Local blast with multiple databases and multiple files

Question

[akang]

I am trying to run a specific query against specific custom database in python. When i just use one database it works fine but doesnt produce any result (just empty output file) when run my queries against multiple databases. Any suggestions?

db1=os.path.join(path, "ref/db1.fasta")
db2=os.path.join(path, "ref/db2.fasta")
db3=os.path.join(path, "ref/db3.fasta")
 subprocess.call([MAKEBLASTDB,"-in",db1,"-dbtype","nucl"])
 subprocess.call([MAKEBLASTDB,"-in",db2,"-dbtype","nucl"])
 subprocess.call([MAKEBLASTDB,"-in",db3,"-dbtype","nucl"])
 for filename in os.listdir(mydir):
      if filename.startswith('AB_A') and filename.endswith('.fa'):
         subprocess.Popen([BLASTN,"-db", db1, "-query", filename ,"-num_alignments","1", "-outfmt","6","-out", filename + "_blast_output.txt"])

      if filename.startswith('HB2_B') and filename.endswith('.fa'):
         subprocess.Popen([BLASTN,"-db", db2, "-query", filename ,"-num_alignments","1", "-outfmt","6","-out", filename + "_blast_output.txt"])