text: user4475: I would to use blastx from command line to analize a library produced with RepeatScout in format .fasta to find new transposable elements.
  I use this command mylaptop$ tblastx OB150DEC_2_repeats.fa
  but it reports an error: 
  USAGE
    tblastx [-h] [-help] [-import_search_strategy filename]
      [-export_search_strategy filename] [-db database_name]
      [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
      [-negative_gilist filename] [-entrez_query entrez_query]
      [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
      [-subject subject_input_file] [-subject_loc range] [-query input_file]
      [-out output_file] [-evalue evalue] [-word_size int_value]
      [-qcov_hsp_perc float_value] [-max_hsps int_value]
      [-xdrop_ungap float_value] [-searchsp int_value] [-sum_stats bool_value]
      [-max_intron_length length] [-seg SEG_options]
      [-soft_masking soft_masking] [-matrix matrix_name]
      [-threshold float_value] [-culling_limit int_value]
      [-best_hit_overhang float_value] [-best_hit_score_edge float_value]
      [-window_size int_value] [-lcase_masking] [-query_loc range]
      [-strand strand] [-parse_deflines] [-query_gencode int_value]
      [-db_gencode int_value] [-outfmt format] [-show_gis]
      [-num_descriptions int_value] [-num_alignments int_value]
      [-line_length line_length] [-html] [-max_target_seqs num_sequences]
      [-num_threads int_value] [-remote] [-version]
  
  DESCRIPTION
     Translated Query-Translated Subject BLAST 2.5.0+
  
  Use '-help' to print detailed descriptions of command line arguments
  ========================================================================
  
  Error: Too many positional arguments (1), the offending value: OB150DEC_2_repeats.fa
  Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: OB150DEC_2_repeats.fa
  
  I don't understand what does it mean too many positional arguments
  
  user77: A positional argument is one that doesn't follow something like -foo or --bar. That is, the variable that it should internally map to depends on it's position in the command. You're looking for something like tblastx -db something -query OB150DEC_2_repeats.fa
  
original_text: 4475: <p>I would to use blastx from command line to analize a library produced with RepeatScout in format .fasta to find new transposable elements.
  I use this command <code>mylaptop$ tblastx OB150DEC_2_repeats.fa</code></p>
  
  <p>but it reports an error: </p>
  
  <pre><code>USAGE
    tblastx [-h] [-help] [-import_search_strategy filename]
      [-export_search_strategy filename] [-db database_name]
      [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
      [-negative_gilist filename] [-entrez_query entrez_query]
      [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
      [-subject subject_input_file] [-subject_loc range] [-query input_file]
      [-out output_file] [-evalue evalue] [-word_size int_value]
      [-qcov_hsp_perc float_value] [-max_hsps int_value]
      [-xdrop_ungap float_value] [-searchsp int_value] [-sum_stats bool_value]
      [-max_intron_length length] [-seg SEG_options]
      [-soft_masking soft_masking] [-matrix matrix_name]
      [-threshold float_value] [-culling_limit int_value]
      [-best_hit_overhang float_value] [-best_hit_score_edge float_value]
      [-window_size int_value] [-lcase_masking] [-query_loc range]
      [-strand strand] [-parse_deflines] [-query_gencode int_value]
      [-db_gencode int_value] [-outfmt format] [-show_gis]
      [-num_descriptions int_value] [-num_alignments int_value]
      [-line_length line_length] [-html] [-max_target_seqs num_sequences]
      [-num_threads int_value] [-remote] [-version]
  
  DESCRIPTION
     Translated Query-Translated Subject BLAST 2.5.0+
  
  Use '-help' to print detailed descriptions of command line arguments
  ========================================================================
  
  Error: Too many positional arguments (1), the offending value: OB150DEC_2_repeats.fa
  Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: OB150DEC_2_repeats.fa
  </code></pre>
  
  <p>I don't understand what does it mean <code>too many positional arguments</code></p>
   77: <p>A positional argument is one that doesn't follow something like <code>-foo</code> or <code>--bar</code>. That is, the variable that it should internally map to depends on it's position in the command. You're looking for something like <code>tblastx -db something -query OB150DEC_2_repeats.fa</code></p>
  