<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 12 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear Vijay,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Parameters you need are:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-p program_name<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-d database_name<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-i input_sequence
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-e evalue (optional)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-o output_file<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Looks me like you are searching nt query sequences against an nt database - if so blastx is also the wrong flavour of BLAST<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">You need something like this<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">blastall -p blastn -d my_database -i my_filename -e 0.1 -o my_output_file<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Avoid underscores in your filenames as they will be misinterpreted but BLAST as command-line arguments - see your error below.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Simon<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> bio-linux-bounces@nebclists.nerc.ac.uk [mailto:bio-linux-bounces@nebclists.nerc.ac.uk]
<b>On Behalf Of </b>Vijay Kumar<br>
<b>Sent:</b> 04 February 2013 10:09<br>
<b>To:</b> bio-linux@nebclists.nerc.ac.uk<br>
<b>Subject:</b> [Bio-Linux] help regarding BLAST running<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222">dear sir,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> 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<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222">vijayakumar@vijayakumar-SVE14112ENB[bioinf_files] blastx -db blastdb/nr.02 -query sra_data contig list - nucleotide_ sequences.fasta -evalue
0.1 > vijay.blastx<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222">USAGE<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> blastx [-h] [-help] [-import_search_strategy filename]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-export_search_strategy filename] [-db database_name]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-dbsize num_letters] [-gilist filename] [-seqidlist filename]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-negative_gilist filename] [-entrez_query entrez_query]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-subject subject_input_file] [-subject_loc range] [-query input_file]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-out output_file] [-evalue evalue] [-word_size int_value]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-gapopen open_penalty] [-gapextend extend_penalty]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-xdrop_ungap float_value] [-xdrop_gap float_value]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-xdrop_gap_final float_value] [-searchsp int_value]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-max_hsps_per_subject int_value] [-frame_shift_penalty frameshift]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-max_intron_length length] [-seg SEG_options]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-soft_masking soft_masking] [-matrix matrix_name]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-threshold float_value] [-culling_limit int_value]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-best_hit_overhang float_value] [-best_hit_score_edge float_value]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc range]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-strand strand] [-parse_deflines] [-query_gencode int_value]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-outfmt format] [-show_gis] [-num_descriptions int_value]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-num_alignments int_value] [-html] [-max_target_seqs num_sequences]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> [-num_threads int_value] [-remote] [-version]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222">DESCRIPTION<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"> Translated Query-Protein Subject BLAST 2.2.26+<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222">Use '-help' to print detailed descriptions of command line arguments<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222">========================================================================<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222">Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: contig<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222">Error: (CArgException::eSynopsis) Application's initialization failed<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#222222">vijayakumar@vijayakumar-SVE14112ENB[bioinf_files]<o:p></o:p></span></p>
</div>
</div>
</body>
</html>