jenny Archibald
@jenarch
Oct 26 2017 20:16
@dereneaton @isaacovercast Hi! It appears I am having the same problem asked about recently by @tommydevitt. When running bpp in a jupyter notebook, ipyclient.wait() said "True" a few seconds after submitting A00 jobs, but when I tried to parse the mcmc table, it gave an error including:
IOError: File /panfs/pfs.local/scratch/bi/jkarch/cam/ch8/bppH/analysis-bpp/A00-nodata_r0.mcmc.txt does not exist
And I cannot find any output files. Any thoughts?
Matt McElroy
@Mattalac_twitter
Oct 26 2017 23:00
Hi all, is there a flag or strategy for implementing a minimum allele frequency cutoff? I've found this to be pretty important to implement when running stacks. Thanks!