You must specify a path to the directory containing Stacks output files.
rxstacks 1.35
rxstacks -b batch_id -P path [-o path] [-t threads] [-v] [-h]
  b: Batch ID to examine when exporting from the catalog.
  P: path to the Stacks output files.
  o: output path to write results.
  t: number of threads to run in parallel sections of code.
  v: print program version.
  h: display this help messsage.

  Filtering options:
    --lnl_filter: filter catalog loci based on the mean log likelihood of the catalog locus in the population.
      --lnl_lim <limit>: minimum log likelihood required to keep a catalog locus.
      --lnl_dist: print distribution of mean log likelihoods for catalog loci.
    --conf_filter: filter confounded loci.
    --conf_lim <limit>: between 0.0 and 1.0 (default 0.75), proportion of loci in population that must be confounded relative to the catalog locus.
    --prune_haplo: prune out non-biological haplotypes unlikely to occur in the population.
    --max_haplo <limit>: only consider haplotypes for pruning if they occur in fewer than max_haplo_cnt samples.
  Model options:
    --model_type <type>: either 'snp' (default), 'bounded', or 'fixed'
    For the SNP or Bounded SNP model:
      --alpha <num>: chi square significance level required to call a heterozygote or homozygote, either 0.1 (default), 0.05, 0.01, or 0.001.
    For the Bounded SNP model:
      --bound_low <num>: lower bound for epsilon, the error rate, between 0 and 1.0 (default 0).
      --bound_high <num>: upper bound for epsilon, the error rate, between 0 and 1.0 (default 1).
  Logging Options:
      --verbose: extended logging, including coordinates of all changed nucleotides (forces single-threaded execution).