has been a while since I used blobTools, but if I remember correctly you should have a file called blast.out that should look like this:

contig_1    979556  200
contig_2    979556  500
contig_2    979556  1000
contig_2    979556  500
contig_2    979556  300
contig_3    979556  10000
contig_4    979556  1000
contig_5    6252    2000
contig_6    232323  2000
contig_6    6252    2000
contig_6    979556  2000
contig_6    232323  2000
contig_7    6252    2000
contig_8    6252    2000
contig_8    979556  2000
contig_9    6252    200

The second column is the NCBI taxonomy ID. Use this information to extract the reads mapping to a specific set of contigs by using the blobtools module bamfilter