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:

  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]

   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


1 Answer 1


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

  • $\begingroup$ ok. I have to download a database to use? $\endgroup$
    – jonny
    May 15, 2019 at 8:57
  • $\begingroup$ Or point it to a remote one. $\endgroup$
    – Devon Ryan
    May 15, 2019 at 8:58
  • $\begingroup$ 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 $\endgroup$
    – jonny
    May 15, 2019 at 9:05
  • $\begingroup$ 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. $\endgroup$
    – Devon Ryan
    May 15, 2019 at 9:06
  • $\begingroup$ 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::] $\endgroup$
    – jonny
    May 15, 2019 at 9:10

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