Answers.Body: <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>
  
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Answers.Text: ok. I have to download a database to use?
Answers.UserDisplayName: jonny
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Answers.Text: Or point it to a remote one.
Answers.UserDisplayName: Devon Ryan
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Answers.Text: I've never used blast from command line before. Could you explain to me how to point it from remote one? I'm working with a cephalopoda genome
Answers.UserDisplayName: jonny
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Answers.Text: Just use `nt` and I think it will figure it out. We only use local databases, so if that doesn't work you'll need to read the documentation.
Answers.UserDisplayName: Devon Ryan
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Answers.Text: ok. I've tried but the message is `BLAST Database error: No alias or index file found for nucleotide database [nt] in search path [/mydirectory/OB150DEC::]`
Answers.UserDisplayName: jonny
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Answers.Text: Use the `-remote` option https://www.ncbi.nlm.nih.gov/books/NBK279680/
Answers.UserDisplayName: Devon Ryan
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Answers.Text: Thank you for your help, but it doesn't work. It reminds a lot of errors. I'll try downloading an nt database
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Answers.UserDisplayName: Devon Ryan
Body: <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>
  
Tags: <blast>
Title: blast command line
ThreadText: # blast command line
  
  (Asked by: username_0 on 2019-05-15)
  
  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`
  
  **Tags:** blast
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-05-15. Score: 1 | Accepted answer
  
  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`
  
  > **Comments:**
  > **username_0**: ok. I have to download a database to use?  
  > **username_1**: Or point it to a remote one.  
  > **username_0**: I've never used blast from command line before. Could you explain to me how to point it from remote one? I'm working with a cephalopoda genome  
  > **username_1**: Just use `nt` and I think it will figure it out. We only use local databases, so if that doesn't work you'll need to read the documentation.  
  > **username_0**: ok. I've tried but the message is `BLAST Database error: No alias or index file found for nucleotide database [nt] in search path [/mydirectory/OB150DEC::]`  
  > **username_1**: Use the `-remote` option https://www.ncbi.nlm.nih.gov/books/NBK279680/  
  > **username_0**: Thank you for your help, but it doesn't work. It reminds a lot of errors. I'll try downloading an nt database  
  
  ---
  
  