You must specify an input file of a supported type.
ustacks 1.35
ustacks -t file_type -f file_path [-d] [-r] [-o path] [-i id] [-m min_cov] [-M max_dist] [-p num_threads] [-R] [-H] [-h]
  t: input file Type. Supported types: fasta, fastq, gzfasta, or gzfastq.
  f: input file path.
  o: output path to write results.
  i: SQL ID to insert into the output to identify this sample.
  m: Minimum depth of coverage required to create a stack (default 3).
  M: Maximum distance (in nucleotides) allowed between stacks (default 2).
  N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2).
  R: retain unused reads.
  H: disable calling haplotypes from secondary reads.
  p: enable parallel execution with num_threads threads.
  h: display this help messsage.

  Stack assembly options:
    r: enable the Removal algorithm, to drop highly-repetitive stacks (and nearby errors) from the algorithm.
    d: enable the Deleveraging algorithm, used for resolving over merged tags.
    --max_locus_stacks <num>: maximum number of stacks at a single de novo locus (default 3).
     --k_len <len>: specify k-mer size for matching between alleles and loci (automatically calculated by default).

  Model options:
    --model_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, 0.05 (default), 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).
    For the Fixed model:
      --bc_err_freq <num>: specify the barcode error frequency, between 0 and 1.0.