<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>

CC BY-SA 4.0
2019-05-15T08:57:45.597Z
ok. I have to download a database to use?
jonny
CC BY-SA 4.0
2019-05-15T08:58:55.400Z
Or point it to a remote one.
Devon Ryan
CC BY-SA 4.0
2019-05-15T09:05:25.710Z
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
jonny
CC BY-SA 4.0
2019-05-15T09:06:33.540Z
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.
Devon Ryan
CC BY-SA 4.0
2019-05-15T09:10:06.213Z
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::]`
jonny
CC BY-SA 4.0
2019-05-15T09:23:07.523Z
Use the `-remote` option https://www.ncbi.nlm.nih.gov/books/NBK279680/
Devon Ryan
CC BY-SA 4.0
2019-05-15T09:30:22.890Z
Thank you for your help, but it doesn't work. It reminds a lot of errors. I'll try downloading an nt database
jonny
CC BY-SA 4.0
2019-05-15T08:53:46.587Z
2019-05-15T08:53:46.587Z
Devon Ryan
<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>

<blast>
blast command line
# 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  

---

