[Bio-Linux] help regarding BLAST running

[Wagstaff, Simon]

Dear Vijay,
The problems are with your BLAST syntax. If you do a quick Google search you will find lots of web sites that will help you construct your BLAST search e.g. http://www.mathworks.co.uk/help/bioinfo/ref/blastlocal.html. You can also go to the NCBI documentation.

Parameters you need are:

-p program_name
-d database_name
-i input_sequence
-e evalue (optional)
-o output_file

Looks me like you are searching nt query sequences against an nt database - if so blastx is also the wrong flavour of BLAST

You need something like this
blastall -p blastn -d my_database -i my_filename -e 0.1 -o my_output_file

Avoid underscores in your filenames as they will be misinterpreted but BLAST as command-line arguments - see your error below.

Simon

From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Vijay Kumar
Sent: 04 February 2013 10:09
To: bio-linux at nebclists.nerc.ac.uk
Subject: [Bio-Linux] help regarding BLAST running

dear sir,
 i am Dr.VIJAY using BIOLINUX 7 for last 2 months.its really working good for biologist with own PC.  now i face problem while working with BLAST run in terminal. when ever i run the BLAST i am getting error message like below for both single sequences and multiple sequences too. please help me( i am biology student, so i am not  exposure to linux commend and error problem.THANK U SIR


vijayakumar at vijayakumar-SVE14112ENB[bioinf_files] blastx -db blastdb/nr.02 -query sra_data contig list - nucleotide_ sequences.fasta -evalue 0.1 > vijay.blastx
USAGE
  blastx [-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]
    [-gapopen open_penalty] [-gapextend extend_penalty]
    [-xdrop_ungap float_value] [-xdrop_gap float_value]
    [-xdrop_gap_final float_value] [-searchsp int_value]
    [-max_hsps_per_subject int_value] [-frame_shift_penalty frameshift]
    [-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] [-ungapped] [-lcase_masking] [-query_loc range]
    [-strand strand] [-parse_deflines] [-query_gencode int_value]
    [-outfmt format] [-show_gis] [-num_descriptions int_value]
    [-num_alignments int_value] [-html] [-max_target_seqs num_sequences]
    [-num_threads int_value] [-remote] [-version]

DESCRIPTION
   Translated Query-Protein Subject BLAST 2.2.26+

Use '-help' to print detailed descriptions of command line arguments
========================================================================
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: contig
Error: (CArgException::eSynopsis) Application's initialization failed
vijayakumar at vijayakumar-SVE14112ENB[bioinf_files]
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