Lastal aligner not detecting queery sequences

Question

[robert.murphy]

I am using the LAST aligner to align a reference to a denvo assembled genome to identify contamination. I have run lastdb on the reference to create the database but when using lastal I get no significant output:

lastal $db_name $denovo_assembly > $outfile

# LAST version 1060
    #
    # a=21 b=9 A=21 B=9 e=139 d=102 x=138 y=44 z=138 D=1e+06 E=6941.95
    # R=01 u=0 s=2 S=0 M=0 T=0 m=10 l=1 n=10 k=1 w=1000 t=4.36661 j=3 Q=0
    # termitodb
    # Reference sequences=47 normal letters=70034757
    # lambda=0.228526 K=0.433378
    #
    #     A   C   G   T   M   S   K   W   R   Y   B   D   H   V
    # A   6 -18 -18 -18   3 -18 -18   3   3 -18 -18   1   1   1
    # C -18   6 -18 -18   3   3 -18 -18 -18   3   1 -18   1   1
    # G -18 -18   6 -18 -18   3   3 -18   3 -18   1   1 -18   1
    # T -18 -18 -18   6 -18 -18   3   3 -18   3   1   1   1 -18
    # M   3   3 -18 -18   3   0 -18   0   0   0  -2  -2   1   1
    # S -18   3   3 -18   0   3   0 -18   0   0   1  -2  -2   1
    # K -18 -18   3   3 -18   0   3   0   0   0   1   1  -2  -2
    # W   3 -18 -18   3   0 -18   0   3   0   0  -2   1   1  -2
    # R   3 -18   3 -18   0   0   0   0   3 -18  -2   1  -2   1
    # Y -18   3 -18   3   0   0   0   0 -18   3   1  -2   1  -2
    # B -18   1   1   1  -2   1   1  -2  -2   1   1  -1  -1  -1
    # D   1 -18   1   1  -2  -2   1   1   1  -2  -1   1  -1  -1
    # H   1   1 -18   1   1  -2  -2   1  -2   1  -1  -1   1  -1
    # V   1   1   1 -18   1   1  -2  -2   1  -2  -1  -1  -1   1
    #
    # Coordinates are 0-based.  For - strand matches, coordinates
    # in the reverse complement of the 2nd sequence are used.
    #
    # name start alnSize strand seqSize alignment
    #
    # Query sequences=0

It seems as though no query sequences are being detected but the de novo assemblies are in the correct fasta format eg:

    >scaffold03054
GACATTCCTTCCCATGTTGCCCATGAAGTTACCGATCCCTCCACTAATTTTCTCTGGGACGAGATCAACACCACCAACCAAGCCTACTCCAAGCATGCCAATGCCCAATGCAAACCAACTCCTAACTGGCCCCCCAGCACCTTAGTCTGGCTTGATCAATGAATCTCAAGACCTAGAGGCCCTCTATCAAGCTTGAACACAAACAACTCAGCCCCTTCAAGATTCTCTAAAAAGTCTCAATGCATGCTTACAA
     >scaffold03288
     GCGGCGTGGAGAAAGACTTTGGAGAGATAAACTTGAAGAAAGTACAAAAATGATCTAGGAGAATTATGTAAGTGCCATGTGGATTTGGAGCGATTTTGGCTGGGGAACCATGCATTCGAGCGGACATAACCCTTCTCTCATTACTTATGTAAGAGAGTCGGGGATGTTGAGGTCGAAACAACCAACACACAACAGAACTG TAGCATCTCCACACTATTAGAAGTGGCCTCTTGAGAA

I anyone able to assist or suggest an alternative?