Hi all, when I run the following command for a local Blastp, I get no results returned even though there should be results.
blastp -out /Users/Wes/Desktop/new_pairwise/blast.xml -outfmt 5 -query /Users/Wes/Desktop/new_pairwise/gyra_ref.txt -db blastdb
Here is the XML output from blastp:
<?xml version="1.0"?><!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"><BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>BLASTP 2.2.28+</BlastOutput_version>
<BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
<BlastOutput_db>blastdb</BlastOutput_db>
<BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
<BlastOutput_query-def>gi|85676699|dbj|BAE77949.1| 30S ribosomal subunit protein S12 [Escherichia coli str. K12 substr. W3110]</BlastOutput_query-def>
<BlastOutput_query-len>124</BlastOutput_query-len>
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>10</Parameters_expect>
<Parameters_gap-open> ...
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