You must specify a path to the directory containing Stacks output files.
phasedstacks 1.35
phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h]
  b: Stacks batch ID.
  P: path to the phased output files.
  S: path to the Stacks output files.
  t: input file type. Supported types: fastphase, and beagle.
  p: number of processes to run in parallel sections of code.
  M: path to the population map, a tab separated file describing which individuals belong in which population.
  v: print program version.
  h: display this help messsage.
  --haplotypes: data were phased as RAD locus haplotypes.
  --dprime_bin_size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value.
  --dprime_threshold <val>: if D' values fall above <val>, set the D' to 1, otherwise set D' to 0.

  Filtering options:
  --skip_zeros: do not include D' values of zero in the D' output.
  --minor_allele_freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5).
  --min_inform_pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9).